Megaruptor^® 2

Notice (8): Undefined variable: solution_of_interest [APP/View/Products/view.ctp, line 755]
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<p><span><strong><span style="text-decoration: underline;">Note</span>:&nbsp;</strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a><span>&nbsp;</span><span>are sold separately.</span></span></p>',
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			'name' => '次世代シーケンシング',
			'description' => '<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2 style="font-size: 22px;">DNA断片化、ライブラリー調製、自動化：NGSのワンストップショップ</h2>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-12 medium-12 large-12 columns">
<h4>1. 断片化装置を選択してください：150 bp〜75 kbの範囲でDNAを断片化します。</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-pico-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/bioruptor_pico.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/megaruptor2-1-unit"><img src="https://www.diagenode.com/img/product/shearing_technologies/B06010001_megaruptor2.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-one-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/br-one-profil.png" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns">5&mu;lまで断片化：150 bp〜2 kb<br />NGS DNAライブラリー調製およびFFPE核酸抽出に最適で、</td>
<td class="small-4 medium-4 large-4 columns">2 kb〜75 kbの範囲をできます。<br />メイトペアライブラリー調製および長いフラグメントDNAシーケンシングに最適で、この軽量デスクトップデバイスで</td>
<td class="small-4 medium-4 large-4 columns">20または50&mu;lの断片化が可能です。</td>
</tr>
</tbody>
</table>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-8 medium-8 large-8 columns">
<h4>2. 最適化されたライブラリー調整キットを選択してください。</h4>
</th>
<th class="small-4 medium-4 large-4 columns">
<h4>3. ライブラリー前処理自動化を選択して、比類のないデータ再現性を実感</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><img src="https://www.diagenode.com/img/product/kits/microPlex_library_preparation.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns"><img src="https://www.diagenode.com/img/product/kits/box_kit.jpg" style="display: block; margin-left: auto; margin-right: auto;" height="173" width="250" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/sx-8g-ip-star-compact-automated-system-1-unit"><img src="https://www.diagenode.com/img/product/automation/B03000002%20_ipstar_compact.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">50pgの低入力：MicroPlex Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">5ng以上：iDeal&nbsp;Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">Achieve great NGS data easily</td>
</tr>
</tbody>
</table>
</div>
</div>
<blockquote>
<div class="row">
<div class="small-12 medium-12 large-12 columns"><span class="label" style="margin-bottom: 16px; margin-left: -22px; font-size: 15px;">DiagenodeがNGS研究にぴったりなプロバイダーである理由</span>
<p>Diagenodeは15年以上もエピジェネティクス研究に専念、専門としています。 ChIP研究クロマチン用のユニークな断片化システムの開発から始まり、 専門知識を活かし、5&mu;lのせん断体積まで可能で、NGS DNAライブラリーの調製に最適な最先端DNA断片化装置の開発にたどり着きました。 我々は以来、ChIP-seq、Methyl-seq、NGSライブラリー調製用キットを研究開発し、業界をリードする免疫沈降研究と同様に、ライブラリー調製を自動化および完結させる独自の自動化システムを開発にも成功しました。</p>
<ul>
<li>信頼されるせん断装置</li>
<li>様々なインプットからのライブラリ作成キット</li>
<li>独自の自動化デバイス</li>
</ul>
</div>
</div>
</blockquote>
<div class="row">
<div class="small-12 columns">
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#panel1a">次世代シーケンシングへの理解とその専門知識</a>
<div id="panel1a" class="content">
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong>次世代シーケンシング (NGS)</strong> ）は、著しいスケールとハイスループットでシーケンシングを行い、1日に数十億もの塩基生成を可能にします。 NGSのハイスループットは迅速でありながら正確で、再現性のあるデータセットを実現し、さらにシーケンシング費用を削減します。 NGSは、ゲノムシーケンシング、ゲノム再シーケンシング、デノボシーケンシング、トランスクリプトームシーケンシング、その他にDNA-タンパク質相互作用の検出やエピゲノムなどを示します。 指数関数的に増加するシーケンシングデータの需要は、計算分析の障害や解釈、データストレージなどの課題を解決します。</p>
<p>アプリケーションおよび出発物質に応じて、数百万から数十億の鋳型DNA分子を大規模に並行してシーケンシングすることが可能です。その為に、異なる化学物質を使用するいくつかの市販のNGSプラットフォームを利用することができます。 NGSプラットフォームの種類によっては、事前準備とライブラリー作成が必要です。</p>
<p>NGSにとっても、特にデータ処理と分析に関した大きな課題はあります。第3世代技術はゲノミクス研究にさらに革命を起こすであろうと大きく期待されています。</p>
</div>
</div>
<div class="row">
<div class="small-6 medium-6 large-6 columns">
<p><strong>NGS アプリケーション</strong></p>
<ul>
<li>全ゲノム配列決定</li>
<li>デノボシーケンシング</li>
<li>標的配列</li>
<li>Exomeシーケンシング</li>
<li>トランスクリプトーム配列決定</li>
<li>ゲノム配列決定</li>
<li>ミトコンドリア配列決定</li>
<li>DNA-タンパク質相互作用（ChIP-seq</li>
<li>バリアント検出</li>
<li>ゲノム仕上げ</li>
</ul>
</div>
<div class="small-6 medium-6 large-6 columns">
<p><strong>研究分野におけるNGS:</strong></p>
<ul>
<li>腫瘍学</li>
<li>リプロダクティブ・ヘルス</li>
<li>法医学ゲノミクス</li>
<li>アグリゲノミックス</li>
<li>複雑な病気</li>
<li>微生物ゲノミクス</li>
<li>食品・環境ゲノミクス</li>
<li>創薬ゲノミクス - パーソナライズド・メディカル</li>
</ul>
</div>
<div class="small-12 medium-12 large-12 columns">
<p><strong>NGSの用語</strong></p>
<dl>
<dt>リード（読み取り）</dt>
<dd>この装置から得られた連続した単一のストレッチ</dd>
<dt>断片リード</dt>
<dd>フラグメントライブラリからの読み込み。 シーケンシングプラットフォームに応じて、読み取りは通常約100〜300bp。</dd>
<dt>断片ペアエンドリード</dt>
<dd>断片ライブラリーからDNA断片の各末端2つの読み取り。</dd>
<dt>メイトペアリード</dt>
<dd>大きなDNA断片（通常は予め定義されたサイズ範囲）の各末端から2つの読み取り。</dd>
<dt>カバレッジ（例）</dt>
<dd>30&times;適用範囲とは、参照ゲノム中の各塩基対が平均30回の読み取りを示す。</dd>
</dl>
</div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2>NGSプラットフォーム</h2>
<h3><a href="http://www.illumina.com" target="_blank">イルミナ</a></h3>
<p>イルミナは、クローン的に増幅された鋳型DNA（クラスター）上に位置する、蛍光標識された可逆的鎖ターミネーターヌクレオチドを用いた配列別合成技術を使用。 DNAクラスターは、ガラスフローセルの表面上に固定化され、 ワークフローは、4つのヌクレオチド（それぞれ異なる蛍光色素で標識された）の組み込み、4色イメージング、色素や末端基の切断、取り込み、イメージングなどを繰り返します。フローセルは大規模な並列配列決定を受ける。 この方法により、単一蛍光標識されたヌクレオチドの制御添加によるモノヌクレオチドのエラーを回避する可能性があります。 読み取りの長さは、通常約100〜150 bpです。</p>
<h3><a href="http://www.lifetechnologies.com" target="_blank">イオン トレント</a></h3>
<p>イオントレントは、半導体技術チップを用いて、合成中にヌクレオチドを取り込む際に放出されたプロトンを検出します。 これは、イオン球粒子と呼ばれるビーズの表面にエマルションPCR（emPCR）を使用し、リンクされた特定のアダプターを用いてDNA断片を増幅します。 各ビーズは1種類のDNA断片で覆われていて、異なるDNA断片を有するビーズは次いで、チップの陽子感知ウェル内に配置されます。 チップには一度に4つのヌクレオチドのうちの1つが浸水し、このプロセスは異なるヌクレオチドで15秒ごとに繰り返されます。 配列決定の間に4つの塩基の各々が1つずつ導入されます、組み込みの場合はプロトンが放出され、電圧信号が取り込みに比例して検出されます。.</p>
<h3><a href="http://www.pacificbiosciences.com" target="_blank">パシフィック バイオサイエンス</a></h3>
<p>パシフィックバイオサイエンスでは、20kbを超える塩基対の読み取りも、単一分子リアルタイム（SMRT）シーケンシングによる構造および細胞タイプの変化を観察することができます。 このプラットフォームでは、超長鎖二本鎖DNA（dsDNA）断片が、Megaruptor（登録商標）のようなDiagenode装置を用いたランダムシアリングまたは目的の標的領域の増幅によって生成されます。 SMRTbellライブラリーは、ユニバーサルヘアピンアダプターをDNA断片の各末端に連結することによって生成します。 サイズ選択条件による洗浄ステップの後、配列決定プライマーをSMRTbellテンプレートにアニーリングし、鋳型DNAに結合したDNAポリメラーゼを含む配列決定を、蛍光標識ヌクレオチドの存在下で開始。 各塩基が取り込まれると、異なる蛍光のパルスをリアルタイムで検出します。</p>
<h3><a href="https://nanoporetech.com" target="_blank">オックスフォード ナノポア</a></h3>
<p>Oxford Nanoporeは、単一のDNA分子配列決定に基づく技術を開発します。その技術により生物学的分子、すなわちDNAが一群の電気抵抗性高分子膜として位置するナノスケールの孔（ナノ細孔）またはその近くを通過し、イオン電流が変化します。 この変化に関する情報は、例えば4つのヌクレオチド（AまたはG r CまたはT）ならびに修飾されたヌクレオチドすべてを区別することによって分子情報に訳されます。 シーケンシングミニオンデバイスのフローセルは、数百個のナノポアチャネルのセンサアレイを含みます。 DNAサンプルは、Diagenode社のMegaruptor（登録商標）を用いてランダムシアリングによって生成され得る超長鎖DNAフラグメントが必要です。</p>
<h3><a href="http://www.lifetechnologies.com/be/en/home/life-science/sequencing/next-generation-sequencing/solid-next-generation-sequencing.html" target="_blank">SOLiD</a></h3>
<p>SOLiDは、ユニークな化学作用により、何千という個々のDNA分子の同時配列決定を可能にします。 それは、アダプター対ライブラリーのフラグメントが適切で、せん断されたゲノムDNAへのアダプターのライゲーションによるライブラリー作製から始まります。 次のステップでは、エマルジョンPCR（emPCR）を実施して、ビーズの表面上の個々の鋳型DNA分子をクローン的に増幅。 emPCRでは、個々の鋳型DNAをPCR試薬と混合し、水中油型エマルジョン内の疎水性シェルで囲まれた水性液滴内のプライマーコートビーズを、配列決定のためにロードするスライドガラスの表面にランダムに付着。 この技術は、シークエンシングプライマーへのライゲーションで競合する4つの蛍光標識されたジ塩基プローブのセットを使用します。</p>
<h3><a href="http://454.com/products/technology.asp" target="_blank">454</a></h3>
<p>454は、大規模並列パイロシーケンシングを利用しています。 始めに全ゲノムDNAまたは標的遺伝子断片の300〜800bp断片のライブラリー調製します。 次に、DNAフラグメントへのアダプターの付着および単一のDNA鎖の分離。 その後アダプターに連結されたDNAフラグメントをエマルジョンベースのクローン増幅（emPCR）で処理し、DNAライブラリーフラグメントをミクロンサイズのビーズ上に配置します。 各DNA結合ビーズを光ファイバーチップ上のウェルに入れ、器具に挿入します。 4つのDNAヌクレオチドは、配列決定操作中に固定された順序で連続して加えられ、並行して配列決定されます。</p>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>&reg;</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>&reg;</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor<sup>&reg;</sup></a>.</div>
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<p></p>
<div class="row">
<div class="small-7 medium-7 large-7 columns text-center"><img src="https://www.diagenode.com/img/applications/true-flexibility-with-br-ngs.jpg" /></div>
<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>&reg;</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 &micro;l volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 &micro;l volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A &amp; B:</b> peak electropherogram view. <b>Panel C &amp; D:</b> virtual gel view.</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor&reg; using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
</div>
<p><br /><br /></p>
<div class="row">
<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor&reg; using long fragment size Hydropores. &nbsp;</strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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			'description' => '<div class="row" style="text-align: center;">
<h3><strong>Your partner in long-read sequencing</strong></h3>
<p>Sequencing technologies have revolutionized genomics and biology researches. Long read sequencing enables researchers to access a more comprehensive view of genomes with higher accuracy. However, one of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size. The Megaruptor gives state-of-art shearing performance providing optimal long-read sequencing using <strong>PacBio&reg; and Oxford Nanopore<sup>TM</sup>technologies.</strong></p>
<p><strong></strong></p>
<center><a href="https://www.diagenode.com/p/megaruptor-cassette-12" class="tiny details button">CHECK OUT THE NEW 12-SAMPLE CASSETTE. RUN 50% MORE SAMPLES ON YOUR MEGARUPTOR 3!</a></center>
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<p><a href="https://www.diagenode.com/en/documents/pacbio-megaruptor-application-note"><img src="https://www.diagenode.com/img/banners/pacbio-mega-banner.png" /></a></p>
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<center>
<h4 style="font-size: 22px;"><a href="https://www.diagenode.com/en/p/megaruptor-3">Click here to discover our latest innovation</a></h4>
</center>
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<p><span>We have designed the Megaruptor</span>&reg;&nbsp;<span>2 using our highest level of knowledge in shearing so that it exceeds your expectations. This device will serve your research needs for many years and will provide the best experience with long DNA molecules preparation. </span></p>
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<p><span>The Megaruptor</span><span>&reg; </span><span>2 was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA in the range of 3 kb - 75 kb </span><span>(contact us for the 3 kb setting)</span><span>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly interface allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design. </span></p>
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			'description' => '<p>Several methods exist today for shearing genomic DNA, but few are reliable for generating DNA fragments &gt;50 kb necessary for assembly of many microbial, human, plant and animal genomes <em>de novo</em>. Pacific Biosciences highly recommends the Megaruptor<sup>TM</sup> System for shearing genomic DNA to large fragments for long-read sequencing in the Sequel&reg; System.</p>',
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			'name' => 'Detection and Quantitation of DNA Damage on a Genome-wide ScaleUsing RADAR-seq.',
			'authors' => 'Zatopek  Kelly M et al.',
			'description' => '<p>The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate DNA damage sites across a genome enable an understanding of the consequences of DNA damage as well as how damage is repaired, which can have key diagnostic and therapeutic implications. Importantly, advancements in technology have enabled the development of high-throughput sequencing-based DNA damage detection methods. These methods require DNA enrichment or amplification steps that limit the ability to quantitate the DNA damage sites. Further, each of these methods is typically tailored to detect only a specific type of damage. RAre DAmage and Repair (RADAR) sequencing is a DNA sequencing workflow that overcomes these limitations and enables detection and quantitation of DNA damage sites in any organism on a genome-wide scale. RADAR-seq works by replacing DNA damage sites with a patch of modified bases that can be directly detected by Pacific Biosciences Single-Molecule Real Time sequencing. Here, we present three protocols that enable detection of thymine dimers and ribonucleotides in bacterial and archaeal genomes. Basic Protocol 1 enables construction of a reference genome required for RADAR-seq analyses. Basic Protocol 2 describes how to locate, quantitate, and compare thymine dimer levels in Escherichia coli exposed to varying amounts of UV light. Basic Protocol 3 describes how to locate, quantitate, and compare ribonucleotide levels in wild-type and &Delta;RNaseH2 Thermococcus kodakarensis. Importantly, all three protocols provide in-depth steps for data analysis. Together they serve as proof-of-principle experiments that will allow users to adapt the protocols to locate and quantitate a wide variety of DNA damage sites in any organism. &copy; 2022 New England Biolabs. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Constructing a reference genome utilizing SMRT sequencing Basic Protocol 2: Mapping and quantitating genomic thymine dimer formation in untreated versus UV-irradiated E. coli using RADAR-seq Basic Protocol 3: Mapping and quantitating genomic ribonucleotide incorporation in wildtype versus &Delta;RNaseH2 T. kodakarensis using RADAR-seq.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36374013',
			'doi' => '10.1002/cpz1.595',
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			'name' => 'Predictable and stable epimutations induced during clonal plantpropagation with embryonic transcription factor.',
			'authors' => 'Wibowo  Anjar Tri et al.',
			'description' => '<p>Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.</p>',
			'date' => '2022-11-01',
			'pmid' => '/',
			'doi' => '10.1371/journal.pgen.1010479',
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			'id' => '4536',
			'name' => 'Benchmarking second and third-generation sequencing platforms formicrobial metagenomics.',
			'authors' => 'Meslier  Victoria et al.',
			'description' => '<p>Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36369227',
			'doi' => '10.1038/s41597-022-01762-z',
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			'name' => 'Mitochondrial RNA editing in Trypanoplasma borreli: new tools, newrevelations',
			'authors' => 'Gerasimov  Evgeny S. et al.',
			'description' => '<p>The kinetoplastids are unicellular flagellates that derive their name from the &lsquo;kinetoplast&rsquo;, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein products of this mitochondrial genome are encoded as cryptogenes; their transcripts require editing to generate an open reading frame. This happens through RNA editing, whereby small regulatory guide (g)RNAs direct the proper insertion and deletion of one or more uridines at each editing site within specific transcript regions. An accurate perspective of the kDNA expansion and evolution of their unique uridine insertion/deletion editing across kinetoplastids has been difficult to achieve. Here, we resolved the kDNA structure and editing patterns in the early-branching kinetoplastid Trypanoplasma borreli and compare them with those of the well-studied trypanosomatids. We find that its kDNA consists of circular molecules of about 42 kb that harbor the rRNA and protein-coding genes, and 17 different contigs of approximately 70 kb carrying an average of 23 putative gRNA loci per contig. These contigs may be linear molecules, as they contain repetitive termini. Our analysis uncovered a putative gRNA population with unique length and sequence parameters that is massive relative to the editing needs of this parasite. We validated or determined the sequence identity of four edited mRNAs, including one coding for ATP synthase 6 that was previously thought to be missing. We utilized computational methods to show that the T. borreli transcriptome includes a substantial number of transcripts with inconsistent editing patterns, apparently products of non-canonical editing. This species utilizes the most extensive uridine deletion compared to other studied kinetoplastids to enforce amino acid conservation of cryptogene products, although insertions still remain more frequent. Finally, in three tested mitochondrial transcriptomes of kinetoplastids, uridine deletions are more common in the raw mitochondrial reads than aligned to the fully edited, translationally competent mRNAs. We conclude that the organization of kDNA across known kinetoplastids represents variations on partitioned coding and repetitive regions of circular molecules encoding mRNAs and rRNAs, while gRNA loci are positioned on a highly unstable population of molecules that differ in relative abundance across strains. Likewise, while all kinetoplastids possess conserved machinery performing RNA editing of the uridine insertion/deletion type, its output parameters are species-specific.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.csbj.2022.11.023',
			'doi' => '10.1016/j.csbj.2022.11.023',
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			'id' => '4737',
			'name' => 'Evaluation of the pathogenesis of non-typical strain with α-hemolysin,Vibrio parahaemolyticus 353, isolated from Chinese seafood throughcomparative genome and transcriptome analysis.',
			'authors' => 'Zha  Fei et al.',
			'description' => '<p>Vibrio parahaemolyticus outbreaks frequently occur, causing gastrointestinal sickness owing to the consumption of aquatic foods by various virulence factors; however, the mechanism of pathogenesis is still unknown. In this study, a non-typical strain of V. parahaemolyticus, named VP353, was isolated from shrimp in China. Its comparative genome and transcriptome after infection with Caco-2 cells were examined to illustrate the mechanisms of its pathogenesis. VP353 was a tdh-trh- strain but uncommonly manifested robust cytotoxicity towards Caco-2 cells. Compared with the standard strain RIMD2210633, VP353 harbored alpha-hemolysins (hlyA, hlyB, hlyC, and hlyD) was first reported in V. parahaemolyticus and showed high diversity in the T3SS2 gene cluster. Moreover, the expression of flagella, T2SS, quorum sensing-related genes, hlyA, hlyC were up-regulated, and hlyB, hlyD were down-regulated. In summary, our results demonstrate that some novel virulence factors contribute to the pathogenesis of V. parahaemolyticus infection.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36437125',
			'doi' => '10.1016/j.marpolbul.2022.114276',
			'modified' => '2023-03-07 08:55:16',
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			'id' => '4476',
			'name' => 'Rapid and comprehensive diagnostic method for repeat expansion diseasesusing nanopore sequencing.',
			'authors' => 'Miyatake  S. et al.',
			'description' => '<p>We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36289212',
			'doi' => '10.1038/s41525-022-00331-y',
			'modified' => '2022-11-18 12:21:42',
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			'id' => '4478',
			'name' => 'Characterization of somatic structural variations in 528 Chineseindividuals with Esophageal squamous cell carcinoma.',
			'authors' => 'Cui   H. et al.',
			'description' => '<p>Esophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations' mechanisms and biological functions. SVs show multi-mode distributions in size, indicating distinct mutational processes. We develop a tool and define five types of complex rearrangements with templated insertions. We highlight a type of fold-back inversion, which is associated with poor outcomes. Distinct rearrangement signatures demonstrate variable genomic metrics such as replicating time, spatial proximity, and chromatin accessibility. Specifically, fold-back inversion tends to occur near the centrosome; TD-c2 (Tandem duplication-cluster2) is significantly enriched in chromatin-accessibility and early-replication region compared to other signatures. Analyses of TD-c2 signature reveal 9 TD hotspots, of which we identify a hotspot consisting of a super-enhancer of PTHLH. We confirm the oncogenic effect of the PTHLH gene and its interaction with enhancers through functional experiments. Finally, extrachromosomal circular DNAs (ecDNAs) are present in 14\% of ESCCs and have strong selective advantages to driver genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36272974',
			'doi' => '10.1038/s41467-022-33994-3',
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			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4483',
			'name' => 'The Capparis spinosa var. herbacea genome provides the first genomicinstrument for a diversity and evolution study of the Capparaceae family.',
			'authors' => 'Wang  Lei et al.',
			'description' => '<p>BACKGROUND: The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS: We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23\% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28\%, and transposable element sequences accounted for 43.98\%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55\% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82\% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS: This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36310248',
			'doi' => '10.1093/gigascience/giac106',
			'modified' => '2022-11-18 12:30:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4484',
			'name' => 'Genomic Characterization and Antimicrobial Susceptibility ofDromedary-Associated  from the Horn of Africa.',
			'authors' => 'Akarsu  H. et al.',
			'description' => '<p>Members of the family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized strains from apparently healthy and diseased camels ( = 84) and cattle ( = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by (K), /, /, /, , , , and , respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the and families, reported here for the first time for certain species of . All strains contained at least one intact prophage sequence, mainly belonging to the family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct clades and species. Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226992',
			'doi' => '10.1128/aem.01146-22',
			'modified' => '2022-11-18 12:31:20',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4418',
			'name' => 'Complete Genome Sequences of the Soil Oxalotrophic BacteriumCupriavidus oxalaticus Strain Ox1 and Its DerivedmCherry-Tagged Strain.',
			'authors' => 'Palmieri  Fabio et al. ',
			'description' => '<p>Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69&thinsp;Mb, with a GC content of 66.9\%. The genome sequence of Ox1 contains a complete operon for the degradation and assimilation of oxalate.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35924938',
			'doi' => '10.1128/mra.00181-22',
			'modified' => '2022-09-27 14:42:06',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4442',
			'name' => 'The improved genome of the nematode Parapristionchus giblindavisiprovides insights into lineage-specific gene family evolution.',
			'authors' => 'Röseler  W. et al. ',
			'description' => '<p>Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricted genes. To trace back the evolution of such new or rapidly evolving genes, a robust phylogenomic framework is indispensable. Here, we present an improved version of the genome of Parapristionchus giblindavisi which is the only known member of the sister group of Pristionchus. Relative to the previous short read assembly, the new genome is based on long reads and displays higher levels of contiguity, completeness, and correctness. Specifically, the number of contigs dropped from over 7303 to 735 resulting in an N50 increase from 112&thinsp;kb to 791&thinsp;kb. We made use of the new genome to revisit the evolution of multiple gene families. This revealed Pristionchus-specific expansions of several environmentally responsive gene families and a Pristionchus-specific loss of the de novo purine biosynthesis pathway. Focusing on the evolution of sulfatases and sulfotransferases, which control the mouth form plasticity in P. pacificus, reveals differences in copy number and genomic configurations between the genera Pristionchus and Parapristionchus. Altogether, this demonstrates the utility of the P. giblindavisi genome to date and polarize lineage-specific patterns.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35980151',
			'doi' => '10.1093/g3journal/jkac215',
			'modified' => '2022-10-14 16:33:33',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4443',
			'name' => 'The chromosome-level genome of Gypsophila paniculata reveals themolecular mechanism of floral development and ethylene insensitivity',
			'authors' => 'Fan  Li et al. ',
			'description' => '<p>Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the worldwide famous cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with a total size of 749.58 Mb. Whole-genome duplication signatures unveil two major duplication events in its evolutionary history, an ancient one occurring before the divergence of Caryophyllaceae and a more recent one shared with Dianthus caryophyllus. The integrative analyses combining genomic and transcriptomic data reveal the mechanisms regulating floral development and ethylene response of G. paniculata. The reduction of AGAMOUS expression probably caused by sequence polymorphism and the mutation in miR172 binding site of PETALOSA are associated with the double flower formation in G. paniculata. The low expression of ERS (ETHYLENE RESPONSE SENSOR) and the reduction of downstream ERF (ETHYLENE RESPONSE FACTOR) gene copy number collectively lead to the ethylene insensitivity of G. paniculata, affecting flower senescence and making it capable of making dried flowers. This study provides a cornerstone for understanding the underlying principles governing floral development and flower senescence, which could accelerate the molecular breeding of the Caryophyllaceae species.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac176/6674669',
			'doi' => '10.1093/hr/uhac176',
			'modified' => '2022-10-14 16:34:34',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4445',
			'name' => 'Patients with biallelic GGC repeat expansions in NOTCH2NLCexhibiting a typical neuronal intranuclear inclusion disease phenotype.',
			'authors' => 'Kameyama  Shinichi et al.',
			'description' => '<p>We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of the entire NOTCH2NLC GGC repeat expansion and DNA methylation were comprehensively evaluated using fluorescent amplicon length PCR (AL-PCR), Southern blotting and targeted long-read sequencing, and detailed genetic/epigenetic and clinical features were described. In AL-PCR, we could not recognize the wild-type allele in both patients. Targeted long-read sequencing revealed that one patient harbored a homozygous repeat expansion. The other patient harbored compound heterozygous repeat expansions. The GGC repeats and the nearest CpG island were hypomethylated in all expanded alleles in both patients. Both patients harboring the biallelic GGC repeat expansion showed a typical dementia-dominant NIID phenotype. In conclusion, the biallelic GGC repeat expansion in two typical NIID patients indicated that NOTCH2NLC-related diseases could be completely dominant.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36041634',
			'doi' => '10.1016/j.ygeno.2022.110469',
			'modified' => '2022-10-21 09:28:25',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4453',
			'name' => 'A haplotype resolved chromosomal level avocado genome allows analysis ofnovel avocado genes',
			'authors' => 'Onkar N. et al. ',
			'description' => '<p>Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80\% of the world&rsquo;s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8\% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48&thinsp;915 avocado genes of which 39&thinsp;207 could be ascribed functions. The genome contained 62.6\% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac157/6652665',
			'doi' => 'https://doi.org/10.1093/hr/uhac157',
			'modified' => '2022-10-21 09:36:02',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4432',
			'name' => 'Identification of Laportea bulbifera using the Complete ChloroplastGenome as a Super-Barcode',
			'authors' => 'Wang  Wenting et al.',
			'description' => '<p>Laportea bulbifera, a Miao medicine grown in karst areas, has exerts a unique curative effect on skin itching in the elderly, with an annual sales of &gt; 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation highthroughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence used as a super-barcode and the highly variable regions (ycf1, matK, and ndhD), especially matK, can be used as specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1793400%2Fv1',
			'doi' => '10.21203/rs.3.rs-1793400/v1',
			'modified' => '2022-09-28 09:10:15',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4435',
			'name' => 'Oxford Nanopore R10.4 long-read sequencing enables the generation ofnear-finished bacterial genomes from pure cultures and metagenomes withoutshort-read or reference polishing.',
			'authors' => 'Sereika  Mantas et al.',
			'description' => '<p>Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35789207',
			'doi' => '10.1038/s41592-022-01539-7',
			'modified' => '2022-09-28 09:21:29',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4462',
			'name' => 'Complete Genome Sequences of Multidrug-Resistant Campylobactercoli Strains YH501, YH503, and YH504, from Retail Chicken.',
			'authors' => 'He  Yiping et al.',
			'description' => '<p>Campylobacter coli is an important foodborne pathogen that can cause inflammation of the intestine and diarrhea in humans. The complete genomes, including megaplasmids, of C. coli strains YH501, YH503, and YH504 from retail chicken were sequenced and assembled. Whole-genome analysis revealed a number of virulence and antibiotic resistance genes, suggesting significant potential for these poultry-originating isolates to cause human disease.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35862903',
			'doi' => '10.1128/mra.00237-22',
			'modified' => '2022-10-21 09:48:05',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4463',
			'name' => 'High-Quality Genome Assembly of Nannochloris desiccata 2437 andIts Associated Bacterial Community.',
			'authors' => 'Sanders  Claire K et al.',
			'description' => '<p>High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assembled in 29 contigs.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35770994',
			'doi' => '10.1128/mra.00710-21',
			'modified' => '2022-10-21 09:48:45',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4461',
			'name' => 'Long-read Oxford nanopore sequencing reveals a de novo case of complexchromosomal rearrangement involving chromosomes 2, 7, and 13.',
			'authors' => 'Xing  Lingling et al.',
			'description' => '<p>BACKGROUND: Complex chromosomal rearrangements (CCRs) are associated with high reproductive risk, infertility, abnormalities in offspring, and recurrent miscarriage in women. It is essential to accurately characterize apparently balanced chromosome rearrangements in unaffected individuals. METHODS: A CCR young couple who suffered two spontaneous abortions and underwent labor induction due to fetal chromosomal abnormalities was studied using long-read sequencing(LRS), single-nucleotide polymorphism (SNP) array, G-banding karyotype analysis (550-band resolution), and Sanger sequencing. RESULTS: SNP analysis of the amniotic fluid cells during the third pregnancy revealed a 9.9-Mb duplication at 7q21.11q21.2 and a 24.8-Mb heterozygous deletion at 13q21.1q31.1. The unaffected female partner was a carrier of a three-way CCR [46,XX,? ins(7;13)(q21.1;q21.1q22)t(2;13)(p23;q22)]. Subsequent LRS analysis revealed the exact breakpoint locations on the derivative chromosomes and the specific method of chromosome rearrangement, indicating that the CCR carrier was a more complex structural rearrangement comprising five breakpoints. Furthermore, LRS detected an inserted fragment of chromosome 13 in chromosome 7. CONCLUSIONS: LRS is effective for analyzing the complex structural variations of the human genome and may be used to clarify the specific CCRs for effective genetic counseling and appropriate intervention.</p>',
			'date' => '2022-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35758276',
			'doi' => '10.1002/mgg3.2011',
			'modified' => '2022-10-21 09:47:15',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4361',
			'name' => 'Accumulation of endosymbiont genomes in an insect autosome followed byendosymbiont replacement.',
			'authors' => 'Tvedte  Eric S. et al. ',
			'description' => '<p>Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT). A prominent source of LGT is Wolbachia, a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells. The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive and has been localized to chromosome 4, contributing to chromosome expansion in this lineage. As has happened frequently with claims of bacteria-to-eukaryote LGT, the contribution of wAna transfers to the expanded size of D.&nbsp;ananassae chromosome 4 has been specifically contested owing to an assembly where Wolbachia sequences were classified as contaminants and removed. Here, long-read sequencing with DNA from a Wolbachia-cured line enabled assembly of 4.9 Mbp of nuclear Wolbachia transfers (nuwts) in D.&nbsp;ananassae and a 24-kbp nuclear mitochondrial transfer. The nuwts are &lt;8,000 years old in at least two locations in chromosome 4 with at least one whole-genome integration followed by rapid extensive duplication of most of the genome with regions that have up to 10 copies. The genes in nuwts are accumulating small indels and mobile element insertions. Among the highly duplicated genes are cifA and cifB, two genes associated with Wolbachia-mediated Drosophila cytoplasmic incompatibility. The wAna strain that was the source of nuwts was subsequently replaced by a different wAna endosymbiont. Direct RNA Nanopore sequencing of Wolbachia-cured lines identified nuwt transcripts, including spliced transcripts, but functionality, if any, remains elusive.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35671755',
			'doi' => '10.1016/j.cub.2022.05.024',
			'modified' => '2022-08-04 15:47:25',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '4363',
			'name' => 'DNA Hypermethylation and a Specific Methylation Spectrum on theX Chromosome in Turner Syndrome as Determined by NanoporeSequencing',
			'authors' => 'Fan  Xin et al.',
			'description' => '<p>The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate TS. Results: Thirteen TS (45X0) patients and eight controls were enrolled. Trio-WES analysis did not find any pathogenetic or likely pathogenic variants except X chromosome (chrX) deletion. The average methylation levels and patterns of chrX in 45X0 and 46XY were similar, and significantly higher than in 46XX (p = 2.22 &times; 10&minus;16). Both hyper-methylation and hypo-methylation were detected in the CpG island (CGI), CGI_shore, promoter, genebody, and PAR1-region, while in the transposon element inactivation regions of the chrX and hypermethylation were predominant. A total of 125 differentially methylated genes were identified in 45X0 compared to 46XX, including 8 and 117 hypermethylated and hypomethylated genes, respectively, with the enrichment terms of mitophagy, regulation of DNA-binding transcription factor activity, etc. Conclusions: The results suggest that the methylation profile in patients with TS might be determined by the number of X chromosomes; the patterns of methylation in TS were precisely associated with the maintenance of genomic stability and improvement of gene expression. Differentially methylated genes/pathways might reveal the potential epigenetic modulation and lead to better understanding of TS.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://doi.org/10.3390%2Fjpm12060872',
			'doi' => '10.3390/jpm12060872',
			'modified' => '2022-08-04 15:49:32',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '4530',
			'name' => 'The genome sequence of Anoplius nigerrimus (Scopoli, 1763), a spiderwasp',
			'authors' => 'Falk  Steven and Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual Anoplius nigerrimus (Arthropoda; Insecta; Hymenoptera; Pompilidae) of unknown sex. The genome sequence is 624 megabases in span. In total, 45.75\% of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 17.5 kilobases in length.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17814.1',
			'doi' => '10.12688/wellcomeopenres.17814.1',
			'modified' => '2023-02-17 08:59:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4522',
			'name' => 'Familial long-read sequencing increases yield of de novo mutations.',
			'authors' => 'Noyes  Michelle D et al.',
			'description' => '<p>Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20\% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5\% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41&nbsp;&times; 10 substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by &gt;25\% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35290762',
			'doi' => '10.1016/j.ajhg.2022.02.014',
			'modified' => '2023-02-17 09:01:49',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4525',
			'name' => 'Transposon activity, local duplications and propagation of structuralvariants across haplotypes drive the evolution of the Drosophila S2cell line.',
			'authors' => 'Lewerentz  Jacob et al.',
			'description' => '<p>BACKGROUND: Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure. RESULTS: Using a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (&gt;&thinsp;80\% of SVs), with Gypsy retrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in other D. melanogaster cell lines. CONCLUSIONS: The S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35392795',
			'doi' => '10.1186/s12864-022-08472-1',
			'modified' => '2023-02-17 09:02:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4466',
			'name' => 'Phylogenomics and Comparative Genomics Highlight SpecificGenetic Features in  Species.',
			'authors' => 'Sun  Yi-Fei et al.',
			'description' => '<p>The species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven genomes, including three new genomes, , , and . The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the species.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35330313',
			'doi' => '10.3390/jof8030311',
			'modified' => '2022-10-21 09:50:01',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4366',
			'name' => 'Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes',
			'authors' => 'Rabanal  Fernando A. and Gräff  Maike and Lanz  Christa andFritschi  Katrin and Llaca  Victor and Lang  Michelle andCarbonell-Bejerano  Pablo and Henderson  Ian and Weigel Detlef',
			'description' => '<p><span>Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant&nbsp;</span><em>Arabidopsis thaliana</em><span>, other than the reference accession Col-0, all other accessions<span>&nbsp;</span></span><em>de novo</em><span><span>&nbsp;</span>assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of &gt;85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two<span>&nbsp;</span></span><em>A. thaliana</em><span><span>&nbsp;</span>accessions.</span></p>',
			'date' => '2022-02-15',
			'pmid' => 'https://doi.org/10.1101%2F2022.02.15.480579',
			'doi' => '10.1101/2022.02.15.480579',
			'modified' => '2022-08-04 16:02:44',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4362',
			'name' => 'Chromosomal rearrangements with stable repertoires of genes andtransposable elements in an invasive forest-pathogenic fungus',
			'authors' => 'Demené A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2021.03.09.434572v5',
			'doi' => '/',
			'modified' => '2022-08-04 15:48:42',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4374',
			'name' => 'Genomic characterisation of three GES-producing Enterobacteralesisolated in the Czech Republic.',
			'authors' => 'Finianos  M. et al.',
			'description' => '<p>OBJECTIVES: The aim of the study is to characterise the genomic features of three GES-producing Enterobacterales isolates from Czech hospitals. METHODS: In 2020, during a routine screening of the hospital's surfaces in Prague General Hospital, two strains (CZ862 and CZ863) that belonged to the Enterobacter cloacae complex were found to be bla positive. Another bla positive strain identified as Klebsiella oxytoca was recovered from a patient hospitalised in Pilsen. Antibiotic susceptibility profiling was done with broth microdilution assay. Conjugation/transformation experiments were performed on all three strains. Genomic DNA of the three isolates was subjected to whole genome sequencing using PacBio platform. RESULTS: Multilocus sequence types typing of CZ862 and CZ863 identified the strains as ST837 and a novel ST (ST1622). Both bla harbouring plasmids showed high sequence similarity and complete query coverage (100\% and 99.98\%) with pEcl-35771cz. Both plasmids had two copies of bla instead of one copy as found in pEcl-35771cz. The clinical isolate CZ598 belonged to ST180. The plasmid harboured bla gene, cat and aac(6')-lb and the novel variant bla No similar sequences were observed, suggesting a novel plasmid. CONCLUSION: The detection of the two bla-positive plasmids in the same hospital environment, the first report after 3 years, suggests a hidden source. This highlights the importance of the hidden sources and evolution of such plasmids on the route of spreading into clinical settings. Also, the detection of the new bla, which is thought in this case to be associated with carbapenem resistance, imposes a health risk if disseminated, limiting therapeutic options.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35231657',
			'doi' => '10.1016/j.jgar.2022.02.016',
			'modified' => '2022-08-04 16:18:16',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4254',
			'name' => 'Improved chromosome-level genome assembly of the Glanville fritillarybutterfly () integrating Pacific Biosciences long reads and ahigh-density linkage map',
			'authors' => 'Smolander Olli-Pekka et al.',
			'description' => '<p>Abstract Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92&ndash;94\% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35022701',
			'doi' => '10.1093/gigascience/giab097',
			'modified' => '2022-05-20 09:45:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '4284',
			'name' => 'PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs,and methylation.',
			'authors' => 'Mahmoud Medhat et al.',
			'description' => '<p>Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34521442',
			'doi' => '10.1186/s13059-021-02486-w',
			'modified' => '2022-05-24 09:07:16',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '4286',
			'name' => 'Establishing community reference samples, data and call sets forbenchmarking cancer mutation detection using whole-genome sequencing.',
			'authors' => 'Fang Li Tai et al.',
			'description' => '<p>The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with &gt;2,000-fold coverage, spanning 82\% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34504347',
			'doi' => '10.1038/s41587-021-00993-6',
			'modified' => '2022-05-24 09:09:41',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4291',
			'name' => 'LeafGo: Leaf to Genome, a quick workflow to produce high-quality denovo plant genomes using long-read sequencing technology.',
			'authors' => 'Driguez Patrick et al.',
			'description' => '<p>Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34479618',
			'doi' => '10.1186/s13059-021-02475-z',
			'modified' => '2022-05-24 09:16:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4310',
			'name' => 'Targeted long-read sequencing identifies missing disease-causingvariation.',
			'authors' => 'Miller Danny E et al.',
			'description' => '<p>Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.ajhg.2021.06.006',
			'doi' => '10.1016/j.ajhg.2021.06.006',
			'modified' => '2022-06-22 09:26:54',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4342',
			'name' => 'Evidence of an epidemic spread of KPC-producing  in Czech hospitals',
			'authors' => 'Kraftova Lucie et al.',
			'description' => '<p>The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018&ndash;2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n&thinsp;=&thinsp;12), N (n&thinsp;=&thinsp;5), C (n&thinsp;=&thinsp;1) and P6 (n&thinsp;=&thinsp;1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn&rsquo;t be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34344951',
			'doi' => '10.1038/s41598-021-95285-z',
			'modified' => '2022-06-22 09:33:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => array(
			'id' => '4309',
			'name' => 'The USDA-ARS Ag100Pest Initiative: High-Quality GenomeAssemblies for Agricultural Pest Arthropod Research',
			'authors' => 'Childers  A.K. et al.',
			'description' => '<p>Simple Summary High-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technical challenge of isolating the necessary quantity and quality of DNA from many species. Sequencing methods have now improved such that many insect genomes can be sequenced and assembled at scale. We created the Ag100Pest Initiative to propel agricultural research forward by assembling reference-quality genomes of important arthropod pest species. Here, we describe the Ag100Pest Initiative&rsquo;s processes and experimental procedures. We show that the Ag100Pest Initiative will greatly expand the diversity of publicly available arthropod genome assemblies. We also demonstrate the high quality of preliminary contig assemblies. We share arthropod-specific technical details and insights that we have gained during the project. The methods and preliminary results presented herein should help other researchers attain similarly high-quality assemblies, effectively changing the landscape of insect genomics. Abstract The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture&rsquo;s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale.</p>',
			'date' => '2021-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34357286',
			'doi' => '10.3390/insects12070626',
			'modified' => '2022-08-03 16:18:33',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 35 => array(
			'id' => '4311',
			'name' => 'The American lobster genome reveals insights on longevity, neural, andimmune adaptations.',
			'authors' => 'Polinski J. M. et al. ',
			'description' => '<p>The American lobster, , is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we report a high-quality draft assembly of the genome with 25,284 predicted gene models. Analysis of the neural gene complement revealed extraordinary development of the chemosensory machinery, including a profound diversification of ligand-gated ion channels and secretory molecules. The discovery of a novel class of chimeric receptors coupling pattern recognition and neurotransmitter binding suggests a deep integration between the neural and immune systems. A robust repertoire of genes involved in innate immunity, genome stability, cell survival, chemical defense, and cuticle formation represents a diversity of defense mechanisms essential to thrive in the benthic marine environment. Together, these unique evolutionary adaptations contribute to the longevity and ecological success of this long-lived benthic predator.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34162536',
			'doi' => '10.1126/sciadv.abe8290',
			'modified' => '2022-08-03 16:19:34',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => array(
			'id' => '4316',
			'name' => 'Analysis of the Coptis chinensis genome reveals the diversification ofprotoberberine-type alkaloids.',
			'authors' => 'Liu Y. et al. ',
			'description' => '<p>Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34078898',
			'doi' => '10.1038/s41467-021-23611-0',
			'modified' => '2022-08-03 16:20:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 37 => array(
			'id' => '4348',
			'name' => 'Infectivity assessment of porcine endogenous retrovirus usinghigh-throughput sequencing technologies.',
			'authors' => 'Kono K. et al.',
			'description' => '<p>Xenogenic cell-based therapeutic products are expected to alleviate the chronic shortage of human donor organs. For example, porcine islet cell products are currently under development for the treatment of human diabetes. As porcine cells possess endogenous retrovirus (PERV), which can replicate in human cells in vitro, the potential transmission of PERV has raised concerns in the case of products that use living pig cells as raw materials. Although several PERV sequences exist in the porcine genome, not all have the ability to infect human cells. Therefore, polymerase chain reaction analysis, which amplifies a portion of the target gene, may not accurately assess the infection risk. Here, we determined porcine genome sequences and evaluated the infectivity of PERVs using high-throughput sequencing technologies. RNA sequencing was performed on both PERV-infected human cells and porcine cells, and reads mapped to PERV sequences were examined. The normalized number of the reads mapped to PERV regions was able to predict the infectivity of PERVs, indicating that it would be useful for evaluation of the PERV infection risk prior to transplantation of porcine products.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.biologicals.2021.05.001',
			'doi' => '10.1016/j.biologicals.2021.05.001',
			'modified' => '2022-08-03 16:57:04',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 38 => array(
			'id' => '4128',
			'name' => 'Chromosomal inversion polymorphisms in two sympatric ascidian lineages.',
			'authors' => 'Satou, Yutaka and Sato, Atsuko and Yasuo, Hitoyoshi and Mihirogi, Yukie andBishop, John and Fujie, Manabu and Kawamitsu, Mayumi and Hisata, Kanako andSatoh, Noriyuki',
			'description' => '<p>Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. While these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. While the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33822040',
			'doi' => '10.1093/gbe/evab068',
			'modified' => '2021-12-07 10:17:37',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4186',
			'name' => 'Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.',
			'authors' => 'Formenti G. et al.',
			'description' => '<p>BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (&gt;&thinsp;10&nbsp;kbp, PacBio or Nanopore) and short (100-300&thinsp;bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33910595',
			'doi' => '10.1186/s13059-021-02336-9',
			'modified' => '2022-01-05 15:01:11',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => array(
			'id' => '4140',
			'name' => 'Chromosomal rearrangements but no change of genes and transposable elementsrepertoires in an invasive forest-pathogenic fungus',
			'authors' => 'Demené, A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long-reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that C. parasitica genome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high quality assembled genomes, and question the role of structural variations on the invasive success of this fungal pathogen species.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1101%2F2021.03.09.434572',
			'doi' => '10.1101/2021.03.09.434572',
			'modified' => '2021-12-13 09:19:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 41 => array(
			'id' => '4191',
			'name' => 'A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.',
			'authors' => 'Liu H. et al. ',
			'description' => '<p>Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population resulting from the mating of Pekin ducks (white-shelled eggs) and mallards (green-shelled eggs). We further narrowed the candidate region to a 30-kb interval by comparing genome divergence in seven indigenous duck populations. Among the genes located in the finely mapped region, only one transcript of the ABCG2 gene (XM_013093252.2) exhibited higher uterine expression in green-shelled individuals than in white-shelled individuals, as supported by transcriptome data from four populations. ABCG2 has been reported to encode a protein that functions as a membrane transporter for biliverdin. Sanger sequencing of the whole 30-kb candidate region (Chr4: 47.41-47.44&nbsp;Mb) and a plasmid reporter assay helped to identify a single nucleotide polymorphism (Chr4: 47,418,074 G&gt;A) located in a conserved predicted promoter region whose variation may alter ABCG2 transcription activity. We provide a useful molecular marker for duck breeding and contribute data to the research on ecological evolution based on egg colour patterns among birds.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33372351',
			'doi' => '10.1111/mec.15785',
			'modified' => '2022-01-05 15:13:30',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => array(
			'id' => '4131',
			'name' => 'Genomic Characterization of VIM and MCR Co-Producers: The First TwoClinical Cases, in Italy.',
			'authors' => 'Marchetti, Vittoria Mattioni and Bitar, Ibrahim and Sarti, Mario andFogato, Elena and Scaltriti, Erika and Bracchi, Chiara and Hrabak, Jaroslavand Pongolini, Stefano and Migliavacca, Roberta',
			'description' => '<p>BACKGROUND: the co-production of carbapenemases and -genes represents a worrisome event in the treatment of infections. The aim of the study was to characterize the genomic features of two clinical complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. METHODS: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the and - type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). RESULTS: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The gene was harbored on a conjugative IncHI2 plasmid, while the determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: gene and its two component regulatory genes for increased expression on the chromosome, on non-conjugative (yet co-transferable) ColE plasmid, and on a non-conjugative IncA plasmid. CONCLUSIONS: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33418979',
			'doi' => '10.3390/diagnostics11010079',
			'modified' => '2021-12-07 10:22:20',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 43 => array(
			'id' => '4190',
			'name' => 'Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).',
			'authors' => 'Xia Z. et al.',
			'description' => '<p>Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7&thinsp;Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~1327.18&thinsp;Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33419990',
			'doi' => '10.1038/s41438-020-00455-1',
			'modified' => '2022-01-05 15:12:13',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 44 => array(
			'id' => '4205',
			'name' => 'Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.',
			'authors' => 'Suzuki Y. et al.',
			'description' => '<p>Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals characterizing rapid, haplotype-specific evolution of human centromeric arrays, while frequent single-nucleotide variants are largely conserved. We found a characteristic pattern shared among prevalent variants in human and chimpanzee. Our findings pave the way for studying sequence evolution in human and primate centromeres.</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33310858',
			'doi' => '10.1126/sciadv.abd9230',
			'modified' => '2022-01-06 15:00:50',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 45 => array(
			'id' => '4212',
			'name' => 'Efficient hybrid de novo assembly of human genomes with WENGAN.',
			'authors' => 'Di Genova A. et al. ',
			'description' => '<p>Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24-80.64&thinsp;Mb), few assembly errors (contig NGA50: 11.8-59.59&thinsp;Mb), good consensus quality (QV: 27.84-42.88) and high gene completeness (BUSCO complete: 94.6-95.2\%), while consuming low computational resources (CPU hours: 187-1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64&thinsp;Mb (NGA50: 59.59&thinsp;Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88&thinsp;Mb).</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33318652',
			'doi' => '10.1038/s41587-020-00747-w',
			'modified' => '2022-01-13 15:09:21',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 46 => array(
			'id' => '4000',
			'name' => 'Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.',
			'authors' => 'von der Heyde B, Emmanouilidou A, Mazzaferro E, Vicenzi S, Höijer I, Klingström T, Jumaa S, Dethlefsen O, Snieder H, de Geus E, Ameur A, Ingelsson E, Allalou A, Brooke HL, den Hoed M',
			'description' => '<p>A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30&nbsp;s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5&nbsp;days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25&nbsp;&micro;M ivabradine-an open channel blocker of HCNs-for 24&nbsp;h resulted in a dose-dependent higher HRV and lower heart rate at 5&nbsp;days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).</p>',
			'date' => '2020-07-16',
			'pmid' => 'http://www.pubmed.gov/32678143',
			'doi' => '10.1038/s41598-020-68567-1',
			'modified' => '2020-09-01 14:40:20',
			'created' => '2020-08-21 16:41:39',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4016',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69Escherichia coli Strain in Italy',
			'authors' => 'Mattioni, Marchetti Vittoria and Bitar, Ibrahim and Piazza, Aurora andMercato, Alessandra and Fogato, Elena and Hrabak, Jaroslav and Migliavacca,Roberta',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-15',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2020-12-16 17:36:09',
			'created' => '2020-10-12 14:54:59',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4359',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a ClinicalST69 Escherichia coli Strain in Italy',
			'authors' => 'Mattioni MV et al. ',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-01',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2022-08-03 17:12:43',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '3974',
			'name' => 'Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.',
			'authors' => 'Oulghazi S, Moumni M, Khayi S, Robic K, Sarfraz S, Lopez-Roques C, Vandecasteele C, Faure D',
			'description' => '<p>Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.</p>',
			'date' => '2020-06-13',
			'pmid' => 'http://www.pubmed.gov/32545839',
			'doi' => '10.3390/microorganisms8060895',
			'modified' => '2020-08-12 09:28:31',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '3972',
			'name' => 'Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.',
			'authors' => 'Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J',
			'description' => '<p>Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.</p>',
			'date' => '2020-06-08',
			'pmid' => 'http://www.pubmed.gov/32553272',
			'doi' => '10.1016/j.cell.2020.05.021',
			'modified' => '2020-08-12 09:27:28',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 51 => array(
			'id' => '3869',
			'name' => 'Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.',
			'authors' => 'Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J',
			'description' => '<p>Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the&nbsp;evolutionary trajectory and functional distribution&nbsp;of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S.&nbsp;epidermidis genomes from 5 healthy individuals, we found that skin S.&nbsp;epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.</p>',
			'date' => '2020-02-06',
			'pmid' => 'http://www.pubmed.gov/32004459',
			'doi' => '10.1016/j.cell.2020.01.006',
			'modified' => '2020-03-20 17:45:40',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 52 => array(
			'id' => '4247',
			'name' => 'LongQC: A Quality Control Tool for Third GenerationSequencing Long Read Data',
			'authors' => 'Fukasawa Yoshinori et al.',
			'description' => '<p>We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key statistics were optimized for long read data, and LongQC covers all major TGS platforms. LongQC processes and visualizes those statistics automatically and quickly.</p>',
			'date' => '2020-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32041730',
			'doi' => '10.1534/g3.119.400864',
			'modified' => '2022-05-24 09:03:08',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 53 => array(
			'id' => '3863',
			'name' => 'Genome Sequence of  sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.',
			'authors' => 'Anton BP, DasSarma P, Martinez FL, DasSarma SL, Al Madadha M, Roberts RJ, DasSarma S',
			'description' => '<p>An extremely halophilic archaeon, sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorporated into HaloWeb (https://halo.umbc.edu/).</p>',
			'date' => '2020-01-30',
			'pmid' => 'http://www.pubmed.gov/32001568',
			'doi' => '10.1128/MRA.01505-19.',
			'modified' => '2020-03-20 17:52:34',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 54 => array(
			'id' => '3864',
			'name' => 'The round goby genome provides insights into mechanisms that may facilitate biological invasions.',
			'authors' => 'Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S',
			'description' => '<p>BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. RESULTS: We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. CONCLUSIONS: The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.</p>',
			'date' => '2020-01-28',
			'pmid' => 'http://www.pubmed.gov/31992286',
			'doi' => '10.1186/s12915-019-0731-8',
			'modified' => '2020-03-20 17:51:48',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 55 => array(
			'id' => '3857',
			'name' => 'The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.',
			'authors' => 'Kan SL, Shen TT, Gong P, Ran JH, Wang XQ',
			'description' => '<p>BACKGROUND: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. RESULTS: Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. CONCLUSIONS: We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.</p>',
			'date' => '2020-01-20',
			'pmid' => 'http://www.pubmed.gov/31959109',
			'doi' => '10.1186/s12862-020-1582-1',
			'modified' => '2020-03-20 17:57:35',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 56 => array(
			'id' => '3858',
			'name' => 'A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).',
			'authors' => 'Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, Hiller M, Hundsdoerfer AK',
			'description' => '<p>BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged &sim;7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51&times; Pacific Biosciences long reads with an average read length of 8.9&nbsp;kb. Pacific Biosciences reads longer than 4&nbsp;kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.</p>',
			'date' => '2020-01-08',
			'pmid' => 'http://www.pubmed.gov/31972020',
			'doi' => '10.1093/gigascience/giaa001',
			'modified' => '2020-03-20 17:56:37',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 57 => array(
			'id' => '3823',
			'name' => 'Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of .',
			'authors' => 'Hovde BT, Daligault HE, Hanschen ER, Kunde YA, Johnson MB, Starkenburg SR, Johnson SL',
			'description' => '<p>The sequenced genome and the leaf transcriptome of a near relative of and was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (&lt;1 mbp) the cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified and we observed substantial diversity of genes and predicted gene products in and previously characterized toxins this suggests diverse toxin repertoires within potentially the results of rapid toxin evolution.</p>',
			'date' => '2019-11-25',
			'pmid' => 'http://www.pubmed.gov/31775284',
			'doi' => '10.3390/toxins11120691',
			'modified' => '2020-02-25 14:47:48',
			'created' => '2020-02-13 10:02:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 58 => array(
			'id' => '3813',
			'name' => 'NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.',
			'authors' => 'De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D'Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K',
			'description' => '<p>Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30&times; human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.</p>',
			'date' => '2019-11-14',
			'pmid' => 'http://www.pubmed.gov/31727106',
			'doi' => '10.1186/s13059-019-1856-3',
			'modified' => '2019-12-05 10:59:42',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 59 => array(
			'id' => '3791',
			'name' => 'Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull.',
			'authors' => 'Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL',
			'description' => '<p>Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (Pp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20&times; coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring P Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the P Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.</p>',
			'date' => '2019-10-07',
			'pmid' => 'http://www.pubmed.gov/31591551',
			'doi' => '10.1038/s41587-019-0266-0',
			'modified' => '2019-12-05 11:47:39',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 60 => array(
			'id' => '3788',
			'name' => 'Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef.',
			'authors' => 'Sekizuka T, Lee K, Kimata K, Isobe J, Kuroda M, Iyoda S, Ohnishi M, Sata T, Watahiki M',
			'description' => '<p>We present the complete genome sequence of an enterohemorrhagic O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.</p>',
			'date' => '2019-10-03',
			'pmid' => 'http://www.pubmed.gov/31582455',
			'doi' => '10.1128/MRA.00882-19.',
			'modified' => '2019-12-05 11:58:13',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 61 => array(
			'id' => '3772',
			'name' => 'Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions.',
			'authors' => 'Zhang S, Liang F, Lei C, Wu J, Fu J, Yang Q, Luo X, Yu G, Wang D, Zhang Y, Lu D, Sun X, Liang Y, Xu C',
			'description' => '<p>BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos that carry balanced inversion from those with a normal karyotype. We aim to evaluate the use of long-read sequencing in combination with haplotype linkage analysis to address this challenge. METHODS: Long-read sequencing on Oxford Nanopore platform was employed to identify the precise positions of inversion break points in four patients. Comprehensive chromosomal screening and genome-wide haplotype linkage analysis were performed based on SNP microarray. The haplotypes, including the break point regions, the whole chromosomes involved in the inversion and the corresponding homologous chromosomes, were established using informative SNPs. RESULTS: All the inversion break points were successfully identified by long-read sequencing and validated by Sanger sequencing, and on average only 13 bp differences were observed between break points inferred by long-read sequencing and Sanger sequencing. Eighteen blastocysts were biopsied and tested, in which 10 were aneuploid or unbalanced and eight were diploid with normal or balanced inversion karyotypes. Diploid embryos were transferred back to patients, the predictive results of the current methodology were consistent with fetal karyotypes of amniotic fluid or cord blood. CONCLUSIONS: Nanopore long-read sequencing is a powerful method to assay chromosomal inversions and identify exact break points. Identification of inversion break points combined with haplotype linkage analysis is an efficient strategy to distinguish embryos with normal or balanced inversion karyotypes, facilitating PGT applications.</p>',
			'date' => '2019-08-22',
			'pmid' => 'http://www.pubmed.gov/31439719',
			'doi' => '10.1136/jmedgenet-2018-105976',
			'modified' => '2019-10-02 17:08:37',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 62 => array(
			'id' => '3760',
			'name' => 'Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.',
			'authors' => 'Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, L',
			'description' => '<p>The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5&thinsp;kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions &lt;50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of &gt;15&thinsp;megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.<br /><!--50--></p>',
			'date' => '2019-08-12',
			'pmid' => 'http://www.pubmed.gov/31406327',
			'doi' => '10.1038/s41587-019-0217-9',
			'modified' => '2019-10-03 10:05:13',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 63 => array(
			'id' => '3749',
			'name' => 'Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.',
			'authors' => 'Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC',
			'description' => '<p>BACKGROUND: Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS: By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS: We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.</p>',
			'date' => '2019-07-08',
			'pmid' => 'http://www.pubmed.gov/31286858',
			'doi' => '10.1186/s12864-019-5909-5',
			'modified' => '2019-08-06 16:06:34',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 64 => array(
			'id' => '3721',
			'name' => 'Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.',
			'authors' => 'Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH',
			'description' => '<p>BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruy&egrave;re and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS: Two NWCs from Swiss Gruy&egrave;re producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS: Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.</p>',
			'date' => '2019-06-25',
			'pmid' => 'http://www.pubmed.gov/31238873',
			'doi' => '10.1186/s12866-019-1500-0',
			'modified' => '2019-07-04 18:06:26',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 65 => array(
			'id' => '3712',
			'name' => 'A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).',
			'authors' => 'Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z',
			'description' => '<p>BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential. FINDINGS: We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (&sim;211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants. CONCLUSION: This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.</p>',
			'date' => '2019-06-01',
			'pmid' => 'http://www.pubmed.gov/31216035',
			'doi' => '10.1093/gigascience/giz072',
			'modified' => '2019-07-05 14:29:16',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 66 => array(
			'id' => '3650',
			'name' => 'Genome Sequence and Methylation Patterns of  sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.',
			'authors' => 'Priya DasSarma, Anton BP, DasSarma S, Laye VJ, Guzman D, Roberts RJ, DasSarma S',
			'description' => '<p>sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Database (http://halo.umbc.edu). The polyextremophilic character and high-elevation environment make the microbe of interest for astrobiology.</p>',
			'date' => '2019-05-09',
			'pmid' => 'http://www.pubmed.gov/31072883',
			'doi' => '10.1016/j.gexplo.2004.07.001.',
			'modified' => '2019-06-07 10:11:11',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 67 => array(
			'id' => '3707',
			'name' => 'The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.',
			'authors' => 'Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C',
			'description' => '<p>Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4'-deoxyflavone synthesis in the genus&nbsp;Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30999079',
			'doi' => '10.1016/j.molp.2019.04.002',
			'modified' => '2019-07-05 14:35:57',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 68 => array(
			'id' => '3602',
			'name' => 'Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.',
			'authors' => 'Palmieri V, Dalchiele EA, Perini G, Motta A, De Spirito M, Zanoni R, Marrani AG, Papi M',
			'description' => '<p>We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoids GO-mediated oxidation of glutathione. This method offers new opportunities for the production of green biocompatible rGO and NAC-based therapies.</p>',
			'date' => '2019-03-20',
			'pmid' => 'http://www.pubmed.gov/30892320',
			'doi' => '10.1039/C9CC00429G.',
			'modified' => '2019-04-17 14:56:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 69 => array(
			'id' => '3725',
			'name' => 'The alternative reality of plant mitochondrial DNA',
			'authors' => 'Alexander Kozik, Beth A. Rowan, Dean Lavelle, Lidija Berke, M. Eric Schranz, Richard W. Michelmore, and Alan C. Christensen',
			'description' => '<p>Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative genomic arrangements (isoforms). Most mitochondrial genomes have been assembled using methods that were unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. This allowed us to characterize a comprehensive, complex set of isoforms within each species and to compare genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched linear, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement, and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms evident in our data, we inferred that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other lettuce species can be largely explained by rare recombination events that rearrange the structure. Our data demonstrate that representations of plant mitochondrial DNA as simple, genome-sized circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.</p>',
			'date' => '2019-03-01',
			'pmid' => 'https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008373',
			'doi' => '10.1101/564278.',
			'modified' => '2022-05-18 18:58:47',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 70 => array(
			'id' => '3615',
			'name' => 'Characterizing the Major Structural Variant Alleles of the Human Genome.',
			'authors' => 'Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE',
			'description' => '<p>In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30661756',
			'doi' => '10.1016/j.cell.2018.12.019',
			'modified' => '2019-04-16 13:55:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 71 => array(
			'id' => '3645',
			'name' => 'Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.',
			'authors' => 'Martínez FL, Anton BP, DasSarma P, Rajal V, Irazusta V, Roberts RJ, DasSarma S',
			'description' => '<p>Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30701250',
			'doi' => '10.1128/MRA',
			'modified' => '2019-06-07 10:15:47',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 72 => array(
			'id' => '3656',
			'name' => 'Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present  tuberculosis vaccine',
			'authors' => 'Katlyn Borgersa,Jheng-Yang Ouc, Po-Xing Zhengc, Petra Tielsa, Annelies Van Heckea, Evelyn Pletsa, Gitte Michielsena, Nele Festjensa, Nico Callewaerta, Yao-Cheng Lin',
			'description' => '<p>Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence of BCG Danish 1331 (07/270), one of the WHO reference strains for BCG vaccines. We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of this vaccine strain.</p>',
			'date' => '2018-12-26',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/31286858/',
			'doi' => '10.1101/513408.',
			'modified' => '2022-05-18 18:52:29',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 73 => array(
			'id' => '3454',
			'name' => 'SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).',
			'authors' => 'Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N',
			'description' => '<p>Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica). Findings: As part of the Genome10K (G10K) effort on generating high quality vertebrate genomes, we have assembled a highly contiguous genome assembly using Single Molecule Real-Time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from the Direct Label and Stain (DLS) technologies. As proposed by Bionano, the DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of over 25.95 Mbp. Conclusions: This high-quality genome assembly represents a valuable resource for further studies of population genetics and genomics in the barn swallow, and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.</p>',
			'date' => '2018-11-29',
			'pmid' => 'http://www.pubmed.gov/30496513',
			'doi' => '10.1093/gigascience/giy142/5202456',
			'modified' => '2019-02-15 20:35:16',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 74 => array(
			'id' => '3429',
			'name' => 'Improved reference genome of Aedes aegypti informs arbovirus vector control.',
			'authors' => 'Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gl',
			'description' => '<p>Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology&nbsp;of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.</p>',
			'date' => '2018-11-14',
			'pmid' => 'http://www.pubmed.gov/30429615',
			'doi' => '10.1038/s41586-018-0692-z',
			'modified' => '2018-12-31 11:15:00',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 75 => array(
			'id' => '3413',
			'name' => 'Whole-genome landscape of Medicago truncatula symbiotic genes.',
			'authors' => 'Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Mu',
			'description' => '<p>Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.</p>',
			'date' => '2018-11-05',
			'pmid' => 'http://www.pubmed.gov/30397259',
			'doi' => '10.1038/s41477-018-0286-7',
			'modified' => '2018-12-31 11:17:32',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 76 => array(
			'id' => '3517',
			'name' => 'Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.',
			'authors' => 'Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, ',
			'description' => '<p>Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions. However, even though genome assemblies based on long reads exhibit high contig N50s (&gt;1&thinsp;Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of &gt;5&thinsp;Mb and contain scaffolds that represent entire chromosomes or chromosome arms.</p>',
			'date' => '2018-11-02',
			'pmid' => 'http://www.pubmed.gov/30390080',
			'doi' => '10.1038/s41477-018-0289-4',
			'modified' => '2019-02-27 15:41:40',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 77 => array(
			'id' => '3441',
			'name' => 'The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.',
			'authors' => 'Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B',
			'description' => '<p>Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is&nbsp;found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H.&nbsp;axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H.&nbsp;axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of &sim;170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that&nbsp;highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.</p>',
			'date' => '2018-10-22',
			'pmid' => 'http://www.pubmed.gov/30146156',
			'doi' => '10.1016/j.cub.2018.08.023',
			'modified' => '2019-02-15 20:42:22',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 78 => array(
			'id' => '3412',
			'name' => 'Long-read sequence capture of the hemoglobin gene clusters across gadid species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes. This article is protected by copyright. All rights reserved.</p>',
			'date' => '2018-10-17',
			'pmid' => 'http://www.pubmed.org/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2018-12-31 11:19:03',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 79 => array(
			'id' => '3399',
			'name' => 'Genomic Structural Variations Within Five Continental Populations of .',
			'authors' => 'Long E, Evans C, Chaston J, Udall JA',
			'description' => '<p>Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing genes. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent diverse populations within the species. We used long-read sequencing and optical mapping technologies to identify SVs in these genomes. Among the five lines examined, we found an average of 2,928 structural variants within these genomes. These structural variations varied greatly in size and location, included many exonic regions, and could impact adaptation and genomic evolution.</p>',
			'date' => '2018-10-03',
			'pmid' => 'http://www.pubmed.gov/30111620',
			'doi' => '10.1534/g3.118.200631',
			'modified' => '2018-11-09 11:49:08',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 80 => array(
			'id' => '3403',
			'name' => 'Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.',
			'authors' => 'Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K, Zhang Q',
			'description' => '<p>Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect disease causal structural variants (SVs) from short reads sequencing technologies. Long reads sequencing can produce longer reads (typically 1000&nbsp;bp or longer), therefore offering greatly improved ability to detect SVs that may be missed by short-read sequencing. Results: Here we describe a case study, where WES identified only one heterozygous pathogenic variant for an individual suspected to have glycogen storage disease type Ia (GSD-Ia), which is an autosomal recessive disease caused by bi-allelic mutations in the gene. Through Nanopore long-read whole-genome sequencing, we identified a 7.1&nbsp;kb deletion covering two exons on the other allele, suggesting that complex structural variants (SVs) may explain a fraction of cases when the second pathogenic allele is missing from WES on recessive diseases. Both breakpoints of the deletion are within Alu elements, and we designed Sanger sequencing and quantitative PCR assays based on the breakpoints for preimplantation genetic diagnosis (PGD) for the family planning on another child. Four embryos were obtained after in vitro fertilization (IVF), and an embryo without deletion in was transplanted after PGD and was confirmed by prenatal diagnosis, postnatal diagnosis, and subsequent lack of disease symptoms after birth. Conclusions: In summary, we present one of the first examples of using long-read sequencing to identify causal yet complex SVs in exome-negative patients, which subsequently enabled successful personalized PGD.</p>',
			'date' => '2018-09-28',
			'pmid' => 'http://www.pubmed.gov/30279644',
			'doi' => '10.1186/s41065-018-0069-1',
			'modified' => '2018-11-09 11:27:02',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 81 => array(
			'id' => '3525',
			'name' => 'Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.',
			'authors' => 'Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD',
			'description' => '<p>BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences' (PacBio) and Oxford Nanopore Technologies' (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing GC repeat expansion. We also report the first long-read sequencing data characterizing the C9orf72 GC repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9. RESULTS: Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinION was a challenge for whole-genome sequencing; we were unable to attain reads covering the human C9orf72 repeat expansion using 15 flow cells. We obtained 8&times; coverage across the C9orf72 locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained &gt;&thinsp;800&times; coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual's repeat region was &gt;&thinsp;99% GC content, though we cannot rule out small interruptions. CONCLUSIONS: Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in C9orf72 expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-GC content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.</p>',
			'date' => '2018-08-21',
			'pmid' => 'http://www.pubmed.gov/30126445',
			'doi' => '10.1186/s13024-018-0274-4',
			'modified' => '2019-02-28 10:13:27',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 82 => array(
			'id' => '3524',
			'name' => 'The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.',
			'authors' => 'Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J',
			'description' => '<p>DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (&gt;94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.</p>',
			'date' => '2018-08-14',
			'pmid' => 'http://www.pubmed.gov/30108278',
			'doi' => '10.1038/s41598-018-30620-5',
			'modified' => '2019-02-28 10:12:41',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 83 => array(
			'id' => '3638',
			'name' => 'Long-read sequence capture of the haemoglobin gene clusters across codfish species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100&nbsp;kb) and MN (~200&nbsp;kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.</p>',
			'date' => '2018-08-03',
			'pmid' => 'http://www.pubmed.gov/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2019-06-07 10:24:26',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 84 => array(
			'id' => '3512',
			'name' => 'A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.',
			'authors' => 'Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Are',
			'description' => '<p>Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512&thinsp;Mb with N50 of 3.4&thinsp;Mb and 564 contigs). The length of 512&thinsp;Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.</p>',
			'date' => '2018-06-11',
			'pmid' => 'http://www.pubmed.gov/29892093',
			'doi' => '10.1038/s41477-018-0166-1',
			'modified' => '2019-02-28 10:35:49',
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			'id' => '3483',
			'name' => 'Overview of Next-Generation Sequencing Technologies.',
			'authors' => 'Slatko BE, Gardner AF, Ausubel FM',
			'description' => '<p>High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. &copy; 2018 by John Wiley &amp; Sons, Inc.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29851291',
			'doi' => '10.1002/cpmb.59',
			'modified' => '2019-02-14 17:07:52',
			'created' => '2019-02-14 15:01:22',
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			'id' => '3474',
			'name' => 'Draft genome of the Peruvian scallop Argopecten purpuratus.',
			'authors' => 'Li C, Liu X, Liu B, Ma B, Liu F, Liu G, Shi Q, Wang C',
			'description' => '<p>Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. Findings: A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. Conclusions: We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29617765',
			'doi' => '10.1093/gigascience/giy031',
			'modified' => '2019-02-15 20:33:41',
			'created' => '2019-02-14 15:01:22',
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		(int) 87 => array(
			'id' => '3544',
			'name' => 'Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.',
			'authors' => 'Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F',
			'description' => '<p>BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS: In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.</p>',
			'date' => '2018-01-16',
			'pmid' => 'http://www.pubmed.gov/29338683',
			'doi' => '10.1186/s12864-017-4429-4',
			'modified' => '2019-02-28 10:58:38',
			'created' => '2019-02-27 12:54:44',
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		(int) 88 => array(
			'id' => '3308',
			'name' => 'Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.',
			'authors' => 'Rödelsperger C. et al.',
			'description' => '<p>The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P.&nbsp;pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P.&nbsp;pacificus. Despite widespread conservation of synteny between P.&nbsp;pacificus and C.&nbsp;elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C.&nbsp;elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P.&nbsp;pacificus.</p>',
			'date' => '2017-10-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045848',
			'doi' => '',
			'modified' => '2018-01-04 10:15:03',
			'created' => '2018-01-04 10:15:03',
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		(int) 89 => array(
			'id' => '3279',
			'name' => 'De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads',
			'authors' => 'Korlach J. et al.',
			'description' => '<p>Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.</p>',
			'date' => '2017-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29020750',
			'doi' => '',
			'modified' => '2017-10-16 10:27:47',
			'created' => '2017-10-16 10:27:47',
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		(int) 90 => array(
			'id' => '3041',
			'name' => 'DNA fragmentation and quality control analysis ',
			'authors' => 'Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian',
			'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
<p><strong>Introduction</strong></p>
<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
<p><strong>Results</strong></p>
<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
<p><strong>Conclusion</strong></p>
<p>Unbiased DNA fragmentation with the Diagenode One, the Bioruptor<sup>&reg;</sup>&nbsp;Pico, or the Megaruptor<sup>&reg;</sup>&nbsp;for short- or long-read sequencing combined with sizing on the Fragment Analyzer<sup>&trade;</sup>&nbsp;delivers an efficient workflow solution for preparing and analyzing libraries with even distribution and representation of the genome.</p>
<p></p>',
			'date' => '2016-09-29',
			'pmid' => 'http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.f.397.html',
			'doi' => '',
			'modified' => '2016-10-20 16:37:08',
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			'name' => 'DNA Link Megaruptor',
			'description' => '<p>Established in March 15<span>th </span><span>2000, DNA Link, Inc. has developed as one of the leading full genomic service provider with its extensive 17 years of experience. DNA Link has been involved in numerous genomic researches including many national projects, and contributed to the expansion of the genomic industry. </span></p>
<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p>',
			'author' => 'Hyeyoon, Jang - Lab Manager - Seoul, Korea',
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			'description' => '<p><span>The system performance was very good. High molecular weight DNA of different plants (Arabidopsis Alm, Hops polaris and wine Villard Blanc) was isolated and diluted to 50ng/&micro;l or 70ng/&micro;l. We aimed for fragment length 30kb at the volume 150&micro;l.</span><br /><span>We achieved good results and we will continue with bead purification and library preps for PacBio sequencing. &nbsp;I like the user friendly interface of the Megaruptor<sup>&reg;</sup>&nbsp;2. Just two parameters had to be specified: volume of each sample and desired mean fragment size. The processed DNA has a narrow size distribution at around 30kb.</span></p>',
			'author' => 'Christa Lanz and Julia Hildebrandt, Max Planck Institute for Developmental Biology, Tübingen, Germany',
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<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p><cite>Hyeyoon, Jang - Lab Manager - Seoul, Korea</cite></blockquote>
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            <h6 style="height:60px">Hydropore - short</h6>
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<p><span><strong><span style="text-decoration: underline;">Note</span>:&nbsp;</strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a><span>&nbsp;</span><span>are sold separately.</span></span></p>',
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<p><strong>Storage</strong><br />Store at room temperature</p>
<p><strong>Precautions</strong><br />This product is for research use only. Not for use in diagnostic or therapeutic procedures</p>
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	'description' => '<p>Several methods exist today for shearing genomic DNA, but few are reliable for generating DNA fragments &gt;50 kb necessary for assembly of many microbial, human, plant and animal genomes <em>de novo</em>. Pacific Biosciences highly recommends the Megaruptor<sup>TM</sup> System for shearing genomic DNA to large fragments for long-read sequencing in the Sequel&reg; System.</p>',
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	'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
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<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
<p><strong>Results</strong></p>
<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
<p><strong>Conclusion</strong></p>
<p>Unbiased DNA fragmentation with the Diagenode One, the Bioruptor<sup>&reg;</sup>&nbsp;Pico, or the Megaruptor<sup>&reg;</sup>&nbsp;for short- or long-read sequencing combined with sizing on the Fragment Analyzer<sup>&trade;</sup>&nbsp;delivers an efficient workflow solution for preparing and analyzing libraries with even distribution and representation of the genome.</p>
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<h6 style="text-align: center;">Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. <strong>A:</strong> DNA was analyzed by pulsedfield gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software. <strong>B:</strong> Fragment Analyzer profiles of human genomic DNA (25 ng/&mu;l; 200 &mu;l/sample) sheared at different software settings of 10, 15, 20, 30 and 40 kb. (High Sensitivity Large Fragment Analysis Kit; Advanced Analytical Technologies, Inc. was used for separation and fragment sizing).</h6>
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<h6 style="text-align: center;">Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. <strong>A:</strong> DNA was analyzed by pulsedfield gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software. <strong>B:</strong> Fragment Analyzer profiles of human genomic DNA (25 ng/&mu;l; 200 &mu;l/sample) sheared at different software settings of 10, 15, 20, 30 and 40 kb. (High Sensitivity Large Fragment Analysis Kit; Advanced Analytical Technologies, Inc. was used for separation and fragment sizing).</h6>
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<p></p>
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			'description' => '<p><span>The shearing devices (Hydropores) have been especially designed for being used with the Megaruptor</span><sup>&reg;</sup><span>&nbsp;(B06010002). The&nbsp;Hydropore - long&nbsp;allows reproducible DNA shearing of&nbsp;</span><span><strong>10 - 75 kb</strong>.</span></p>
<p><strong><span style="text-decoration: underline;">Note</span>: </strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a>&nbsp;are sold separately.</p>
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			'label1' => 'Characteristics',
			'info1' => '<p>Sterile hydropore are intended for single use</p>
<p><strong>Storage</strong><br />Store at room temperature</p>
<p><strong>Precautions</strong><br />This product is for research use only. Not for use in diagnostic or therapeutic procedures</p>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>
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			'antibody_id' => null,
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<p><span><strong><span style="text-decoration: underline;">Note</span>:&nbsp;</strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a><span>&nbsp;</span><span>are sold separately.</span></span></p>',
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<p><strong>Storage</strong><br />Store at room temperature</p>
<p><strong>Precautions</strong><br />This product is for research use only. Not for use in diagnostic or therapeutic procedures</p>
<script src="chrome-extension://hhojmcideegachlhfgfdhailpfhgknjm/web_accessible_resources/index.js"></script>
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			'id' => '3',
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			'name' => '次世代シーケンシング',
			'description' => '<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2 style="font-size: 22px;">DNA断片化、ライブラリー調製、自動化：NGSのワンストップショップ</h2>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-12 medium-12 large-12 columns">
<h4>1. 断片化装置を選択してください：150 bp〜75 kbの範囲でDNAを断片化します。</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-pico-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/bioruptor_pico.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/megaruptor2-1-unit"><img src="https://www.diagenode.com/img/product/shearing_technologies/B06010001_megaruptor2.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-one-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/br-one-profil.png" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns">5&mu;lまで断片化：150 bp〜2 kb<br />NGS DNAライブラリー調製およびFFPE核酸抽出に最適で、</td>
<td class="small-4 medium-4 large-4 columns">2 kb〜75 kbの範囲をできます。<br />メイトペアライブラリー調製および長いフラグメントDNAシーケンシングに最適で、この軽量デスクトップデバイスで</td>
<td class="small-4 medium-4 large-4 columns">20または50&mu;lの断片化が可能です。</td>
</tr>
</tbody>
</table>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-8 medium-8 large-8 columns">
<h4>2. 最適化されたライブラリー調整キットを選択してください。</h4>
</th>
<th class="small-4 medium-4 large-4 columns">
<h4>3. ライブラリー前処理自動化を選択して、比類のないデータ再現性を実感</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><img src="https://www.diagenode.com/img/product/kits/microPlex_library_preparation.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns"><img src="https://www.diagenode.com/img/product/kits/box_kit.jpg" style="display: block; margin-left: auto; margin-right: auto;" height="173" width="250" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/sx-8g-ip-star-compact-automated-system-1-unit"><img src="https://www.diagenode.com/img/product/automation/B03000002%20_ipstar_compact.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">50pgの低入力：MicroPlex Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">5ng以上：iDeal&nbsp;Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">Achieve great NGS data easily</td>
</tr>
</tbody>
</table>
</div>
</div>
<blockquote>
<div class="row">
<div class="small-12 medium-12 large-12 columns"><span class="label" style="margin-bottom: 16px; margin-left: -22px; font-size: 15px;">DiagenodeがNGS研究にぴったりなプロバイダーである理由</span>
<p>Diagenodeは15年以上もエピジェネティクス研究に専念、専門としています。 ChIP研究クロマチン用のユニークな断片化システムの開発から始まり、 専門知識を活かし、5&mu;lのせん断体積まで可能で、NGS DNAライブラリーの調製に最適な最先端DNA断片化装置の開発にたどり着きました。 我々は以来、ChIP-seq、Methyl-seq、NGSライブラリー調製用キットを研究開発し、業界をリードする免疫沈降研究と同様に、ライブラリー調製を自動化および完結させる独自の自動化システムを開発にも成功しました。</p>
<ul>
<li>信頼されるせん断装置</li>
<li>様々なインプットからのライブラリ作成キット</li>
<li>独自の自動化デバイス</li>
</ul>
</div>
</div>
</blockquote>
<div class="row">
<div class="small-12 columns">
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#panel1a">次世代シーケンシングへの理解とその専門知識</a>
<div id="panel1a" class="content">
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong>次世代シーケンシング (NGS)</strong> ）は、著しいスケールとハイスループットでシーケンシングを行い、1日に数十億もの塩基生成を可能にします。 NGSのハイスループットは迅速でありながら正確で、再現性のあるデータセットを実現し、さらにシーケンシング費用を削減します。 NGSは、ゲノムシーケンシング、ゲノム再シーケンシング、デノボシーケンシング、トランスクリプトームシーケンシング、その他にDNA-タンパク質相互作用の検出やエピゲノムなどを示します。 指数関数的に増加するシーケンシングデータの需要は、計算分析の障害や解釈、データストレージなどの課題を解決します。</p>
<p>アプリケーションおよび出発物質に応じて、数百万から数十億の鋳型DNA分子を大規模に並行してシーケンシングすることが可能です。その為に、異なる化学物質を使用するいくつかの市販のNGSプラットフォームを利用することができます。 NGSプラットフォームの種類によっては、事前準備とライブラリー作成が必要です。</p>
<p>NGSにとっても、特にデータ処理と分析に関した大きな課題はあります。第3世代技術はゲノミクス研究にさらに革命を起こすであろうと大きく期待されています。</p>
</div>
</div>
<div class="row">
<div class="small-6 medium-6 large-6 columns">
<p><strong>NGS アプリケーション</strong></p>
<ul>
<li>全ゲノム配列決定</li>
<li>デノボシーケンシング</li>
<li>標的配列</li>
<li>Exomeシーケンシング</li>
<li>トランスクリプトーム配列決定</li>
<li>ゲノム配列決定</li>
<li>ミトコンドリア配列決定</li>
<li>DNA-タンパク質相互作用（ChIP-seq</li>
<li>バリアント検出</li>
<li>ゲノム仕上げ</li>
</ul>
</div>
<div class="small-6 medium-6 large-6 columns">
<p><strong>研究分野におけるNGS:</strong></p>
<ul>
<li>腫瘍学</li>
<li>リプロダクティブ・ヘルス</li>
<li>法医学ゲノミクス</li>
<li>アグリゲノミックス</li>
<li>複雑な病気</li>
<li>微生物ゲノミクス</li>
<li>食品・環境ゲノミクス</li>
<li>創薬ゲノミクス - パーソナライズド・メディカル</li>
</ul>
</div>
<div class="small-12 medium-12 large-12 columns">
<p><strong>NGSの用語</strong></p>
<dl>
<dt>リード（読み取り）</dt>
<dd>この装置から得られた連続した単一のストレッチ</dd>
<dt>断片リード</dt>
<dd>フラグメントライブラリからの読み込み。 シーケンシングプラットフォームに応じて、読み取りは通常約100〜300bp。</dd>
<dt>断片ペアエンドリード</dt>
<dd>断片ライブラリーからDNA断片の各末端2つの読み取り。</dd>
<dt>メイトペアリード</dt>
<dd>大きなDNA断片（通常は予め定義されたサイズ範囲）の各末端から2つの読み取り。</dd>
<dt>カバレッジ（例）</dt>
<dd>30&times;適用範囲とは、参照ゲノム中の各塩基対が平均30回の読み取りを示す。</dd>
</dl>
</div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2>NGSプラットフォーム</h2>
<h3><a href="http://www.illumina.com" target="_blank">イルミナ</a></h3>
<p>イルミナは、クローン的に増幅された鋳型DNA（クラスター）上に位置する、蛍光標識された可逆的鎖ターミネーターヌクレオチドを用いた配列別合成技術を使用。 DNAクラスターは、ガラスフローセルの表面上に固定化され、 ワークフローは、4つのヌクレオチド（それぞれ異なる蛍光色素で標識された）の組み込み、4色イメージング、色素や末端基の切断、取り込み、イメージングなどを繰り返します。フローセルは大規模な並列配列決定を受ける。 この方法により、単一蛍光標識されたヌクレオチドの制御添加によるモノヌクレオチドのエラーを回避する可能性があります。 読み取りの長さは、通常約100〜150 bpです。</p>
<h3><a href="http://www.lifetechnologies.com" target="_blank">イオン トレント</a></h3>
<p>イオントレントは、半導体技術チップを用いて、合成中にヌクレオチドを取り込む際に放出されたプロトンを検出します。 これは、イオン球粒子と呼ばれるビーズの表面にエマルションPCR（emPCR）を使用し、リンクされた特定のアダプターを用いてDNA断片を増幅します。 各ビーズは1種類のDNA断片で覆われていて、異なるDNA断片を有するビーズは次いで、チップの陽子感知ウェル内に配置されます。 チップには一度に4つのヌクレオチドのうちの1つが浸水し、このプロセスは異なるヌクレオチドで15秒ごとに繰り返されます。 配列決定の間に4つの塩基の各々が1つずつ導入されます、組み込みの場合はプロトンが放出され、電圧信号が取り込みに比例して検出されます。.</p>
<h3><a href="http://www.pacificbiosciences.com" target="_blank">パシフィック バイオサイエンス</a></h3>
<p>パシフィックバイオサイエンスでは、20kbを超える塩基対の読み取りも、単一分子リアルタイム（SMRT）シーケンシングによる構造および細胞タイプの変化を観察することができます。 このプラットフォームでは、超長鎖二本鎖DNA（dsDNA）断片が、Megaruptor（登録商標）のようなDiagenode装置を用いたランダムシアリングまたは目的の標的領域の増幅によって生成されます。 SMRTbellライブラリーは、ユニバーサルヘアピンアダプターをDNA断片の各末端に連結することによって生成します。 サイズ選択条件による洗浄ステップの後、配列決定プライマーをSMRTbellテンプレートにアニーリングし、鋳型DNAに結合したDNAポリメラーゼを含む配列決定を、蛍光標識ヌクレオチドの存在下で開始。 各塩基が取り込まれると、異なる蛍光のパルスをリアルタイムで検出します。</p>
<h3><a href="https://nanoporetech.com" target="_blank">オックスフォード ナノポア</a></h3>
<p>Oxford Nanoporeは、単一のDNA分子配列決定に基づく技術を開発します。その技術により生物学的分子、すなわちDNAが一群の電気抵抗性高分子膜として位置するナノスケールの孔（ナノ細孔）またはその近くを通過し、イオン電流が変化します。 この変化に関する情報は、例えば4つのヌクレオチド（AまたはG r CまたはT）ならびに修飾されたヌクレオチドすべてを区別することによって分子情報に訳されます。 シーケンシングミニオンデバイスのフローセルは、数百個のナノポアチャネルのセンサアレイを含みます。 DNAサンプルは、Diagenode社のMegaruptor（登録商標）を用いてランダムシアリングによって生成され得る超長鎖DNAフラグメントが必要です。</p>
<h3><a href="http://www.lifetechnologies.com/be/en/home/life-science/sequencing/next-generation-sequencing/solid-next-generation-sequencing.html" target="_blank">SOLiD</a></h3>
<p>SOLiDは、ユニークな化学作用により、何千という個々のDNA分子の同時配列決定を可能にします。 それは、アダプター対ライブラリーのフラグメントが適切で、せん断されたゲノムDNAへのアダプターのライゲーションによるライブラリー作製から始まります。 次のステップでは、エマルジョンPCR（emPCR）を実施して、ビーズの表面上の個々の鋳型DNA分子をクローン的に増幅。 emPCRでは、個々の鋳型DNAをPCR試薬と混合し、水中油型エマルジョン内の疎水性シェルで囲まれた水性液滴内のプライマーコートビーズを、配列決定のためにロードするスライドガラスの表面にランダムに付着。 この技術は、シークエンシングプライマーへのライゲーションで競合する4つの蛍光標識されたジ塩基プローブのセットを使用します。</p>
<h3><a href="http://454.com/products/technology.asp" target="_blank">454</a></h3>
<p>454は、大規模並列パイロシーケンシングを利用しています。 始めに全ゲノムDNAまたは標的遺伝子断片の300〜800bp断片のライブラリー調製します。 次に、DNAフラグメントへのアダプターの付着および単一のDNA鎖の分離。 その後アダプターに連結されたDNAフラグメントをエマルジョンベースのクローン増幅（emPCR）で処理し、DNAライブラリーフラグメントをミクロンサイズのビーズ上に配置します。 各DNA結合ビーズを光ファイバーチップ上のウェルに入れ、器具に挿入します。 4つのDNAヌクレオチドは、配列決定操作中に固定された順序で連続して加えられ、並行して配列決定されます。</p>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>&reg;</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>&reg;</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor<sup>&reg;</sup></a>.</div>
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<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>&reg;</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 &micro;l volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 &micro;l volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A &amp; B:</b> peak electropherogram view. <b>Panel C &amp; D:</b> virtual gel view.</small></div>
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<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor&reg; using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
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<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor&reg; using long fragment size Hydropores. &nbsp;</strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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<h3><strong>Your partner in long-read sequencing</strong></h3>
<p>Sequencing technologies have revolutionized genomics and biology researches. Long read sequencing enables researchers to access a more comprehensive view of genomes with higher accuracy. However, one of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size. The Megaruptor gives state-of-art shearing performance providing optimal long-read sequencing using <strong>PacBio&reg; and Oxford Nanopore<sup>TM</sup>technologies.</strong></p>
<p><strong></strong></p>
<center><a href="https://www.diagenode.com/p/megaruptor-cassette-12" class="tiny details button">CHECK OUT THE NEW 12-SAMPLE CASSETTE. RUN 50% MORE SAMPLES ON YOUR MEGARUPTOR 3!</a></center>
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<h4 style="font-size: 22px;"><a href="https://www.diagenode.com/en/p/megaruptor-3">Click here to discover our latest innovation</a></h4>
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<p><span>We have designed the Megaruptor</span>&reg;&nbsp;<span>2 using our highest level of knowledge in shearing so that it exceeds your expectations. This device will serve your research needs for many years and will provide the best experience with long DNA molecules preparation. </span></p>
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<p><span>The Megaruptor</span><span>&reg; </span><span>2 was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA in the range of 3 kb - 75 kb </span><span>(contact us for the 3 kb setting)</span><span>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly interface allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design. </span></p>
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			'name' => 'Detection and Quantitation of DNA Damage on a Genome-wide ScaleUsing RADAR-seq.',
			'authors' => 'Zatopek  Kelly M et al.',
			'description' => '<p>The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate DNA damage sites across a genome enable an understanding of the consequences of DNA damage as well as how damage is repaired, which can have key diagnostic and therapeutic implications. Importantly, advancements in technology have enabled the development of high-throughput sequencing-based DNA damage detection methods. These methods require DNA enrichment or amplification steps that limit the ability to quantitate the DNA damage sites. Further, each of these methods is typically tailored to detect only a specific type of damage. RAre DAmage and Repair (RADAR) sequencing is a DNA sequencing workflow that overcomes these limitations and enables detection and quantitation of DNA damage sites in any organism on a genome-wide scale. RADAR-seq works by replacing DNA damage sites with a patch of modified bases that can be directly detected by Pacific Biosciences Single-Molecule Real Time sequencing. Here, we present three protocols that enable detection of thymine dimers and ribonucleotides in bacterial and archaeal genomes. Basic Protocol 1 enables construction of a reference genome required for RADAR-seq analyses. Basic Protocol 2 describes how to locate, quantitate, and compare thymine dimer levels in Escherichia coli exposed to varying amounts of UV light. Basic Protocol 3 describes how to locate, quantitate, and compare ribonucleotide levels in wild-type and &Delta;RNaseH2 Thermococcus kodakarensis. Importantly, all three protocols provide in-depth steps for data analysis. Together they serve as proof-of-principle experiments that will allow users to adapt the protocols to locate and quantitate a wide variety of DNA damage sites in any organism. &copy; 2022 New England Biolabs. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Constructing a reference genome utilizing SMRT sequencing Basic Protocol 2: Mapping and quantitating genomic thymine dimer formation in untreated versus UV-irradiated E. coli using RADAR-seq Basic Protocol 3: Mapping and quantitating genomic ribonucleotide incorporation in wildtype versus &Delta;RNaseH2 T. kodakarensis using RADAR-seq.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36374013',
			'doi' => '10.1002/cpz1.595',
			'modified' => '2023-02-17 08:48:37',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '4533',
			'name' => 'Predictable and stable epimutations induced during clonal plantpropagation with embryonic transcription factor.',
			'authors' => 'Wibowo  Anjar Tri et al.',
			'description' => '<p>Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.</p>',
			'date' => '2022-11-01',
			'pmid' => '/',
			'doi' => '10.1371/journal.pgen.1010479',
			'modified' => '2023-02-17 08:50:15',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '4536',
			'name' => 'Benchmarking second and third-generation sequencing platforms formicrobial metagenomics.',
			'authors' => 'Meslier  Victoria et al.',
			'description' => '<p>Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36369227',
			'doi' => '10.1038/s41597-022-01762-z',
			'modified' => '2023-02-17 08:52:35',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '4543',
			'name' => 'Mitochondrial RNA editing in Trypanoplasma borreli: new tools, newrevelations',
			'authors' => 'Gerasimov  Evgeny S. et al.',
			'description' => '<p>The kinetoplastids are unicellular flagellates that derive their name from the &lsquo;kinetoplast&rsquo;, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein products of this mitochondrial genome are encoded as cryptogenes; their transcripts require editing to generate an open reading frame. This happens through RNA editing, whereby small regulatory guide (g)RNAs direct the proper insertion and deletion of one or more uridines at each editing site within specific transcript regions. An accurate perspective of the kDNA expansion and evolution of their unique uridine insertion/deletion editing across kinetoplastids has been difficult to achieve. Here, we resolved the kDNA structure and editing patterns in the early-branching kinetoplastid Trypanoplasma borreli and compare them with those of the well-studied trypanosomatids. We find that its kDNA consists of circular molecules of about 42 kb that harbor the rRNA and protein-coding genes, and 17 different contigs of approximately 70 kb carrying an average of 23 putative gRNA loci per contig. These contigs may be linear molecules, as they contain repetitive termini. Our analysis uncovered a putative gRNA population with unique length and sequence parameters that is massive relative to the editing needs of this parasite. We validated or determined the sequence identity of four edited mRNAs, including one coding for ATP synthase 6 that was previously thought to be missing. We utilized computational methods to show that the T. borreli transcriptome includes a substantial number of transcripts with inconsistent editing patterns, apparently products of non-canonical editing. This species utilizes the most extensive uridine deletion compared to other studied kinetoplastids to enforce amino acid conservation of cryptogene products, although insertions still remain more frequent. Finally, in three tested mitochondrial transcriptomes of kinetoplastids, uridine deletions are more common in the raw mitochondrial reads than aligned to the fully edited, translationally competent mRNAs. We conclude that the organization of kDNA across known kinetoplastids represents variations on partitioned coding and repetitive regions of circular molecules encoding mRNAs and rRNAs, while gRNA loci are positioned on a highly unstable population of molecules that differ in relative abundance across strains. Likewise, while all kinetoplastids possess conserved machinery performing RNA editing of the uridine insertion/deletion type, its output parameters are species-specific.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.csbj.2022.11.023',
			'doi' => '10.1016/j.csbj.2022.11.023',
			'modified' => '2023-02-17 08:53:23',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4737',
			'name' => 'Evaluation of the pathogenesis of non-typical strain with α-hemolysin,Vibrio parahaemolyticus 353, isolated from Chinese seafood throughcomparative genome and transcriptome analysis.',
			'authors' => 'Zha  Fei et al.',
			'description' => '<p>Vibrio parahaemolyticus outbreaks frequently occur, causing gastrointestinal sickness owing to the consumption of aquatic foods by various virulence factors; however, the mechanism of pathogenesis is still unknown. In this study, a non-typical strain of V. parahaemolyticus, named VP353, was isolated from shrimp in China. Its comparative genome and transcriptome after infection with Caco-2 cells were examined to illustrate the mechanisms of its pathogenesis. VP353 was a tdh-trh- strain but uncommonly manifested robust cytotoxicity towards Caco-2 cells. Compared with the standard strain RIMD2210633, VP353 harbored alpha-hemolysins (hlyA, hlyB, hlyC, and hlyD) was first reported in V. parahaemolyticus and showed high diversity in the T3SS2 gene cluster. Moreover, the expression of flagella, T2SS, quorum sensing-related genes, hlyA, hlyC were up-regulated, and hlyB, hlyD were down-regulated. In summary, our results demonstrate that some novel virulence factors contribute to the pathogenesis of V. parahaemolyticus infection.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36437125',
			'doi' => '10.1016/j.marpolbul.2022.114276',
			'modified' => '2023-03-07 08:55:16',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4476',
			'name' => 'Rapid and comprehensive diagnostic method for repeat expansion diseasesusing nanopore sequencing.',
			'authors' => 'Miyatake  S. et al.',
			'description' => '<p>We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36289212',
			'doi' => '10.1038/s41525-022-00331-y',
			'modified' => '2022-11-18 12:21:42',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4478',
			'name' => 'Characterization of somatic structural variations in 528 Chineseindividuals with Esophageal squamous cell carcinoma.',
			'authors' => 'Cui   H. et al.',
			'description' => '<p>Esophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations' mechanisms and biological functions. SVs show multi-mode distributions in size, indicating distinct mutational processes. We develop a tool and define five types of complex rearrangements with templated insertions. We highlight a type of fold-back inversion, which is associated with poor outcomes. Distinct rearrangement signatures demonstrate variable genomic metrics such as replicating time, spatial proximity, and chromatin accessibility. Specifically, fold-back inversion tends to occur near the centrosome; TD-c2 (Tandem duplication-cluster2) is significantly enriched in chromatin-accessibility and early-replication region compared to other signatures. Analyses of TD-c2 signature reveal 9 TD hotspots, of which we identify a hotspot consisting of a super-enhancer of PTHLH. We confirm the oncogenic effect of the PTHLH gene and its interaction with enhancers through functional experiments. Finally, extrachromosomal circular DNAs (ecDNAs) are present in 14\% of ESCCs and have strong selective advantages to driver genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36272974',
			'doi' => '10.1038/s41467-022-33994-3',
			'modified' => '2022-11-18 12:23:21',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4483',
			'name' => 'The Capparis spinosa var. herbacea genome provides the first genomicinstrument for a diversity and evolution study of the Capparaceae family.',
			'authors' => 'Wang  Lei et al.',
			'description' => '<p>BACKGROUND: The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS: We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23\% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28\%, and transposable element sequences accounted for 43.98\%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55\% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82\% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS: This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36310248',
			'doi' => '10.1093/gigascience/giac106',
			'modified' => '2022-11-18 12:30:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4484',
			'name' => 'Genomic Characterization and Antimicrobial Susceptibility ofDromedary-Associated  from the Horn of Africa.',
			'authors' => 'Akarsu  H. et al.',
			'description' => '<p>Members of the family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized strains from apparently healthy and diseased camels ( = 84) and cattle ( = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by (K), /, /, /, , , , and , respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the and families, reported here for the first time for certain species of . All strains contained at least one intact prophage sequence, mainly belonging to the family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct clades and species. Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226992',
			'doi' => '10.1128/aem.01146-22',
			'modified' => '2022-11-18 12:31:20',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4418',
			'name' => 'Complete Genome Sequences of the Soil Oxalotrophic BacteriumCupriavidus oxalaticus Strain Ox1 and Its DerivedmCherry-Tagged Strain.',
			'authors' => 'Palmieri  Fabio et al. ',
			'description' => '<p>Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69&thinsp;Mb, with a GC content of 66.9\%. The genome sequence of Ox1 contains a complete operon for the degradation and assimilation of oxalate.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35924938',
			'doi' => '10.1128/mra.00181-22',
			'modified' => '2022-09-27 14:42:06',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4442',
			'name' => 'The improved genome of the nematode Parapristionchus giblindavisiprovides insights into lineage-specific gene family evolution.',
			'authors' => 'Röseler  W. et al. ',
			'description' => '<p>Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricted genes. To trace back the evolution of such new or rapidly evolving genes, a robust phylogenomic framework is indispensable. Here, we present an improved version of the genome of Parapristionchus giblindavisi which is the only known member of the sister group of Pristionchus. Relative to the previous short read assembly, the new genome is based on long reads and displays higher levels of contiguity, completeness, and correctness. Specifically, the number of contigs dropped from over 7303 to 735 resulting in an N50 increase from 112&thinsp;kb to 791&thinsp;kb. We made use of the new genome to revisit the evolution of multiple gene families. This revealed Pristionchus-specific expansions of several environmentally responsive gene families and a Pristionchus-specific loss of the de novo purine biosynthesis pathway. Focusing on the evolution of sulfatases and sulfotransferases, which control the mouth form plasticity in P. pacificus, reveals differences in copy number and genomic configurations between the genera Pristionchus and Parapristionchus. Altogether, this demonstrates the utility of the P. giblindavisi genome to date and polarize lineage-specific patterns.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35980151',
			'doi' => '10.1093/g3journal/jkac215',
			'modified' => '2022-10-14 16:33:33',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4443',
			'name' => 'The chromosome-level genome of Gypsophila paniculata reveals themolecular mechanism of floral development and ethylene insensitivity',
			'authors' => 'Fan  Li et al. ',
			'description' => '<p>Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the worldwide famous cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with a total size of 749.58 Mb. Whole-genome duplication signatures unveil two major duplication events in its evolutionary history, an ancient one occurring before the divergence of Caryophyllaceae and a more recent one shared with Dianthus caryophyllus. The integrative analyses combining genomic and transcriptomic data reveal the mechanisms regulating floral development and ethylene response of G. paniculata. The reduction of AGAMOUS expression probably caused by sequence polymorphism and the mutation in miR172 binding site of PETALOSA are associated with the double flower formation in G. paniculata. The low expression of ERS (ETHYLENE RESPONSE SENSOR) and the reduction of downstream ERF (ETHYLENE RESPONSE FACTOR) gene copy number collectively lead to the ethylene insensitivity of G. paniculata, affecting flower senescence and making it capable of making dried flowers. This study provides a cornerstone for understanding the underlying principles governing floral development and flower senescence, which could accelerate the molecular breeding of the Caryophyllaceae species.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac176/6674669',
			'doi' => '10.1093/hr/uhac176',
			'modified' => '2022-10-14 16:34:34',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4445',
			'name' => 'Patients with biallelic GGC repeat expansions in NOTCH2NLCexhibiting a typical neuronal intranuclear inclusion disease phenotype.',
			'authors' => 'Kameyama  Shinichi et al.',
			'description' => '<p>We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of the entire NOTCH2NLC GGC repeat expansion and DNA methylation were comprehensively evaluated using fluorescent amplicon length PCR (AL-PCR), Southern blotting and targeted long-read sequencing, and detailed genetic/epigenetic and clinical features were described. In AL-PCR, we could not recognize the wild-type allele in both patients. Targeted long-read sequencing revealed that one patient harbored a homozygous repeat expansion. The other patient harbored compound heterozygous repeat expansions. The GGC repeats and the nearest CpG island were hypomethylated in all expanded alleles in both patients. Both patients harboring the biallelic GGC repeat expansion showed a typical dementia-dominant NIID phenotype. In conclusion, the biallelic GGC repeat expansion in two typical NIID patients indicated that NOTCH2NLC-related diseases could be completely dominant.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36041634',
			'doi' => '10.1016/j.ygeno.2022.110469',
			'modified' => '2022-10-21 09:28:25',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4453',
			'name' => 'A haplotype resolved chromosomal level avocado genome allows analysis ofnovel avocado genes',
			'authors' => 'Onkar N. et al. ',
			'description' => '<p>Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80\% of the world&rsquo;s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8\% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48&thinsp;915 avocado genes of which 39&thinsp;207 could be ascribed functions. The genome contained 62.6\% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac157/6652665',
			'doi' => 'https://doi.org/10.1093/hr/uhac157',
			'modified' => '2022-10-21 09:36:02',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4432',
			'name' => 'Identification of Laportea bulbifera using the Complete ChloroplastGenome as a Super-Barcode',
			'authors' => 'Wang  Wenting et al.',
			'description' => '<p>Laportea bulbifera, a Miao medicine grown in karst areas, has exerts a unique curative effect on skin itching in the elderly, with an annual sales of &gt; 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation highthroughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence used as a super-barcode and the highly variable regions (ycf1, matK, and ndhD), especially matK, can be used as specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1793400%2Fv1',
			'doi' => '10.21203/rs.3.rs-1793400/v1',
			'modified' => '2022-09-28 09:10:15',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4435',
			'name' => 'Oxford Nanopore R10.4 long-read sequencing enables the generation ofnear-finished bacterial genomes from pure cultures and metagenomes withoutshort-read or reference polishing.',
			'authors' => 'Sereika  Mantas et al.',
			'description' => '<p>Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35789207',
			'doi' => '10.1038/s41592-022-01539-7',
			'modified' => '2022-09-28 09:21:29',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4462',
			'name' => 'Complete Genome Sequences of Multidrug-Resistant Campylobactercoli Strains YH501, YH503, and YH504, from Retail Chicken.',
			'authors' => 'He  Yiping et al.',
			'description' => '<p>Campylobacter coli is an important foodborne pathogen that can cause inflammation of the intestine and diarrhea in humans. The complete genomes, including megaplasmids, of C. coli strains YH501, YH503, and YH504 from retail chicken were sequenced and assembled. Whole-genome analysis revealed a number of virulence and antibiotic resistance genes, suggesting significant potential for these poultry-originating isolates to cause human disease.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35862903',
			'doi' => '10.1128/mra.00237-22',
			'modified' => '2022-10-21 09:48:05',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4463',
			'name' => 'High-Quality Genome Assembly of Nannochloris desiccata 2437 andIts Associated Bacterial Community.',
			'authors' => 'Sanders  Claire K et al.',
			'description' => '<p>High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assembled in 29 contigs.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35770994',
			'doi' => '10.1128/mra.00710-21',
			'modified' => '2022-10-21 09:48:45',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4461',
			'name' => 'Long-read Oxford nanopore sequencing reveals a de novo case of complexchromosomal rearrangement involving chromosomes 2, 7, and 13.',
			'authors' => 'Xing  Lingling et al.',
			'description' => '<p>BACKGROUND: Complex chromosomal rearrangements (CCRs) are associated with high reproductive risk, infertility, abnormalities in offspring, and recurrent miscarriage in women. It is essential to accurately characterize apparently balanced chromosome rearrangements in unaffected individuals. METHODS: A CCR young couple who suffered two spontaneous abortions and underwent labor induction due to fetal chromosomal abnormalities was studied using long-read sequencing(LRS), single-nucleotide polymorphism (SNP) array, G-banding karyotype analysis (550-band resolution), and Sanger sequencing. RESULTS: SNP analysis of the amniotic fluid cells during the third pregnancy revealed a 9.9-Mb duplication at 7q21.11q21.2 and a 24.8-Mb heterozygous deletion at 13q21.1q31.1. The unaffected female partner was a carrier of a three-way CCR [46,XX,? ins(7;13)(q21.1;q21.1q22)t(2;13)(p23;q22)]. Subsequent LRS analysis revealed the exact breakpoint locations on the derivative chromosomes and the specific method of chromosome rearrangement, indicating that the CCR carrier was a more complex structural rearrangement comprising five breakpoints. Furthermore, LRS detected an inserted fragment of chromosome 13 in chromosome 7. CONCLUSIONS: LRS is effective for analyzing the complex structural variations of the human genome and may be used to clarify the specific CCRs for effective genetic counseling and appropriate intervention.</p>',
			'date' => '2022-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35758276',
			'doi' => '10.1002/mgg3.2011',
			'modified' => '2022-10-21 09:47:15',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4361',
			'name' => 'Accumulation of endosymbiont genomes in an insect autosome followed byendosymbiont replacement.',
			'authors' => 'Tvedte  Eric S. et al. ',
			'description' => '<p>Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT). A prominent source of LGT is Wolbachia, a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells. The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive and has been localized to chromosome 4, contributing to chromosome expansion in this lineage. As has happened frequently with claims of bacteria-to-eukaryote LGT, the contribution of wAna transfers to the expanded size of D.&nbsp;ananassae chromosome 4 has been specifically contested owing to an assembly where Wolbachia sequences were classified as contaminants and removed. Here, long-read sequencing with DNA from a Wolbachia-cured line enabled assembly of 4.9 Mbp of nuclear Wolbachia transfers (nuwts) in D.&nbsp;ananassae and a 24-kbp nuclear mitochondrial transfer. The nuwts are &lt;8,000 years old in at least two locations in chromosome 4 with at least one whole-genome integration followed by rapid extensive duplication of most of the genome with regions that have up to 10 copies. The genes in nuwts are accumulating small indels and mobile element insertions. Among the highly duplicated genes are cifA and cifB, two genes associated with Wolbachia-mediated Drosophila cytoplasmic incompatibility. The wAna strain that was the source of nuwts was subsequently replaced by a different wAna endosymbiont. Direct RNA Nanopore sequencing of Wolbachia-cured lines identified nuwt transcripts, including spliced transcripts, but functionality, if any, remains elusive.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35671755',
			'doi' => '10.1016/j.cub.2022.05.024',
			'modified' => '2022-08-04 15:47:25',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '4363',
			'name' => 'DNA Hypermethylation and a Specific Methylation Spectrum on theX Chromosome in Turner Syndrome as Determined by NanoporeSequencing',
			'authors' => 'Fan  Xin et al.',
			'description' => '<p>The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate TS. Results: Thirteen TS (45X0) patients and eight controls were enrolled. Trio-WES analysis did not find any pathogenetic or likely pathogenic variants except X chromosome (chrX) deletion. The average methylation levels and patterns of chrX in 45X0 and 46XY were similar, and significantly higher than in 46XX (p = 2.22 &times; 10&minus;16). Both hyper-methylation and hypo-methylation were detected in the CpG island (CGI), CGI_shore, promoter, genebody, and PAR1-region, while in the transposon element inactivation regions of the chrX and hypermethylation were predominant. A total of 125 differentially methylated genes were identified in 45X0 compared to 46XX, including 8 and 117 hypermethylated and hypomethylated genes, respectively, with the enrichment terms of mitophagy, regulation of DNA-binding transcription factor activity, etc. Conclusions: The results suggest that the methylation profile in patients with TS might be determined by the number of X chromosomes; the patterns of methylation in TS were precisely associated with the maintenance of genomic stability and improvement of gene expression. Differentially methylated genes/pathways might reveal the potential epigenetic modulation and lead to better understanding of TS.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://doi.org/10.3390%2Fjpm12060872',
			'doi' => '10.3390/jpm12060872',
			'modified' => '2022-08-04 15:49:32',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '4530',
			'name' => 'The genome sequence of Anoplius nigerrimus (Scopoli, 1763), a spiderwasp',
			'authors' => 'Falk  Steven and Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual Anoplius nigerrimus (Arthropoda; Insecta; Hymenoptera; Pompilidae) of unknown sex. The genome sequence is 624 megabases in span. In total, 45.75\% of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 17.5 kilobases in length.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17814.1',
			'doi' => '10.12688/wellcomeopenres.17814.1',
			'modified' => '2023-02-17 08:59:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4522',
			'name' => 'Familial long-read sequencing increases yield of de novo mutations.',
			'authors' => 'Noyes  Michelle D et al.',
			'description' => '<p>Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20\% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5\% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41&nbsp;&times; 10 substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by &gt;25\% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35290762',
			'doi' => '10.1016/j.ajhg.2022.02.014',
			'modified' => '2023-02-17 09:01:49',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4525',
			'name' => 'Transposon activity, local duplications and propagation of structuralvariants across haplotypes drive the evolution of the Drosophila S2cell line.',
			'authors' => 'Lewerentz  Jacob et al.',
			'description' => '<p>BACKGROUND: Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure. RESULTS: Using a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (&gt;&thinsp;80\% of SVs), with Gypsy retrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in other D. melanogaster cell lines. CONCLUSIONS: The S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35392795',
			'doi' => '10.1186/s12864-022-08472-1',
			'modified' => '2023-02-17 09:02:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4466',
			'name' => 'Phylogenomics and Comparative Genomics Highlight SpecificGenetic Features in  Species.',
			'authors' => 'Sun  Yi-Fei et al.',
			'description' => '<p>The species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven genomes, including three new genomes, , , and . The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the species.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35330313',
			'doi' => '10.3390/jof8030311',
			'modified' => '2022-10-21 09:50:01',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4366',
			'name' => 'Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes',
			'authors' => 'Rabanal  Fernando A. and Gräff  Maike and Lanz  Christa andFritschi  Katrin and Llaca  Victor and Lang  Michelle andCarbonell-Bejerano  Pablo and Henderson  Ian and Weigel Detlef',
			'description' => '<p><span>Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant&nbsp;</span><em>Arabidopsis thaliana</em><span>, other than the reference accession Col-0, all other accessions<span>&nbsp;</span></span><em>de novo</em><span><span>&nbsp;</span>assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of &gt;85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two<span>&nbsp;</span></span><em>A. thaliana</em><span><span>&nbsp;</span>accessions.</span></p>',
			'date' => '2022-02-15',
			'pmid' => 'https://doi.org/10.1101%2F2022.02.15.480579',
			'doi' => '10.1101/2022.02.15.480579',
			'modified' => '2022-08-04 16:02:44',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4362',
			'name' => 'Chromosomal rearrangements with stable repertoires of genes andtransposable elements in an invasive forest-pathogenic fungus',
			'authors' => 'Demené A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2021.03.09.434572v5',
			'doi' => '/',
			'modified' => '2022-08-04 15:48:42',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4374',
			'name' => 'Genomic characterisation of three GES-producing Enterobacteralesisolated in the Czech Republic.',
			'authors' => 'Finianos  M. et al.',
			'description' => '<p>OBJECTIVES: The aim of the study is to characterise the genomic features of three GES-producing Enterobacterales isolates from Czech hospitals. METHODS: In 2020, during a routine screening of the hospital's surfaces in Prague General Hospital, two strains (CZ862 and CZ863) that belonged to the Enterobacter cloacae complex were found to be bla positive. Another bla positive strain identified as Klebsiella oxytoca was recovered from a patient hospitalised in Pilsen. Antibiotic susceptibility profiling was done with broth microdilution assay. Conjugation/transformation experiments were performed on all three strains. Genomic DNA of the three isolates was subjected to whole genome sequencing using PacBio platform. RESULTS: Multilocus sequence types typing of CZ862 and CZ863 identified the strains as ST837 and a novel ST (ST1622). Both bla harbouring plasmids showed high sequence similarity and complete query coverage (100\% and 99.98\%) with pEcl-35771cz. Both plasmids had two copies of bla instead of one copy as found in pEcl-35771cz. The clinical isolate CZ598 belonged to ST180. The plasmid harboured bla gene, cat and aac(6')-lb and the novel variant bla No similar sequences were observed, suggesting a novel plasmid. CONCLUSION: The detection of the two bla-positive plasmids in the same hospital environment, the first report after 3 years, suggests a hidden source. This highlights the importance of the hidden sources and evolution of such plasmids on the route of spreading into clinical settings. Also, the detection of the new bla, which is thought in this case to be associated with carbapenem resistance, imposes a health risk if disseminated, limiting therapeutic options.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35231657',
			'doi' => '10.1016/j.jgar.2022.02.016',
			'modified' => '2022-08-04 16:18:16',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4254',
			'name' => 'Improved chromosome-level genome assembly of the Glanville fritillarybutterfly () integrating Pacific Biosciences long reads and ahigh-density linkage map',
			'authors' => 'Smolander Olli-Pekka et al.',
			'description' => '<p>Abstract Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92&ndash;94\% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35022701',
			'doi' => '10.1093/gigascience/giab097',
			'modified' => '2022-05-20 09:45:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '4284',
			'name' => 'PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs,and methylation.',
			'authors' => 'Mahmoud Medhat et al.',
			'description' => '<p>Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34521442',
			'doi' => '10.1186/s13059-021-02486-w',
			'modified' => '2022-05-24 09:07:16',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '4286',
			'name' => 'Establishing community reference samples, data and call sets forbenchmarking cancer mutation detection using whole-genome sequencing.',
			'authors' => 'Fang Li Tai et al.',
			'description' => '<p>The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with &gt;2,000-fold coverage, spanning 82\% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34504347',
			'doi' => '10.1038/s41587-021-00993-6',
			'modified' => '2022-05-24 09:09:41',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4291',
			'name' => 'LeafGo: Leaf to Genome, a quick workflow to produce high-quality denovo plant genomes using long-read sequencing technology.',
			'authors' => 'Driguez Patrick et al.',
			'description' => '<p>Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34479618',
			'doi' => '10.1186/s13059-021-02475-z',
			'modified' => '2022-05-24 09:16:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4310',
			'name' => 'Targeted long-read sequencing identifies missing disease-causingvariation.',
			'authors' => 'Miller Danny E et al.',
			'description' => '<p>Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.ajhg.2021.06.006',
			'doi' => '10.1016/j.ajhg.2021.06.006',
			'modified' => '2022-06-22 09:26:54',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4342',
			'name' => 'Evidence of an epidemic spread of KPC-producing  in Czech hospitals',
			'authors' => 'Kraftova Lucie et al.',
			'description' => '<p>The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018&ndash;2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n&thinsp;=&thinsp;12), N (n&thinsp;=&thinsp;5), C (n&thinsp;=&thinsp;1) and P6 (n&thinsp;=&thinsp;1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn&rsquo;t be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34344951',
			'doi' => '10.1038/s41598-021-95285-z',
			'modified' => '2022-06-22 09:33:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => array(
			'id' => '4309',
			'name' => 'The USDA-ARS Ag100Pest Initiative: High-Quality GenomeAssemblies for Agricultural Pest Arthropod Research',
			'authors' => 'Childers  A.K. et al.',
			'description' => '<p>Simple Summary High-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technical challenge of isolating the necessary quantity and quality of DNA from many species. Sequencing methods have now improved such that many insect genomes can be sequenced and assembled at scale. We created the Ag100Pest Initiative to propel agricultural research forward by assembling reference-quality genomes of important arthropod pest species. Here, we describe the Ag100Pest Initiative&rsquo;s processes and experimental procedures. We show that the Ag100Pest Initiative will greatly expand the diversity of publicly available arthropod genome assemblies. We also demonstrate the high quality of preliminary contig assemblies. We share arthropod-specific technical details and insights that we have gained during the project. The methods and preliminary results presented herein should help other researchers attain similarly high-quality assemblies, effectively changing the landscape of insect genomics. Abstract The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture&rsquo;s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale.</p>',
			'date' => '2021-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34357286',
			'doi' => '10.3390/insects12070626',
			'modified' => '2022-08-03 16:18:33',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 35 => array(
			'id' => '4311',
			'name' => 'The American lobster genome reveals insights on longevity, neural, andimmune adaptations.',
			'authors' => 'Polinski J. M. et al. ',
			'description' => '<p>The American lobster, , is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we report a high-quality draft assembly of the genome with 25,284 predicted gene models. Analysis of the neural gene complement revealed extraordinary development of the chemosensory machinery, including a profound diversification of ligand-gated ion channels and secretory molecules. The discovery of a novel class of chimeric receptors coupling pattern recognition and neurotransmitter binding suggests a deep integration between the neural and immune systems. A robust repertoire of genes involved in innate immunity, genome stability, cell survival, chemical defense, and cuticle formation represents a diversity of defense mechanisms essential to thrive in the benthic marine environment. Together, these unique evolutionary adaptations contribute to the longevity and ecological success of this long-lived benthic predator.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34162536',
			'doi' => '10.1126/sciadv.abe8290',
			'modified' => '2022-08-03 16:19:34',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => array(
			'id' => '4316',
			'name' => 'Analysis of the Coptis chinensis genome reveals the diversification ofprotoberberine-type alkaloids.',
			'authors' => 'Liu Y. et al. ',
			'description' => '<p>Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34078898',
			'doi' => '10.1038/s41467-021-23611-0',
			'modified' => '2022-08-03 16:20:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 37 => array(
			'id' => '4348',
			'name' => 'Infectivity assessment of porcine endogenous retrovirus usinghigh-throughput sequencing technologies.',
			'authors' => 'Kono K. et al.',
			'description' => '<p>Xenogenic cell-based therapeutic products are expected to alleviate the chronic shortage of human donor organs. For example, porcine islet cell products are currently under development for the treatment of human diabetes. As porcine cells possess endogenous retrovirus (PERV), which can replicate in human cells in vitro, the potential transmission of PERV has raised concerns in the case of products that use living pig cells as raw materials. Although several PERV sequences exist in the porcine genome, not all have the ability to infect human cells. Therefore, polymerase chain reaction analysis, which amplifies a portion of the target gene, may not accurately assess the infection risk. Here, we determined porcine genome sequences and evaluated the infectivity of PERVs using high-throughput sequencing technologies. RNA sequencing was performed on both PERV-infected human cells and porcine cells, and reads mapped to PERV sequences were examined. The normalized number of the reads mapped to PERV regions was able to predict the infectivity of PERVs, indicating that it would be useful for evaluation of the PERV infection risk prior to transplantation of porcine products.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.biologicals.2021.05.001',
			'doi' => '10.1016/j.biologicals.2021.05.001',
			'modified' => '2022-08-03 16:57:04',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 38 => array(
			'id' => '4128',
			'name' => 'Chromosomal inversion polymorphisms in two sympatric ascidian lineages.',
			'authors' => 'Satou, Yutaka and Sato, Atsuko and Yasuo, Hitoyoshi and Mihirogi, Yukie andBishop, John and Fujie, Manabu and Kawamitsu, Mayumi and Hisata, Kanako andSatoh, Noriyuki',
			'description' => '<p>Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. While these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. While the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33822040',
			'doi' => '10.1093/gbe/evab068',
			'modified' => '2021-12-07 10:17:37',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4186',
			'name' => 'Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.',
			'authors' => 'Formenti G. et al.',
			'description' => '<p>BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (&gt;&thinsp;10&nbsp;kbp, PacBio or Nanopore) and short (100-300&thinsp;bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33910595',
			'doi' => '10.1186/s13059-021-02336-9',
			'modified' => '2022-01-05 15:01:11',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => array(
			'id' => '4140',
			'name' => 'Chromosomal rearrangements but no change of genes and transposable elementsrepertoires in an invasive forest-pathogenic fungus',
			'authors' => 'Demené, A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long-reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that C. parasitica genome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high quality assembled genomes, and question the role of structural variations on the invasive success of this fungal pathogen species.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1101%2F2021.03.09.434572',
			'doi' => '10.1101/2021.03.09.434572',
			'modified' => '2021-12-13 09:19:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 41 => array(
			'id' => '4191',
			'name' => 'A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.',
			'authors' => 'Liu H. et al. ',
			'description' => '<p>Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population resulting from the mating of Pekin ducks (white-shelled eggs) and mallards (green-shelled eggs). We further narrowed the candidate region to a 30-kb interval by comparing genome divergence in seven indigenous duck populations. Among the genes located in the finely mapped region, only one transcript of the ABCG2 gene (XM_013093252.2) exhibited higher uterine expression in green-shelled individuals than in white-shelled individuals, as supported by transcriptome data from four populations. ABCG2 has been reported to encode a protein that functions as a membrane transporter for biliverdin. Sanger sequencing of the whole 30-kb candidate region (Chr4: 47.41-47.44&nbsp;Mb) and a plasmid reporter assay helped to identify a single nucleotide polymorphism (Chr4: 47,418,074 G&gt;A) located in a conserved predicted promoter region whose variation may alter ABCG2 transcription activity. We provide a useful molecular marker for duck breeding and contribute data to the research on ecological evolution based on egg colour patterns among birds.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33372351',
			'doi' => '10.1111/mec.15785',
			'modified' => '2022-01-05 15:13:30',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => array(
			'id' => '4131',
			'name' => 'Genomic Characterization of VIM and MCR Co-Producers: The First TwoClinical Cases, in Italy.',
			'authors' => 'Marchetti, Vittoria Mattioni and Bitar, Ibrahim and Sarti, Mario andFogato, Elena and Scaltriti, Erika and Bracchi, Chiara and Hrabak, Jaroslavand Pongolini, Stefano and Migliavacca, Roberta',
			'description' => '<p>BACKGROUND: the co-production of carbapenemases and -genes represents a worrisome event in the treatment of infections. The aim of the study was to characterize the genomic features of two clinical complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. METHODS: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the and - type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). RESULTS: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The gene was harbored on a conjugative IncHI2 plasmid, while the determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: gene and its two component regulatory genes for increased expression on the chromosome, on non-conjugative (yet co-transferable) ColE plasmid, and on a non-conjugative IncA plasmid. CONCLUSIONS: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33418979',
			'doi' => '10.3390/diagnostics11010079',
			'modified' => '2021-12-07 10:22:20',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 43 => array(
			'id' => '4190',
			'name' => 'Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).',
			'authors' => 'Xia Z. et al.',
			'description' => '<p>Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7&thinsp;Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~1327.18&thinsp;Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33419990',
			'doi' => '10.1038/s41438-020-00455-1',
			'modified' => '2022-01-05 15:12:13',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 44 => array(
			'id' => '4205',
			'name' => 'Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.',
			'authors' => 'Suzuki Y. et al.',
			'description' => '<p>Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals characterizing rapid, haplotype-specific evolution of human centromeric arrays, while frequent single-nucleotide variants are largely conserved. We found a characteristic pattern shared among prevalent variants in human and chimpanzee. Our findings pave the way for studying sequence evolution in human and primate centromeres.</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33310858',
			'doi' => '10.1126/sciadv.abd9230',
			'modified' => '2022-01-06 15:00:50',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 45 => array(
			'id' => '4212',
			'name' => 'Efficient hybrid de novo assembly of human genomes with WENGAN.',
			'authors' => 'Di Genova A. et al. ',
			'description' => '<p>Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24-80.64&thinsp;Mb), few assembly errors (contig NGA50: 11.8-59.59&thinsp;Mb), good consensus quality (QV: 27.84-42.88) and high gene completeness (BUSCO complete: 94.6-95.2\%), while consuming low computational resources (CPU hours: 187-1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64&thinsp;Mb (NGA50: 59.59&thinsp;Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88&thinsp;Mb).</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33318652',
			'doi' => '10.1038/s41587-020-00747-w',
			'modified' => '2022-01-13 15:09:21',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 46 => array(
			'id' => '4000',
			'name' => 'Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.',
			'authors' => 'von der Heyde B, Emmanouilidou A, Mazzaferro E, Vicenzi S, Höijer I, Klingström T, Jumaa S, Dethlefsen O, Snieder H, de Geus E, Ameur A, Ingelsson E, Allalou A, Brooke HL, den Hoed M',
			'description' => '<p>A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30&nbsp;s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5&nbsp;days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25&nbsp;&micro;M ivabradine-an open channel blocker of HCNs-for 24&nbsp;h resulted in a dose-dependent higher HRV and lower heart rate at 5&nbsp;days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).</p>',
			'date' => '2020-07-16',
			'pmid' => 'http://www.pubmed.gov/32678143',
			'doi' => '10.1038/s41598-020-68567-1',
			'modified' => '2020-09-01 14:40:20',
			'created' => '2020-08-21 16:41:39',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4016',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69Escherichia coli Strain in Italy',
			'authors' => 'Mattioni, Marchetti Vittoria and Bitar, Ibrahim and Piazza, Aurora andMercato, Alessandra and Fogato, Elena and Hrabak, Jaroslav and Migliavacca,Roberta',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-15',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2020-12-16 17:36:09',
			'created' => '2020-10-12 14:54:59',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4359',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a ClinicalST69 Escherichia coli Strain in Italy',
			'authors' => 'Mattioni MV et al. ',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-01',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2022-08-03 17:12:43',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '3974',
			'name' => 'Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.',
			'authors' => 'Oulghazi S, Moumni M, Khayi S, Robic K, Sarfraz S, Lopez-Roques C, Vandecasteele C, Faure D',
			'description' => '<p>Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.</p>',
			'date' => '2020-06-13',
			'pmid' => 'http://www.pubmed.gov/32545839',
			'doi' => '10.3390/microorganisms8060895',
			'modified' => '2020-08-12 09:28:31',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '3972',
			'name' => 'Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.',
			'authors' => 'Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J',
			'description' => '<p>Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.</p>',
			'date' => '2020-06-08',
			'pmid' => 'http://www.pubmed.gov/32553272',
			'doi' => '10.1016/j.cell.2020.05.021',
			'modified' => '2020-08-12 09:27:28',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 51 => array(
			'id' => '3869',
			'name' => 'Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.',
			'authors' => 'Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J',
			'description' => '<p>Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the&nbsp;evolutionary trajectory and functional distribution&nbsp;of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S.&nbsp;epidermidis genomes from 5 healthy individuals, we found that skin S.&nbsp;epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.</p>',
			'date' => '2020-02-06',
			'pmid' => 'http://www.pubmed.gov/32004459',
			'doi' => '10.1016/j.cell.2020.01.006',
			'modified' => '2020-03-20 17:45:40',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 52 => array(
			'id' => '4247',
			'name' => 'LongQC: A Quality Control Tool for Third GenerationSequencing Long Read Data',
			'authors' => 'Fukasawa Yoshinori et al.',
			'description' => '<p>We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key statistics were optimized for long read data, and LongQC covers all major TGS platforms. LongQC processes and visualizes those statistics automatically and quickly.</p>',
			'date' => '2020-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32041730',
			'doi' => '10.1534/g3.119.400864',
			'modified' => '2022-05-24 09:03:08',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 53 => array(
			'id' => '3863',
			'name' => 'Genome Sequence of  sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.',
			'authors' => 'Anton BP, DasSarma P, Martinez FL, DasSarma SL, Al Madadha M, Roberts RJ, DasSarma S',
			'description' => '<p>An extremely halophilic archaeon, sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorporated into HaloWeb (https://halo.umbc.edu/).</p>',
			'date' => '2020-01-30',
			'pmid' => 'http://www.pubmed.gov/32001568',
			'doi' => '10.1128/MRA.01505-19.',
			'modified' => '2020-03-20 17:52:34',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 54 => array(
			'id' => '3864',
			'name' => 'The round goby genome provides insights into mechanisms that may facilitate biological invasions.',
			'authors' => 'Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S',
			'description' => '<p>BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. RESULTS: We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. CONCLUSIONS: The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.</p>',
			'date' => '2020-01-28',
			'pmid' => 'http://www.pubmed.gov/31992286',
			'doi' => '10.1186/s12915-019-0731-8',
			'modified' => '2020-03-20 17:51:48',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 55 => array(
			'id' => '3857',
			'name' => 'The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.',
			'authors' => 'Kan SL, Shen TT, Gong P, Ran JH, Wang XQ',
			'description' => '<p>BACKGROUND: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. RESULTS: Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. CONCLUSIONS: We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.</p>',
			'date' => '2020-01-20',
			'pmid' => 'http://www.pubmed.gov/31959109',
			'doi' => '10.1186/s12862-020-1582-1',
			'modified' => '2020-03-20 17:57:35',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 56 => array(
			'id' => '3858',
			'name' => 'A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).',
			'authors' => 'Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, Hiller M, Hundsdoerfer AK',
			'description' => '<p>BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged &sim;7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51&times; Pacific Biosciences long reads with an average read length of 8.9&nbsp;kb. Pacific Biosciences reads longer than 4&nbsp;kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.</p>',
			'date' => '2020-01-08',
			'pmid' => 'http://www.pubmed.gov/31972020',
			'doi' => '10.1093/gigascience/giaa001',
			'modified' => '2020-03-20 17:56:37',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 57 => array(
			'id' => '3823',
			'name' => 'Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of .',
			'authors' => 'Hovde BT, Daligault HE, Hanschen ER, Kunde YA, Johnson MB, Starkenburg SR, Johnson SL',
			'description' => '<p>The sequenced genome and the leaf transcriptome of a near relative of and was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (&lt;1 mbp) the cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified and we observed substantial diversity of genes and predicted gene products in and previously characterized toxins this suggests diverse toxin repertoires within potentially the results of rapid toxin evolution.</p>',
			'date' => '2019-11-25',
			'pmid' => 'http://www.pubmed.gov/31775284',
			'doi' => '10.3390/toxins11120691',
			'modified' => '2020-02-25 14:47:48',
			'created' => '2020-02-13 10:02:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 58 => array(
			'id' => '3813',
			'name' => 'NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.',
			'authors' => 'De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D'Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K',
			'description' => '<p>Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30&times; human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.</p>',
			'date' => '2019-11-14',
			'pmid' => 'http://www.pubmed.gov/31727106',
			'doi' => '10.1186/s13059-019-1856-3',
			'modified' => '2019-12-05 10:59:42',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 59 => array(
			'id' => '3791',
			'name' => 'Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull.',
			'authors' => 'Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL',
			'description' => '<p>Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (Pp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20&times; coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring P Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the P Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.</p>',
			'date' => '2019-10-07',
			'pmid' => 'http://www.pubmed.gov/31591551',
			'doi' => '10.1038/s41587-019-0266-0',
			'modified' => '2019-12-05 11:47:39',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 60 => array(
			'id' => '3788',
			'name' => 'Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef.',
			'authors' => 'Sekizuka T, Lee K, Kimata K, Isobe J, Kuroda M, Iyoda S, Ohnishi M, Sata T, Watahiki M',
			'description' => '<p>We present the complete genome sequence of an enterohemorrhagic O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.</p>',
			'date' => '2019-10-03',
			'pmid' => 'http://www.pubmed.gov/31582455',
			'doi' => '10.1128/MRA.00882-19.',
			'modified' => '2019-12-05 11:58:13',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 61 => array(
			'id' => '3772',
			'name' => 'Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions.',
			'authors' => 'Zhang S, Liang F, Lei C, Wu J, Fu J, Yang Q, Luo X, Yu G, Wang D, Zhang Y, Lu D, Sun X, Liang Y, Xu C',
			'description' => '<p>BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos that carry balanced inversion from those with a normal karyotype. We aim to evaluate the use of long-read sequencing in combination with haplotype linkage analysis to address this challenge. METHODS: Long-read sequencing on Oxford Nanopore platform was employed to identify the precise positions of inversion break points in four patients. Comprehensive chromosomal screening and genome-wide haplotype linkage analysis were performed based on SNP microarray. The haplotypes, including the break point regions, the whole chromosomes involved in the inversion and the corresponding homologous chromosomes, were established using informative SNPs. RESULTS: All the inversion break points were successfully identified by long-read sequencing and validated by Sanger sequencing, and on average only 13 bp differences were observed between break points inferred by long-read sequencing and Sanger sequencing. Eighteen blastocysts were biopsied and tested, in which 10 were aneuploid or unbalanced and eight were diploid with normal or balanced inversion karyotypes. Diploid embryos were transferred back to patients, the predictive results of the current methodology were consistent with fetal karyotypes of amniotic fluid or cord blood. CONCLUSIONS: Nanopore long-read sequencing is a powerful method to assay chromosomal inversions and identify exact break points. Identification of inversion break points combined with haplotype linkage analysis is an efficient strategy to distinguish embryos with normal or balanced inversion karyotypes, facilitating PGT applications.</p>',
			'date' => '2019-08-22',
			'pmid' => 'http://www.pubmed.gov/31439719',
			'doi' => '10.1136/jmedgenet-2018-105976',
			'modified' => '2019-10-02 17:08:37',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 62 => array(
			'id' => '3760',
			'name' => 'Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.',
			'authors' => 'Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, L',
			'description' => '<p>The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5&thinsp;kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions &lt;50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of &gt;15&thinsp;megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.<br /><!--50--></p>',
			'date' => '2019-08-12',
			'pmid' => 'http://www.pubmed.gov/31406327',
			'doi' => '10.1038/s41587-019-0217-9',
			'modified' => '2019-10-03 10:05:13',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 63 => array(
			'id' => '3749',
			'name' => 'Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.',
			'authors' => 'Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC',
			'description' => '<p>BACKGROUND: Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS: By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS: We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.</p>',
			'date' => '2019-07-08',
			'pmid' => 'http://www.pubmed.gov/31286858',
			'doi' => '10.1186/s12864-019-5909-5',
			'modified' => '2019-08-06 16:06:34',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 64 => array(
			'id' => '3721',
			'name' => 'Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.',
			'authors' => 'Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH',
			'description' => '<p>BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruy&egrave;re and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS: Two NWCs from Swiss Gruy&egrave;re producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS: Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.</p>',
			'date' => '2019-06-25',
			'pmid' => 'http://www.pubmed.gov/31238873',
			'doi' => '10.1186/s12866-019-1500-0',
			'modified' => '2019-07-04 18:06:26',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 65 => array(
			'id' => '3712',
			'name' => 'A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).',
			'authors' => 'Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z',
			'description' => '<p>BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential. FINDINGS: We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (&sim;211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants. CONCLUSION: This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.</p>',
			'date' => '2019-06-01',
			'pmid' => 'http://www.pubmed.gov/31216035',
			'doi' => '10.1093/gigascience/giz072',
			'modified' => '2019-07-05 14:29:16',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 66 => array(
			'id' => '3650',
			'name' => 'Genome Sequence and Methylation Patterns of  sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.',
			'authors' => 'Priya DasSarma, Anton BP, DasSarma S, Laye VJ, Guzman D, Roberts RJ, DasSarma S',
			'description' => '<p>sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Database (http://halo.umbc.edu). The polyextremophilic character and high-elevation environment make the microbe of interest for astrobiology.</p>',
			'date' => '2019-05-09',
			'pmid' => 'http://www.pubmed.gov/31072883',
			'doi' => '10.1016/j.gexplo.2004.07.001.',
			'modified' => '2019-06-07 10:11:11',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 67 => array(
			'id' => '3707',
			'name' => 'The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.',
			'authors' => 'Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C',
			'description' => '<p>Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4'-deoxyflavone synthesis in the genus&nbsp;Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30999079',
			'doi' => '10.1016/j.molp.2019.04.002',
			'modified' => '2019-07-05 14:35:57',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 68 => array(
			'id' => '3602',
			'name' => 'Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.',
			'authors' => 'Palmieri V, Dalchiele EA, Perini G, Motta A, De Spirito M, Zanoni R, Marrani AG, Papi M',
			'description' => '<p>We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoids GO-mediated oxidation of glutathione. This method offers new opportunities for the production of green biocompatible rGO and NAC-based therapies.</p>',
			'date' => '2019-03-20',
			'pmid' => 'http://www.pubmed.gov/30892320',
			'doi' => '10.1039/C9CC00429G.',
			'modified' => '2019-04-17 14:56:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 69 => array(
			'id' => '3725',
			'name' => 'The alternative reality of plant mitochondrial DNA',
			'authors' => 'Alexander Kozik, Beth A. Rowan, Dean Lavelle, Lidija Berke, M. Eric Schranz, Richard W. Michelmore, and Alan C. Christensen',
			'description' => '<p>Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative genomic arrangements (isoforms). Most mitochondrial genomes have been assembled using methods that were unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. This allowed us to characterize a comprehensive, complex set of isoforms within each species and to compare genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched linear, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement, and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms evident in our data, we inferred that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other lettuce species can be largely explained by rare recombination events that rearrange the structure. Our data demonstrate that representations of plant mitochondrial DNA as simple, genome-sized circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.</p>',
			'date' => '2019-03-01',
			'pmid' => 'https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008373',
			'doi' => '10.1101/564278.',
			'modified' => '2022-05-18 18:58:47',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 70 => array(
			'id' => '3615',
			'name' => 'Characterizing the Major Structural Variant Alleles of the Human Genome.',
			'authors' => 'Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE',
			'description' => '<p>In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30661756',
			'doi' => '10.1016/j.cell.2018.12.019',
			'modified' => '2019-04-16 13:55:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 71 => array(
			'id' => '3645',
			'name' => 'Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.',
			'authors' => 'Martínez FL, Anton BP, DasSarma P, Rajal V, Irazusta V, Roberts RJ, DasSarma S',
			'description' => '<p>Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30701250',
			'doi' => '10.1128/MRA',
			'modified' => '2019-06-07 10:15:47',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 72 => array(
			'id' => '3656',
			'name' => 'Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present  tuberculosis vaccine',
			'authors' => 'Katlyn Borgersa,Jheng-Yang Ouc, Po-Xing Zhengc, Petra Tielsa, Annelies Van Heckea, Evelyn Pletsa, Gitte Michielsena, Nele Festjensa, Nico Callewaerta, Yao-Cheng Lin',
			'description' => '<p>Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence of BCG Danish 1331 (07/270), one of the WHO reference strains for BCG vaccines. We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of this vaccine strain.</p>',
			'date' => '2018-12-26',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/31286858/',
			'doi' => '10.1101/513408.',
			'modified' => '2022-05-18 18:52:29',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 73 => array(
			'id' => '3454',
			'name' => 'SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).',
			'authors' => 'Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N',
			'description' => '<p>Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica). Findings: As part of the Genome10K (G10K) effort on generating high quality vertebrate genomes, we have assembled a highly contiguous genome assembly using Single Molecule Real-Time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from the Direct Label and Stain (DLS) technologies. As proposed by Bionano, the DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of over 25.95 Mbp. Conclusions: This high-quality genome assembly represents a valuable resource for further studies of population genetics and genomics in the barn swallow, and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.</p>',
			'date' => '2018-11-29',
			'pmid' => 'http://www.pubmed.gov/30496513',
			'doi' => '10.1093/gigascience/giy142/5202456',
			'modified' => '2019-02-15 20:35:16',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 74 => array(
			'id' => '3429',
			'name' => 'Improved reference genome of Aedes aegypti informs arbovirus vector control.',
			'authors' => 'Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gl',
			'description' => '<p>Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology&nbsp;of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.</p>',
			'date' => '2018-11-14',
			'pmid' => 'http://www.pubmed.gov/30429615',
			'doi' => '10.1038/s41586-018-0692-z',
			'modified' => '2018-12-31 11:15:00',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 75 => array(
			'id' => '3413',
			'name' => 'Whole-genome landscape of Medicago truncatula symbiotic genes.',
			'authors' => 'Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Mu',
			'description' => '<p>Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.</p>',
			'date' => '2018-11-05',
			'pmid' => 'http://www.pubmed.gov/30397259',
			'doi' => '10.1038/s41477-018-0286-7',
			'modified' => '2018-12-31 11:17:32',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 76 => array(
			'id' => '3517',
			'name' => 'Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.',
			'authors' => 'Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, ',
			'description' => '<p>Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions. However, even though genome assemblies based on long reads exhibit high contig N50s (&gt;1&thinsp;Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of &gt;5&thinsp;Mb and contain scaffolds that represent entire chromosomes or chromosome arms.</p>',
			'date' => '2018-11-02',
			'pmid' => 'http://www.pubmed.gov/30390080',
			'doi' => '10.1038/s41477-018-0289-4',
			'modified' => '2019-02-27 15:41:40',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 77 => array(
			'id' => '3441',
			'name' => 'The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.',
			'authors' => 'Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B',
			'description' => '<p>Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is&nbsp;found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H.&nbsp;axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H.&nbsp;axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of &sim;170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that&nbsp;highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.</p>',
			'date' => '2018-10-22',
			'pmid' => 'http://www.pubmed.gov/30146156',
			'doi' => '10.1016/j.cub.2018.08.023',
			'modified' => '2019-02-15 20:42:22',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 78 => array(
			'id' => '3412',
			'name' => 'Long-read sequence capture of the hemoglobin gene clusters across gadid species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes. This article is protected by copyright. All rights reserved.</p>',
			'date' => '2018-10-17',
			'pmid' => 'http://www.pubmed.org/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2018-12-31 11:19:03',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 79 => array(
			'id' => '3399',
			'name' => 'Genomic Structural Variations Within Five Continental Populations of .',
			'authors' => 'Long E, Evans C, Chaston J, Udall JA',
			'description' => '<p>Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing genes. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent diverse populations within the species. We used long-read sequencing and optical mapping technologies to identify SVs in these genomes. Among the five lines examined, we found an average of 2,928 structural variants within these genomes. These structural variations varied greatly in size and location, included many exonic regions, and could impact adaptation and genomic evolution.</p>',
			'date' => '2018-10-03',
			'pmid' => 'http://www.pubmed.gov/30111620',
			'doi' => '10.1534/g3.118.200631',
			'modified' => '2018-11-09 11:49:08',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 80 => array(
			'id' => '3403',
			'name' => 'Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.',
			'authors' => 'Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K, Zhang Q',
			'description' => '<p>Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect disease causal structural variants (SVs) from short reads sequencing technologies. Long reads sequencing can produce longer reads (typically 1000&nbsp;bp or longer), therefore offering greatly improved ability to detect SVs that may be missed by short-read sequencing. Results: Here we describe a case study, where WES identified only one heterozygous pathogenic variant for an individual suspected to have glycogen storage disease type Ia (GSD-Ia), which is an autosomal recessive disease caused by bi-allelic mutations in the gene. Through Nanopore long-read whole-genome sequencing, we identified a 7.1&nbsp;kb deletion covering two exons on the other allele, suggesting that complex structural variants (SVs) may explain a fraction of cases when the second pathogenic allele is missing from WES on recessive diseases. Both breakpoints of the deletion are within Alu elements, and we designed Sanger sequencing and quantitative PCR assays based on the breakpoints for preimplantation genetic diagnosis (PGD) for the family planning on another child. Four embryos were obtained after in vitro fertilization (IVF), and an embryo without deletion in was transplanted after PGD and was confirmed by prenatal diagnosis, postnatal diagnosis, and subsequent lack of disease symptoms after birth. Conclusions: In summary, we present one of the first examples of using long-read sequencing to identify causal yet complex SVs in exome-negative patients, which subsequently enabled successful personalized PGD.</p>',
			'date' => '2018-09-28',
			'pmid' => 'http://www.pubmed.gov/30279644',
			'doi' => '10.1186/s41065-018-0069-1',
			'modified' => '2018-11-09 11:27:02',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 81 => array(
			'id' => '3525',
			'name' => 'Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.',
			'authors' => 'Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD',
			'description' => '<p>BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences' (PacBio) and Oxford Nanopore Technologies' (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing GC repeat expansion. We also report the first long-read sequencing data characterizing the C9orf72 GC repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9. RESULTS: Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinION was a challenge for whole-genome sequencing; we were unable to attain reads covering the human C9orf72 repeat expansion using 15 flow cells. We obtained 8&times; coverage across the C9orf72 locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained &gt;&thinsp;800&times; coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual's repeat region was &gt;&thinsp;99% GC content, though we cannot rule out small interruptions. CONCLUSIONS: Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in C9orf72 expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-GC content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.</p>',
			'date' => '2018-08-21',
			'pmid' => 'http://www.pubmed.gov/30126445',
			'doi' => '10.1186/s13024-018-0274-4',
			'modified' => '2019-02-28 10:13:27',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 82 => array(
			'id' => '3524',
			'name' => 'The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.',
			'authors' => 'Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J',
			'description' => '<p>DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (&gt;94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.</p>',
			'date' => '2018-08-14',
			'pmid' => 'http://www.pubmed.gov/30108278',
			'doi' => '10.1038/s41598-018-30620-5',
			'modified' => '2019-02-28 10:12:41',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 83 => array(
			'id' => '3638',
			'name' => 'Long-read sequence capture of the haemoglobin gene clusters across codfish species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100&nbsp;kb) and MN (~200&nbsp;kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.</p>',
			'date' => '2018-08-03',
			'pmid' => 'http://www.pubmed.gov/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2019-06-07 10:24:26',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 84 => array(
			'id' => '3512',
			'name' => 'A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.',
			'authors' => 'Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Are',
			'description' => '<p>Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512&thinsp;Mb with N50 of 3.4&thinsp;Mb and 564 contigs). The length of 512&thinsp;Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.</p>',
			'date' => '2018-06-11',
			'pmid' => 'http://www.pubmed.gov/29892093',
			'doi' => '10.1038/s41477-018-0166-1',
			'modified' => '2019-02-28 10:35:49',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 85 => array(
			'id' => '3483',
			'name' => 'Overview of Next-Generation Sequencing Technologies.',
			'authors' => 'Slatko BE, Gardner AF, Ausubel FM',
			'description' => '<p>High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. &copy; 2018 by John Wiley &amp; Sons, Inc.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29851291',
			'doi' => '10.1002/cpmb.59',
			'modified' => '2019-02-14 17:07:52',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 86 => array(
			'id' => '3474',
			'name' => 'Draft genome of the Peruvian scallop Argopecten purpuratus.',
			'authors' => 'Li C, Liu X, Liu B, Ma B, Liu F, Liu G, Shi Q, Wang C',
			'description' => '<p>Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. Findings: A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. Conclusions: We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29617765',
			'doi' => '10.1093/gigascience/giy031',
			'modified' => '2019-02-15 20:33:41',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 87 => array(
			'id' => '3544',
			'name' => 'Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.',
			'authors' => 'Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F',
			'description' => '<p>BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS: In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.</p>',
			'date' => '2018-01-16',
			'pmid' => 'http://www.pubmed.gov/29338683',
			'doi' => '10.1186/s12864-017-4429-4',
			'modified' => '2019-02-28 10:58:38',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 88 => array(
			'id' => '3308',
			'name' => 'Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.',
			'authors' => 'Rödelsperger C. et al.',
			'description' => '<p>The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P.&nbsp;pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P.&nbsp;pacificus. Despite widespread conservation of synteny between P.&nbsp;pacificus and C.&nbsp;elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C.&nbsp;elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P.&nbsp;pacificus.</p>',
			'date' => '2017-10-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045848',
			'doi' => '',
			'modified' => '2018-01-04 10:15:03',
			'created' => '2018-01-04 10:15:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 89 => array(
			'id' => '3279',
			'name' => 'De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads',
			'authors' => 'Korlach J. et al.',
			'description' => '<p>Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.</p>',
			'date' => '2017-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29020750',
			'doi' => '',
			'modified' => '2017-10-16 10:27:47',
			'created' => '2017-10-16 10:27:47',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 90 => array(
			'id' => '3041',
			'name' => 'DNA fragmentation and quality control analysis ',
			'authors' => 'Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian',
			'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
<p><strong>Introduction</strong></p>
<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
<p><strong>Results</strong></p>
<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
<p><strong>Conclusion</strong></p>
<p>Unbiased DNA fragmentation with the Diagenode One, the Bioruptor<sup>&reg;</sup>&nbsp;Pico, or the Megaruptor<sup>&reg;</sup>&nbsp;for short- or long-read sequencing combined with sizing on the Fragment Analyzer<sup>&trade;</sup>&nbsp;delivers an efficient workflow solution for preparing and analyzing libraries with even distribution and representation of the genome.</p>
<p></p>',
			'date' => '2016-09-29',
			'pmid' => 'http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.f.397.html',
			'doi' => '',
			'modified' => '2016-10-20 16:37:08',
			'created' => '2016-10-07 16:26:28',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
	),
	'Testimonial' => array(
		(int) 0 => array(
			'id' => '64',
			'name' => 'DNA Link Megaruptor',
			'description' => '<p>Established in March 15<span>th </span><span>2000, DNA Link, Inc. has developed as one of the leading full genomic service provider with its extensive 17 years of experience. DNA Link has been involved in numerous genomic researches including many national projects, and contributed to the expansion of the genomic industry. </span></p>
<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p>',
			'author' => 'Hyeyoon, Jang - Lab Manager - Seoul, Korea',
			'featured' => true,
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2017-04-20 12:18:10',
			'created' => '2017-04-11 22:54:52',
			'ProductsTestimonial' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '58',
			'name' => 'MPIDB_Megaruptor 2',
			'description' => '<p><span>The system performance was very good. High molecular weight DNA of different plants (Arabidopsis Alm, Hops polaris and wine Villard Blanc) was isolated and diluted to 50ng/&micro;l or 70ng/&micro;l. We aimed for fragment length 30kb at the volume 150&micro;l.</span><br /><span>We achieved good results and we will continue with bead purification and library preps for PacBio sequencing. &nbsp;I like the user friendly interface of the Megaruptor<sup>&reg;</sup>&nbsp;2. Just two parameters had to be specified: volume of each sample and desired mean fragment size. The processed DNA has a narrow size distribution at around 30kb.</span></p>',
			'author' => 'Christa Lanz and Julia Hildebrandt, Max Planck Institute for Developmental Biology, Tübingen, Germany',
			'featured' => false,
			'slug' => 'MPIDB-Megaruptor',
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<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p><cite>Hyeyoon, Jang - Lab Manager - Seoul, Korea</cite></blockquote>
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<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
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<h6 style="text-align: center;">Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. <strong>A:</strong> DNA was analyzed by pulsedfield gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software. <strong>B:</strong> Fragment Analyzer profiles of human genomic DNA (25 ng/&mu;l; 200 &mu;l/sample) sheared at different software settings of 10, 15, 20, 30 and 40 kb. (High Sensitivity Large Fragment Analysis Kit; Advanced Analytical Technologies, Inc. was used for separation and fragment sizing).</h6>
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<p><strong>Storage</strong><br />Store at room temperature</p>
<p><strong>Precautions</strong><br />This product is for research use only. Not for use in diagnostic or therapeutic procedures</p>
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<p><strong><span style="text-decoration: underline;">Note</span>: </strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a>&nbsp;are sold separately.</p>
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<p><span><strong><span style="text-decoration: underline;">Note</span>:&nbsp;</strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a><span>&nbsp;</span><span>are sold separately.</span></span></p>',
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<div class="small-12 medium-12 large-12 columns">
<h2 style="font-size: 22px;">DNA断片化、ライブラリー調製、自動化：NGSのワンストップショップ</h2>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-12 medium-12 large-12 columns">
<h4>1. 断片化装置を選択してください：150 bp〜75 kbの範囲でDNAを断片化します。</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-pico-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/bioruptor_pico.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/megaruptor2-1-unit"><img src="https://www.diagenode.com/img/product/shearing_technologies/B06010001_megaruptor2.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-one-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/br-one-profil.png" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns">5&mu;lまで断片化：150 bp〜2 kb<br />NGS DNAライブラリー調製およびFFPE核酸抽出に最適で、</td>
<td class="small-4 medium-4 large-4 columns">2 kb〜75 kbの範囲をできます。<br />メイトペアライブラリー調製および長いフラグメントDNAシーケンシングに最適で、この軽量デスクトップデバイスで</td>
<td class="small-4 medium-4 large-4 columns">20または50&mu;lの断片化が可能です。</td>
</tr>
</tbody>
</table>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-8 medium-8 large-8 columns">
<h4>2. 最適化されたライブラリー調整キットを選択してください。</h4>
</th>
<th class="small-4 medium-4 large-4 columns">
<h4>3. ライブラリー前処理自動化を選択して、比類のないデータ再現性を実感</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><img src="https://www.diagenode.com/img/product/kits/microPlex_library_preparation.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns"><img src="https://www.diagenode.com/img/product/kits/box_kit.jpg" style="display: block; margin-left: auto; margin-right: auto;" height="173" width="250" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/sx-8g-ip-star-compact-automated-system-1-unit"><img src="https://www.diagenode.com/img/product/automation/B03000002%20_ipstar_compact.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">50pgの低入力：MicroPlex Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">5ng以上：iDeal&nbsp;Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">Achieve great NGS data easily</td>
</tr>
</tbody>
</table>
</div>
</div>
<blockquote>
<div class="row">
<div class="small-12 medium-12 large-12 columns"><span class="label" style="margin-bottom: 16px; margin-left: -22px; font-size: 15px;">DiagenodeがNGS研究にぴったりなプロバイダーである理由</span>
<p>Diagenodeは15年以上もエピジェネティクス研究に専念、専門としています。 ChIP研究クロマチン用のユニークな断片化システムの開発から始まり、 専門知識を活かし、5&mu;lのせん断体積まで可能で、NGS DNAライブラリーの調製に最適な最先端DNA断片化装置の開発にたどり着きました。 我々は以来、ChIP-seq、Methyl-seq、NGSライブラリー調製用キットを研究開発し、業界をリードする免疫沈降研究と同様に、ライブラリー調製を自動化および完結させる独自の自動化システムを開発にも成功しました。</p>
<ul>
<li>信頼されるせん断装置</li>
<li>様々なインプットからのライブラリ作成キット</li>
<li>独自の自動化デバイス</li>
</ul>
</div>
</div>
</blockquote>
<div class="row">
<div class="small-12 columns">
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#panel1a">次世代シーケンシングへの理解とその専門知識</a>
<div id="panel1a" class="content">
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong>次世代シーケンシング (NGS)</strong> ）は、著しいスケールとハイスループットでシーケンシングを行い、1日に数十億もの塩基生成を可能にします。 NGSのハイスループットは迅速でありながら正確で、再現性のあるデータセットを実現し、さらにシーケンシング費用を削減します。 NGSは、ゲノムシーケンシング、ゲノム再シーケンシング、デノボシーケンシング、トランスクリプトームシーケンシング、その他にDNA-タンパク質相互作用の検出やエピゲノムなどを示します。 指数関数的に増加するシーケンシングデータの需要は、計算分析の障害や解釈、データストレージなどの課題を解決します。</p>
<p>アプリケーションおよび出発物質に応じて、数百万から数十億の鋳型DNA分子を大規模に並行してシーケンシングすることが可能です。その為に、異なる化学物質を使用するいくつかの市販のNGSプラットフォームを利用することができます。 NGSプラットフォームの種類によっては、事前準備とライブラリー作成が必要です。</p>
<p>NGSにとっても、特にデータ処理と分析に関した大きな課題はあります。第3世代技術はゲノミクス研究にさらに革命を起こすであろうと大きく期待されています。</p>
</div>
</div>
<div class="row">
<div class="small-6 medium-6 large-6 columns">
<p><strong>NGS アプリケーション</strong></p>
<ul>
<li>全ゲノム配列決定</li>
<li>デノボシーケンシング</li>
<li>標的配列</li>
<li>Exomeシーケンシング</li>
<li>トランスクリプトーム配列決定</li>
<li>ゲノム配列決定</li>
<li>ミトコンドリア配列決定</li>
<li>DNA-タンパク質相互作用（ChIP-seq</li>
<li>バリアント検出</li>
<li>ゲノム仕上げ</li>
</ul>
</div>
<div class="small-6 medium-6 large-6 columns">
<p><strong>研究分野におけるNGS:</strong></p>
<ul>
<li>腫瘍学</li>
<li>リプロダクティブ・ヘルス</li>
<li>法医学ゲノミクス</li>
<li>アグリゲノミックス</li>
<li>複雑な病気</li>
<li>微生物ゲノミクス</li>
<li>食品・環境ゲノミクス</li>
<li>創薬ゲノミクス - パーソナライズド・メディカル</li>
</ul>
</div>
<div class="small-12 medium-12 large-12 columns">
<p><strong>NGSの用語</strong></p>
<dl>
<dt>リード（読み取り）</dt>
<dd>この装置から得られた連続した単一のストレッチ</dd>
<dt>断片リード</dt>
<dd>フラグメントライブラリからの読み込み。 シーケンシングプラットフォームに応じて、読み取りは通常約100〜300bp。</dd>
<dt>断片ペアエンドリード</dt>
<dd>断片ライブラリーからDNA断片の各末端2つの読み取り。</dd>
<dt>メイトペアリード</dt>
<dd>大きなDNA断片（通常は予め定義されたサイズ範囲）の各末端から2つの読み取り。</dd>
<dt>カバレッジ（例）</dt>
<dd>30&times;適用範囲とは、参照ゲノム中の各塩基対が平均30回の読み取りを示す。</dd>
</dl>
</div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2>NGSプラットフォーム</h2>
<h3><a href="http://www.illumina.com" target="_blank">イルミナ</a></h3>
<p>イルミナは、クローン的に増幅された鋳型DNA（クラスター）上に位置する、蛍光標識された可逆的鎖ターミネーターヌクレオチドを用いた配列別合成技術を使用。 DNAクラスターは、ガラスフローセルの表面上に固定化され、 ワークフローは、4つのヌクレオチド（それぞれ異なる蛍光色素で標識された）の組み込み、4色イメージング、色素や末端基の切断、取り込み、イメージングなどを繰り返します。フローセルは大規模な並列配列決定を受ける。 この方法により、単一蛍光標識されたヌクレオチドの制御添加によるモノヌクレオチドのエラーを回避する可能性があります。 読み取りの長さは、通常約100〜150 bpです。</p>
<h3><a href="http://www.lifetechnologies.com" target="_blank">イオン トレント</a></h3>
<p>イオントレントは、半導体技術チップを用いて、合成中にヌクレオチドを取り込む際に放出されたプロトンを検出します。 これは、イオン球粒子と呼ばれるビーズの表面にエマルションPCR（emPCR）を使用し、リンクされた特定のアダプターを用いてDNA断片を増幅します。 各ビーズは1種類のDNA断片で覆われていて、異なるDNA断片を有するビーズは次いで、チップの陽子感知ウェル内に配置されます。 チップには一度に4つのヌクレオチドのうちの1つが浸水し、このプロセスは異なるヌクレオチドで15秒ごとに繰り返されます。 配列決定の間に4つの塩基の各々が1つずつ導入されます、組み込みの場合はプロトンが放出され、電圧信号が取り込みに比例して検出されます。.</p>
<h3><a href="http://www.pacificbiosciences.com" target="_blank">パシフィック バイオサイエンス</a></h3>
<p>パシフィックバイオサイエンスでは、20kbを超える塩基対の読み取りも、単一分子リアルタイム（SMRT）シーケンシングによる構造および細胞タイプの変化を観察することができます。 このプラットフォームでは、超長鎖二本鎖DNA（dsDNA）断片が、Megaruptor（登録商標）のようなDiagenode装置を用いたランダムシアリングまたは目的の標的領域の増幅によって生成されます。 SMRTbellライブラリーは、ユニバーサルヘアピンアダプターをDNA断片の各末端に連結することによって生成します。 サイズ選択条件による洗浄ステップの後、配列決定プライマーをSMRTbellテンプレートにアニーリングし、鋳型DNAに結合したDNAポリメラーゼを含む配列決定を、蛍光標識ヌクレオチドの存在下で開始。 各塩基が取り込まれると、異なる蛍光のパルスをリアルタイムで検出します。</p>
<h3><a href="https://nanoporetech.com" target="_blank">オックスフォード ナノポア</a></h3>
<p>Oxford Nanoporeは、単一のDNA分子配列決定に基づく技術を開発します。その技術により生物学的分子、すなわちDNAが一群の電気抵抗性高分子膜として位置するナノスケールの孔（ナノ細孔）またはその近くを通過し、イオン電流が変化します。 この変化に関する情報は、例えば4つのヌクレオチド（AまたはG r CまたはT）ならびに修飾されたヌクレオチドすべてを区別することによって分子情報に訳されます。 シーケンシングミニオンデバイスのフローセルは、数百個のナノポアチャネルのセンサアレイを含みます。 DNAサンプルは、Diagenode社のMegaruptor（登録商標）を用いてランダムシアリングによって生成され得る超長鎖DNAフラグメントが必要です。</p>
<h3><a href="http://www.lifetechnologies.com/be/en/home/life-science/sequencing/next-generation-sequencing/solid-next-generation-sequencing.html" target="_blank">SOLiD</a></h3>
<p>SOLiDは、ユニークな化学作用により、何千という個々のDNA分子の同時配列決定を可能にします。 それは、アダプター対ライブラリーのフラグメントが適切で、せん断されたゲノムDNAへのアダプターのライゲーションによるライブラリー作製から始まります。 次のステップでは、エマルジョンPCR（emPCR）を実施して、ビーズの表面上の個々の鋳型DNA分子をクローン的に増幅。 emPCRでは、個々の鋳型DNAをPCR試薬と混合し、水中油型エマルジョン内の疎水性シェルで囲まれた水性液滴内のプライマーコートビーズを、配列決定のためにロードするスライドガラスの表面にランダムに付着。 この技術は、シークエンシングプライマーへのライゲーションで競合する4つの蛍光標識されたジ塩基プローブのセットを使用します。</p>
<h3><a href="http://454.com/products/technology.asp" target="_blank">454</a></h3>
<p>454は、大規模並列パイロシーケンシングを利用しています。 始めに全ゲノムDNAまたは標的遺伝子断片の300〜800bp断片のライブラリー調製します。 次に、DNAフラグメントへのアダプターの付着および単一のDNA鎖の分離。 その後アダプターに連結されたDNAフラグメントをエマルジョンベースのクローン増幅（emPCR）で処理し、DNAライブラリーフラグメントをミクロンサイズのビーズ上に配置します。 各DNA結合ビーズを光ファイバーチップ上のウェルに入れ、器具に挿入します。 4つのDNAヌクレオチドは、配列決定操作中に固定された順序で連続して加えられ、並行して配列決定されます。</p>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>&reg;</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>&reg;</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor<sup>&reg;</sup></a>.</div>
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<p></p>
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<div class="small-7 medium-7 large-7 columns text-center"><img src="https://www.diagenode.com/img/applications/true-flexibility-with-br-ngs.jpg" /></div>
<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>&reg;</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 &micro;l volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 &micro;l volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A &amp; B:</b> peak electropherogram view. <b>Panel C &amp; D:</b> virtual gel view.</small></div>
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<p><br /><br /></p>
<div class="row">
<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor&reg; using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
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<p><br /><br /></p>
<div class="row">
<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor&reg; using long fragment size Hydropores. &nbsp;</strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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<h3><strong>Your partner in long-read sequencing</strong></h3>
<p>Sequencing technologies have revolutionized genomics and biology researches. Long read sequencing enables researchers to access a more comprehensive view of genomes with higher accuracy. However, one of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size. The Megaruptor gives state-of-art shearing performance providing optimal long-read sequencing using <strong>PacBio&reg; and Oxford Nanopore<sup>TM</sup>technologies.</strong></p>
<p><strong></strong></p>
<center><a href="https://www.diagenode.com/p/megaruptor-cassette-12" class="tiny details button">CHECK OUT THE NEW 12-SAMPLE CASSETTE. RUN 50% MORE SAMPLES ON YOUR MEGARUPTOR 3!</a></center>
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<h4 style="font-size: 22px;"><a href="https://www.diagenode.com/en/p/megaruptor-3">Click here to discover our latest innovation</a></h4>
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<p><span>We have designed the Megaruptor</span>&reg;&nbsp;<span>2 using our highest level of knowledge in shearing so that it exceeds your expectations. This device will serve your research needs for many years and will provide the best experience with long DNA molecules preparation. </span></p>
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<p><span>The Megaruptor</span><span>&reg; </span><span>2 was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA in the range of 3 kb - 75 kb </span><span>(contact us for the 3 kb setting)</span><span>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly interface allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design. </span></p>
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			'meta_keywords' => 'Megaruptor 2 flyer',
			'meta_description' => 'Megaruptor 2 flyer',
			'modified' => '2017-05-03 09:38:38',
			'created' => '2017-05-03 09:38:20',
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				[maximum depth reached]
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		),
		(int) 3 => array(
			'id' => '27',
			'name' => 'Application of the Megaruptor® for shearing of ultra-long DNA fragments in the context of Long Read Sequencing using 3rd Gen Sequencing Technologies',
			'description' => '<p><span>The Megaruptor</span><span>&reg; </span><span>provides a simple, robust, and straight forward method for reproducible DNA shearing to obtain ultra-large DNA fragments. The system has been easily integrated into our workflow for long range sequencing of single molecules using the RSII platform from Pacific Biosciences</span><span>&reg;</span><span>. The obtained dense distribution of fragment sizes after shearing and the low content of non-sheared as well as short fragments was beneficial for the performance of the whole library preparation process. </span></p>',
			'image_id' => null,
			'type' => 'Application note',
			'url' => 'files/application_notes/Megaruptor_application_note.pdf',
			'slug' => 'megaruptor-application-note',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2017-05-17 10:07:08',
			'created' => '2015-07-03 16:05:20',
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				[maximum depth reached]
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		),
		(int) 4 => array(
			'id' => '840',
			'name' => 'Megaruptor genomic DNA shearing for large insert sequencing library preparation',
			'description' => '<p>Wageningen University has a strong background in plant genome sequencing including contributions to the Arabidopsis, potato and tomato genome research as partner of various international consortia. The sequencing facility of Wageningen University operates several 2nd and 3rd generation sequencing platforms including a Pacbio RS-II. The rapid developments of this third generation sequencing resulting in continuously increased read length requires a reliable DNA fragmentation into large molecules. The benefit of these large DNA molecules is their ability to span repetitive sequences which appeared to be crucial for de-novo reconstruction of large and complex genomes. To stay ahead of new developments intended for sequencing library preparations we tested the Megaruptor<span>&reg; </span>from Diagenode for optimizing our library preparation procedure targeting very large DNA molecules used for Pacbio sequencing.For this purpose we used the Megaruptor<span>&reg; </span>using large hydropores, evaluating target fragmentation size, fragment range, reproducibility and the ease in usage.</p>',
			'image_id' => null,
			'type' => 'Application note',
			'url' => 'files/application_notes/megaruptor-dna-shearing-application-note.pdf',
			'slug' => 'megaruptor-genomic-dna-shearing',
			'meta_keywords' => 'megaruptor-genomic-dna-shearing',
			'meta_description' => 'megaruptor-genomic-dna-shearing',
			'modified' => '2017-05-17 10:07:32',
			'created' => '2015-10-29 10:57:23',
			'ProductsDocument' => array(
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			)
		),
		(int) 5 => array(
			'id' => '35',
			'name' => 'Bioruptor &reg; Sonicator Brochure',
			'description' => '<p><span>Diagenode&rsquo;s Bioruptor</span><sup>&reg;</sup>&nbsp;<span>uses state-of-the-art shearing device to&nbsp;disrupt, disperse, or shear a variety of sample types for biological, chemical, pharmaceutical, and industrial applications.&nbsp;It is<span>&nbsp;t</span></span><span>he standard for DNA and RNA shearing, chromatin shearing, cell and tissue disruption, FFPE DNA extraction, DNA methylation studies and tissue RNA extraction. </span></p>',
			'image_id' => null,
			'type' => 'Brochure',
			'url' => 'files/brochures/Bioruptor_Sonicator_Brochure.pdf',
			'slug' => 'bioruptor-sonicator-brochure',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2024-06-14 15:35:05',
			'created' => '2015-07-03 16:05:27',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '968',
			'name' => 'Optimal long DNA fragment generation prior to SMRTbell® library preparation',
			'description' => '<p>Several methods exist today for shearing genomic DNA, but few are reliable for generating DNA fragments &gt;50 kb necessary for assembly of many microbial, human, plant and animal genomes <em>de novo</em>. Pacific Biosciences highly recommends the Megaruptor<sup>TM</sup> System for shearing genomic DNA to large fragments for long-read sequencing in the Sequel&reg; System.</p>',
			'image_id' => '247',
			'type' => 'Application note',
			'url' => 'files/application_notes/AN-PacBio-Megaruptor-02_2023.pdf',
			'slug' => 'pacbio-megaruptor-application-note',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2023-02-17 09:57:21',
			'created' => '2017-10-04 14:30:02',
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			)
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			'id' => '2',
			'name' => 'Tight fragment size distribution',
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2015-07-24 17:39:26',
			'created' => '2014-10-18 14:20:50',
			'ProductsFeature' => array(
				[maximum depth reached]
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		),
		(int) 1 => array(
			'id' => '3',
			'name' => 'Hydropores eliminate clogging',
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2015-07-24 17:39:40',
			'created' => '2014-10-07 08:41:12',
			'ProductsFeature' => array(
				[maximum depth reached]
			)
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		(int) 2 => array(
			'id' => '14',
			'name' => 'High quality libraires',
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2015-07-24 17:40:54',
			'created' => '2015-02-25 00:05:53',
			'ProductsFeature' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '36',
			'name' => 'Tuneable to between 3 - 75 kb',
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2019-02-20 17:58:05',
			'created' => '2019-02-20 17:58:05',
			'ProductsFeature' => array(
				[maximum depth reached]
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		(int) 4 => array(
			'id' => '32',
			'name' => '1 to 2 samples in series',
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			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2019-02-20 17:53:19',
			'created' => '2019-02-20 17:53:19',
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		(int) 0 => array(
			'id' => '1745',
			'name' => 'product/shearing_technologies/B06010001_megaruptor2.jpg',
			'alt' => ' DNA Shearing, RNA shearing and Chromatin shearing',
			'modified' => '2020-11-27 06:56:56',
			'created' => '2016-08-30 16:30:47',
			'ProductsImage' => array(
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	'Protocol' => array(),
	'Publication' => array(
		(int) 0 => array(
			'id' => '4531',
			'name' => 'Detection and Quantitation of DNA Damage on a Genome-wide ScaleUsing RADAR-seq.',
			'authors' => 'Zatopek  Kelly M et al.',
			'description' => '<p>The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate DNA damage sites across a genome enable an understanding of the consequences of DNA damage as well as how damage is repaired, which can have key diagnostic and therapeutic implications. Importantly, advancements in technology have enabled the development of high-throughput sequencing-based DNA damage detection methods. These methods require DNA enrichment or amplification steps that limit the ability to quantitate the DNA damage sites. Further, each of these methods is typically tailored to detect only a specific type of damage. RAre DAmage and Repair (RADAR) sequencing is a DNA sequencing workflow that overcomes these limitations and enables detection and quantitation of DNA damage sites in any organism on a genome-wide scale. RADAR-seq works by replacing DNA damage sites with a patch of modified bases that can be directly detected by Pacific Biosciences Single-Molecule Real Time sequencing. Here, we present three protocols that enable detection of thymine dimers and ribonucleotides in bacterial and archaeal genomes. Basic Protocol 1 enables construction of a reference genome required for RADAR-seq analyses. Basic Protocol 2 describes how to locate, quantitate, and compare thymine dimer levels in Escherichia coli exposed to varying amounts of UV light. Basic Protocol 3 describes how to locate, quantitate, and compare ribonucleotide levels in wild-type and &Delta;RNaseH2 Thermococcus kodakarensis. Importantly, all three protocols provide in-depth steps for data analysis. Together they serve as proof-of-principle experiments that will allow users to adapt the protocols to locate and quantitate a wide variety of DNA damage sites in any organism. &copy; 2022 New England Biolabs. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Constructing a reference genome utilizing SMRT sequencing Basic Protocol 2: Mapping and quantitating genomic thymine dimer formation in untreated versus UV-irradiated E. coli using RADAR-seq Basic Protocol 3: Mapping and quantitating genomic ribonucleotide incorporation in wildtype versus &Delta;RNaseH2 T. kodakarensis using RADAR-seq.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36374013',
			'doi' => '10.1002/cpz1.595',
			'modified' => '2023-02-17 08:48:37',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '4533',
			'name' => 'Predictable and stable epimutations induced during clonal plantpropagation with embryonic transcription factor.',
			'authors' => 'Wibowo  Anjar Tri et al.',
			'description' => '<p>Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.</p>',
			'date' => '2022-11-01',
			'pmid' => '/',
			'doi' => '10.1371/journal.pgen.1010479',
			'modified' => '2023-02-17 08:50:15',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '4536',
			'name' => 'Benchmarking second and third-generation sequencing platforms formicrobial metagenomics.',
			'authors' => 'Meslier  Victoria et al.',
			'description' => '<p>Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36369227',
			'doi' => '10.1038/s41597-022-01762-z',
			'modified' => '2023-02-17 08:52:35',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '4543',
			'name' => 'Mitochondrial RNA editing in Trypanoplasma borreli: new tools, newrevelations',
			'authors' => 'Gerasimov  Evgeny S. et al.',
			'description' => '<p>The kinetoplastids are unicellular flagellates that derive their name from the &lsquo;kinetoplast&rsquo;, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein products of this mitochondrial genome are encoded as cryptogenes; their transcripts require editing to generate an open reading frame. This happens through RNA editing, whereby small regulatory guide (g)RNAs direct the proper insertion and deletion of one or more uridines at each editing site within specific transcript regions. An accurate perspective of the kDNA expansion and evolution of their unique uridine insertion/deletion editing across kinetoplastids has been difficult to achieve. Here, we resolved the kDNA structure and editing patterns in the early-branching kinetoplastid Trypanoplasma borreli and compare them with those of the well-studied trypanosomatids. We find that its kDNA consists of circular molecules of about 42 kb that harbor the rRNA and protein-coding genes, and 17 different contigs of approximately 70 kb carrying an average of 23 putative gRNA loci per contig. These contigs may be linear molecules, as they contain repetitive termini. Our analysis uncovered a putative gRNA population with unique length and sequence parameters that is massive relative to the editing needs of this parasite. We validated or determined the sequence identity of four edited mRNAs, including one coding for ATP synthase 6 that was previously thought to be missing. We utilized computational methods to show that the T. borreli transcriptome includes a substantial number of transcripts with inconsistent editing patterns, apparently products of non-canonical editing. This species utilizes the most extensive uridine deletion compared to other studied kinetoplastids to enforce amino acid conservation of cryptogene products, although insertions still remain more frequent. Finally, in three tested mitochondrial transcriptomes of kinetoplastids, uridine deletions are more common in the raw mitochondrial reads than aligned to the fully edited, translationally competent mRNAs. We conclude that the organization of kDNA across known kinetoplastids represents variations on partitioned coding and repetitive regions of circular molecules encoding mRNAs and rRNAs, while gRNA loci are positioned on a highly unstable population of molecules that differ in relative abundance across strains. Likewise, while all kinetoplastids possess conserved machinery performing RNA editing of the uridine insertion/deletion type, its output parameters are species-specific.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.csbj.2022.11.023',
			'doi' => '10.1016/j.csbj.2022.11.023',
			'modified' => '2023-02-17 08:53:23',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4737',
			'name' => 'Evaluation of the pathogenesis of non-typical strain with α-hemolysin,Vibrio parahaemolyticus 353, isolated from Chinese seafood throughcomparative genome and transcriptome analysis.',
			'authors' => 'Zha  Fei et al.',
			'description' => '<p>Vibrio parahaemolyticus outbreaks frequently occur, causing gastrointestinal sickness owing to the consumption of aquatic foods by various virulence factors; however, the mechanism of pathogenesis is still unknown. In this study, a non-typical strain of V. parahaemolyticus, named VP353, was isolated from shrimp in China. Its comparative genome and transcriptome after infection with Caco-2 cells were examined to illustrate the mechanisms of its pathogenesis. VP353 was a tdh-trh- strain but uncommonly manifested robust cytotoxicity towards Caco-2 cells. Compared with the standard strain RIMD2210633, VP353 harbored alpha-hemolysins (hlyA, hlyB, hlyC, and hlyD) was first reported in V. parahaemolyticus and showed high diversity in the T3SS2 gene cluster. Moreover, the expression of flagella, T2SS, quorum sensing-related genes, hlyA, hlyC were up-regulated, and hlyB, hlyD were down-regulated. In summary, our results demonstrate that some novel virulence factors contribute to the pathogenesis of V. parahaemolyticus infection.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36437125',
			'doi' => '10.1016/j.marpolbul.2022.114276',
			'modified' => '2023-03-07 08:55:16',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4476',
			'name' => 'Rapid and comprehensive diagnostic method for repeat expansion diseasesusing nanopore sequencing.',
			'authors' => 'Miyatake  S. et al.',
			'description' => '<p>We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36289212',
			'doi' => '10.1038/s41525-022-00331-y',
			'modified' => '2022-11-18 12:21:42',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4478',
			'name' => 'Characterization of somatic structural variations in 528 Chineseindividuals with Esophageal squamous cell carcinoma.',
			'authors' => 'Cui   H. et al.',
			'description' => '<p>Esophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations' mechanisms and biological functions. SVs show multi-mode distributions in size, indicating distinct mutational processes. We develop a tool and define five types of complex rearrangements with templated insertions. We highlight a type of fold-back inversion, which is associated with poor outcomes. Distinct rearrangement signatures demonstrate variable genomic metrics such as replicating time, spatial proximity, and chromatin accessibility. Specifically, fold-back inversion tends to occur near the centrosome; TD-c2 (Tandem duplication-cluster2) is significantly enriched in chromatin-accessibility and early-replication region compared to other signatures. Analyses of TD-c2 signature reveal 9 TD hotspots, of which we identify a hotspot consisting of a super-enhancer of PTHLH. We confirm the oncogenic effect of the PTHLH gene and its interaction with enhancers through functional experiments. Finally, extrachromosomal circular DNAs (ecDNAs) are present in 14\% of ESCCs and have strong selective advantages to driver genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36272974',
			'doi' => '10.1038/s41467-022-33994-3',
			'modified' => '2022-11-18 12:23:21',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4483',
			'name' => 'The Capparis spinosa var. herbacea genome provides the first genomicinstrument for a diversity and evolution study of the Capparaceae family.',
			'authors' => 'Wang  Lei et al.',
			'description' => '<p>BACKGROUND: The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS: We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23\% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28\%, and transposable element sequences accounted for 43.98\%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55\% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82\% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS: This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36310248',
			'doi' => '10.1093/gigascience/giac106',
			'modified' => '2022-11-18 12:30:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4484',
			'name' => 'Genomic Characterization and Antimicrobial Susceptibility ofDromedary-Associated  from the Horn of Africa.',
			'authors' => 'Akarsu  H. et al.',
			'description' => '<p>Members of the family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized strains from apparently healthy and diseased camels ( = 84) and cattle ( = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by (K), /, /, /, , , , and , respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the and families, reported here for the first time for certain species of . All strains contained at least one intact prophage sequence, mainly belonging to the family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct clades and species. Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226992',
			'doi' => '10.1128/aem.01146-22',
			'modified' => '2022-11-18 12:31:20',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4418',
			'name' => 'Complete Genome Sequences of the Soil Oxalotrophic BacteriumCupriavidus oxalaticus Strain Ox1 and Its DerivedmCherry-Tagged Strain.',
			'authors' => 'Palmieri  Fabio et al. ',
			'description' => '<p>Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69&thinsp;Mb, with a GC content of 66.9\%. The genome sequence of Ox1 contains a complete operon for the degradation and assimilation of oxalate.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35924938',
			'doi' => '10.1128/mra.00181-22',
			'modified' => '2022-09-27 14:42:06',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4442',
			'name' => 'The improved genome of the nematode Parapristionchus giblindavisiprovides insights into lineage-specific gene family evolution.',
			'authors' => 'Röseler  W. et al. ',
			'description' => '<p>Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricted genes. To trace back the evolution of such new or rapidly evolving genes, a robust phylogenomic framework is indispensable. Here, we present an improved version of the genome of Parapristionchus giblindavisi which is the only known member of the sister group of Pristionchus. Relative to the previous short read assembly, the new genome is based on long reads and displays higher levels of contiguity, completeness, and correctness. Specifically, the number of contigs dropped from over 7303 to 735 resulting in an N50 increase from 112&thinsp;kb to 791&thinsp;kb. We made use of the new genome to revisit the evolution of multiple gene families. This revealed Pristionchus-specific expansions of several environmentally responsive gene families and a Pristionchus-specific loss of the de novo purine biosynthesis pathway. Focusing on the evolution of sulfatases and sulfotransferases, which control the mouth form plasticity in P. pacificus, reveals differences in copy number and genomic configurations between the genera Pristionchus and Parapristionchus. Altogether, this demonstrates the utility of the P. giblindavisi genome to date and polarize lineage-specific patterns.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35980151',
			'doi' => '10.1093/g3journal/jkac215',
			'modified' => '2022-10-14 16:33:33',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4443',
			'name' => 'The chromosome-level genome of Gypsophila paniculata reveals themolecular mechanism of floral development and ethylene insensitivity',
			'authors' => 'Fan  Li et al. ',
			'description' => '<p>Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the worldwide famous cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with a total size of 749.58 Mb. Whole-genome duplication signatures unveil two major duplication events in its evolutionary history, an ancient one occurring before the divergence of Caryophyllaceae and a more recent one shared with Dianthus caryophyllus. The integrative analyses combining genomic and transcriptomic data reveal the mechanisms regulating floral development and ethylene response of G. paniculata. The reduction of AGAMOUS expression probably caused by sequence polymorphism and the mutation in miR172 binding site of PETALOSA are associated with the double flower formation in G. paniculata. The low expression of ERS (ETHYLENE RESPONSE SENSOR) and the reduction of downstream ERF (ETHYLENE RESPONSE FACTOR) gene copy number collectively lead to the ethylene insensitivity of G. paniculata, affecting flower senescence and making it capable of making dried flowers. This study provides a cornerstone for understanding the underlying principles governing floral development and flower senescence, which could accelerate the molecular breeding of the Caryophyllaceae species.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac176/6674669',
			'doi' => '10.1093/hr/uhac176',
			'modified' => '2022-10-14 16:34:34',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4445',
			'name' => 'Patients with biallelic GGC repeat expansions in NOTCH2NLCexhibiting a typical neuronal intranuclear inclusion disease phenotype.',
			'authors' => 'Kameyama  Shinichi et al.',
			'description' => '<p>We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of the entire NOTCH2NLC GGC repeat expansion and DNA methylation were comprehensively evaluated using fluorescent amplicon length PCR (AL-PCR), Southern blotting and targeted long-read sequencing, and detailed genetic/epigenetic and clinical features were described. In AL-PCR, we could not recognize the wild-type allele in both patients. Targeted long-read sequencing revealed that one patient harbored a homozygous repeat expansion. The other patient harbored compound heterozygous repeat expansions. The GGC repeats and the nearest CpG island were hypomethylated in all expanded alleles in both patients. Both patients harboring the biallelic GGC repeat expansion showed a typical dementia-dominant NIID phenotype. In conclusion, the biallelic GGC repeat expansion in two typical NIID patients indicated that NOTCH2NLC-related diseases could be completely dominant.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36041634',
			'doi' => '10.1016/j.ygeno.2022.110469',
			'modified' => '2022-10-21 09:28:25',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4453',
			'name' => 'A haplotype resolved chromosomal level avocado genome allows analysis ofnovel avocado genes',
			'authors' => 'Onkar N. et al. ',
			'description' => '<p>Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80\% of the world&rsquo;s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8\% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48&thinsp;915 avocado genes of which 39&thinsp;207 could be ascribed functions. The genome contained 62.6\% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac157/6652665',
			'doi' => 'https://doi.org/10.1093/hr/uhac157',
			'modified' => '2022-10-21 09:36:02',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4432',
			'name' => 'Identification of Laportea bulbifera using the Complete ChloroplastGenome as a Super-Barcode',
			'authors' => 'Wang  Wenting et al.',
			'description' => '<p>Laportea bulbifera, a Miao medicine grown in karst areas, has exerts a unique curative effect on skin itching in the elderly, with an annual sales of &gt; 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation highthroughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence used as a super-barcode and the highly variable regions (ycf1, matK, and ndhD), especially matK, can be used as specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1793400%2Fv1',
			'doi' => '10.21203/rs.3.rs-1793400/v1',
			'modified' => '2022-09-28 09:10:15',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4435',
			'name' => 'Oxford Nanopore R10.4 long-read sequencing enables the generation ofnear-finished bacterial genomes from pure cultures and metagenomes withoutshort-read or reference polishing.',
			'authors' => 'Sereika  Mantas et al.',
			'description' => '<p>Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35789207',
			'doi' => '10.1038/s41592-022-01539-7',
			'modified' => '2022-09-28 09:21:29',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4462',
			'name' => 'Complete Genome Sequences of Multidrug-Resistant Campylobactercoli Strains YH501, YH503, and YH504, from Retail Chicken.',
			'authors' => 'He  Yiping et al.',
			'description' => '<p>Campylobacter coli is an important foodborne pathogen that can cause inflammation of the intestine and diarrhea in humans. The complete genomes, including megaplasmids, of C. coli strains YH501, YH503, and YH504 from retail chicken were sequenced and assembled. Whole-genome analysis revealed a number of virulence and antibiotic resistance genes, suggesting significant potential for these poultry-originating isolates to cause human disease.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35862903',
			'doi' => '10.1128/mra.00237-22',
			'modified' => '2022-10-21 09:48:05',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4463',
			'name' => 'High-Quality Genome Assembly of Nannochloris desiccata 2437 andIts Associated Bacterial Community.',
			'authors' => 'Sanders  Claire K et al.',
			'description' => '<p>High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assembled in 29 contigs.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35770994',
			'doi' => '10.1128/mra.00710-21',
			'modified' => '2022-10-21 09:48:45',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4461',
			'name' => 'Long-read Oxford nanopore sequencing reveals a de novo case of complexchromosomal rearrangement involving chromosomes 2, 7, and 13.',
			'authors' => 'Xing  Lingling et al.',
			'description' => '<p>BACKGROUND: Complex chromosomal rearrangements (CCRs) are associated with high reproductive risk, infertility, abnormalities in offspring, and recurrent miscarriage in women. It is essential to accurately characterize apparently balanced chromosome rearrangements in unaffected individuals. METHODS: A CCR young couple who suffered two spontaneous abortions and underwent labor induction due to fetal chromosomal abnormalities was studied using long-read sequencing(LRS), single-nucleotide polymorphism (SNP) array, G-banding karyotype analysis (550-band resolution), and Sanger sequencing. RESULTS: SNP analysis of the amniotic fluid cells during the third pregnancy revealed a 9.9-Mb duplication at 7q21.11q21.2 and a 24.8-Mb heterozygous deletion at 13q21.1q31.1. The unaffected female partner was a carrier of a three-way CCR [46,XX,? ins(7;13)(q21.1;q21.1q22)t(2;13)(p23;q22)]. Subsequent LRS analysis revealed the exact breakpoint locations on the derivative chromosomes and the specific method of chromosome rearrangement, indicating that the CCR carrier was a more complex structural rearrangement comprising five breakpoints. Furthermore, LRS detected an inserted fragment of chromosome 13 in chromosome 7. CONCLUSIONS: LRS is effective for analyzing the complex structural variations of the human genome and may be used to clarify the specific CCRs for effective genetic counseling and appropriate intervention.</p>',
			'date' => '2022-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35758276',
			'doi' => '10.1002/mgg3.2011',
			'modified' => '2022-10-21 09:47:15',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4361',
			'name' => 'Accumulation of endosymbiont genomes in an insect autosome followed byendosymbiont replacement.',
			'authors' => 'Tvedte  Eric S. et al. ',
			'description' => '<p>Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT). A prominent source of LGT is Wolbachia, a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells. The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive and has been localized to chromosome 4, contributing to chromosome expansion in this lineage. As has happened frequently with claims of bacteria-to-eukaryote LGT, the contribution of wAna transfers to the expanded size of D.&nbsp;ananassae chromosome 4 has been specifically contested owing to an assembly where Wolbachia sequences were classified as contaminants and removed. Here, long-read sequencing with DNA from a Wolbachia-cured line enabled assembly of 4.9 Mbp of nuclear Wolbachia transfers (nuwts) in D.&nbsp;ananassae and a 24-kbp nuclear mitochondrial transfer. The nuwts are &lt;8,000 years old in at least two locations in chromosome 4 with at least one whole-genome integration followed by rapid extensive duplication of most of the genome with regions that have up to 10 copies. The genes in nuwts are accumulating small indels and mobile element insertions. Among the highly duplicated genes are cifA and cifB, two genes associated with Wolbachia-mediated Drosophila cytoplasmic incompatibility. The wAna strain that was the source of nuwts was subsequently replaced by a different wAna endosymbiont. Direct RNA Nanopore sequencing of Wolbachia-cured lines identified nuwt transcripts, including spliced transcripts, but functionality, if any, remains elusive.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35671755',
			'doi' => '10.1016/j.cub.2022.05.024',
			'modified' => '2022-08-04 15:47:25',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '4363',
			'name' => 'DNA Hypermethylation and a Specific Methylation Spectrum on theX Chromosome in Turner Syndrome as Determined by NanoporeSequencing',
			'authors' => 'Fan  Xin et al.',
			'description' => '<p>The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate TS. Results: Thirteen TS (45X0) patients and eight controls were enrolled. Trio-WES analysis did not find any pathogenetic or likely pathogenic variants except X chromosome (chrX) deletion. The average methylation levels and patterns of chrX in 45X0 and 46XY were similar, and significantly higher than in 46XX (p = 2.22 &times; 10&minus;16). Both hyper-methylation and hypo-methylation were detected in the CpG island (CGI), CGI_shore, promoter, genebody, and PAR1-region, while in the transposon element inactivation regions of the chrX and hypermethylation were predominant. A total of 125 differentially methylated genes were identified in 45X0 compared to 46XX, including 8 and 117 hypermethylated and hypomethylated genes, respectively, with the enrichment terms of mitophagy, regulation of DNA-binding transcription factor activity, etc. Conclusions: The results suggest that the methylation profile in patients with TS might be determined by the number of X chromosomes; the patterns of methylation in TS were precisely associated with the maintenance of genomic stability and improvement of gene expression. Differentially methylated genes/pathways might reveal the potential epigenetic modulation and lead to better understanding of TS.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://doi.org/10.3390%2Fjpm12060872',
			'doi' => '10.3390/jpm12060872',
			'modified' => '2022-08-04 15:49:32',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '4530',
			'name' => 'The genome sequence of Anoplius nigerrimus (Scopoli, 1763), a spiderwasp',
			'authors' => 'Falk  Steven and Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual Anoplius nigerrimus (Arthropoda; Insecta; Hymenoptera; Pompilidae) of unknown sex. The genome sequence is 624 megabases in span. In total, 45.75\% of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 17.5 kilobases in length.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17814.1',
			'doi' => '10.12688/wellcomeopenres.17814.1',
			'modified' => '2023-02-17 08:59:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4522',
			'name' => 'Familial long-read sequencing increases yield of de novo mutations.',
			'authors' => 'Noyes  Michelle D et al.',
			'description' => '<p>Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20\% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5\% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41&nbsp;&times; 10 substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by &gt;25\% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35290762',
			'doi' => '10.1016/j.ajhg.2022.02.014',
			'modified' => '2023-02-17 09:01:49',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4525',
			'name' => 'Transposon activity, local duplications and propagation of structuralvariants across haplotypes drive the evolution of the Drosophila S2cell line.',
			'authors' => 'Lewerentz  Jacob et al.',
			'description' => '<p>BACKGROUND: Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure. RESULTS: Using a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (&gt;&thinsp;80\% of SVs), with Gypsy retrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in other D. melanogaster cell lines. CONCLUSIONS: The S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35392795',
			'doi' => '10.1186/s12864-022-08472-1',
			'modified' => '2023-02-17 09:02:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4466',
			'name' => 'Phylogenomics and Comparative Genomics Highlight SpecificGenetic Features in  Species.',
			'authors' => 'Sun  Yi-Fei et al.',
			'description' => '<p>The species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven genomes, including three new genomes, , , and . The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the species.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35330313',
			'doi' => '10.3390/jof8030311',
			'modified' => '2022-10-21 09:50:01',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4366',
			'name' => 'Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes',
			'authors' => 'Rabanal  Fernando A. and Gräff  Maike and Lanz  Christa andFritschi  Katrin and Llaca  Victor and Lang  Michelle andCarbonell-Bejerano  Pablo and Henderson  Ian and Weigel Detlef',
			'description' => '<p><span>Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant&nbsp;</span><em>Arabidopsis thaliana</em><span>, other than the reference accession Col-0, all other accessions<span>&nbsp;</span></span><em>de novo</em><span><span>&nbsp;</span>assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of &gt;85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two<span>&nbsp;</span></span><em>A. thaliana</em><span><span>&nbsp;</span>accessions.</span></p>',
			'date' => '2022-02-15',
			'pmid' => 'https://doi.org/10.1101%2F2022.02.15.480579',
			'doi' => '10.1101/2022.02.15.480579',
			'modified' => '2022-08-04 16:02:44',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4362',
			'name' => 'Chromosomal rearrangements with stable repertoires of genes andtransposable elements in an invasive forest-pathogenic fungus',
			'authors' => 'Demené A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2021.03.09.434572v5',
			'doi' => '/',
			'modified' => '2022-08-04 15:48:42',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4374',
			'name' => 'Genomic characterisation of three GES-producing Enterobacteralesisolated in the Czech Republic.',
			'authors' => 'Finianos  M. et al.',
			'description' => '<p>OBJECTIVES: The aim of the study is to characterise the genomic features of three GES-producing Enterobacterales isolates from Czech hospitals. METHODS: In 2020, during a routine screening of the hospital's surfaces in Prague General Hospital, two strains (CZ862 and CZ863) that belonged to the Enterobacter cloacae complex were found to be bla positive. Another bla positive strain identified as Klebsiella oxytoca was recovered from a patient hospitalised in Pilsen. Antibiotic susceptibility profiling was done with broth microdilution assay. Conjugation/transformation experiments were performed on all three strains. Genomic DNA of the three isolates was subjected to whole genome sequencing using PacBio platform. RESULTS: Multilocus sequence types typing of CZ862 and CZ863 identified the strains as ST837 and a novel ST (ST1622). Both bla harbouring plasmids showed high sequence similarity and complete query coverage (100\% and 99.98\%) with pEcl-35771cz. Both plasmids had two copies of bla instead of one copy as found in pEcl-35771cz. The clinical isolate CZ598 belonged to ST180. The plasmid harboured bla gene, cat and aac(6')-lb and the novel variant bla No similar sequences were observed, suggesting a novel plasmid. CONCLUSION: The detection of the two bla-positive plasmids in the same hospital environment, the first report after 3 years, suggests a hidden source. This highlights the importance of the hidden sources and evolution of such plasmids on the route of spreading into clinical settings. Also, the detection of the new bla, which is thought in this case to be associated with carbapenem resistance, imposes a health risk if disseminated, limiting therapeutic options.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35231657',
			'doi' => '10.1016/j.jgar.2022.02.016',
			'modified' => '2022-08-04 16:18:16',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4254',
			'name' => 'Improved chromosome-level genome assembly of the Glanville fritillarybutterfly () integrating Pacific Biosciences long reads and ahigh-density linkage map',
			'authors' => 'Smolander Olli-Pekka et al.',
			'description' => '<p>Abstract Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92&ndash;94\% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35022701',
			'doi' => '10.1093/gigascience/giab097',
			'modified' => '2022-05-20 09:45:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '4284',
			'name' => 'PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs,and methylation.',
			'authors' => 'Mahmoud Medhat et al.',
			'description' => '<p>Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34521442',
			'doi' => '10.1186/s13059-021-02486-w',
			'modified' => '2022-05-24 09:07:16',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '4286',
			'name' => 'Establishing community reference samples, data and call sets forbenchmarking cancer mutation detection using whole-genome sequencing.',
			'authors' => 'Fang Li Tai et al.',
			'description' => '<p>The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with &gt;2,000-fold coverage, spanning 82\% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34504347',
			'doi' => '10.1038/s41587-021-00993-6',
			'modified' => '2022-05-24 09:09:41',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4291',
			'name' => 'LeafGo: Leaf to Genome, a quick workflow to produce high-quality denovo plant genomes using long-read sequencing technology.',
			'authors' => 'Driguez Patrick et al.',
			'description' => '<p>Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34479618',
			'doi' => '10.1186/s13059-021-02475-z',
			'modified' => '2022-05-24 09:16:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4310',
			'name' => 'Targeted long-read sequencing identifies missing disease-causingvariation.',
			'authors' => 'Miller Danny E et al.',
			'description' => '<p>Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.ajhg.2021.06.006',
			'doi' => '10.1016/j.ajhg.2021.06.006',
			'modified' => '2022-06-22 09:26:54',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4342',
			'name' => 'Evidence of an epidemic spread of KPC-producing  in Czech hospitals',
			'authors' => 'Kraftova Lucie et al.',
			'description' => '<p>The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018&ndash;2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n&thinsp;=&thinsp;12), N (n&thinsp;=&thinsp;5), C (n&thinsp;=&thinsp;1) and P6 (n&thinsp;=&thinsp;1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn&rsquo;t be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34344951',
			'doi' => '10.1038/s41598-021-95285-z',
			'modified' => '2022-06-22 09:33:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => array(
			'id' => '4309',
			'name' => 'The USDA-ARS Ag100Pest Initiative: High-Quality GenomeAssemblies for Agricultural Pest Arthropod Research',
			'authors' => 'Childers  A.K. et al.',
			'description' => '<p>Simple Summary High-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technical challenge of isolating the necessary quantity and quality of DNA from many species. Sequencing methods have now improved such that many insect genomes can be sequenced and assembled at scale. We created the Ag100Pest Initiative to propel agricultural research forward by assembling reference-quality genomes of important arthropod pest species. Here, we describe the Ag100Pest Initiative&rsquo;s processes and experimental procedures. We show that the Ag100Pest Initiative will greatly expand the diversity of publicly available arthropod genome assemblies. We also demonstrate the high quality of preliminary contig assemblies. We share arthropod-specific technical details and insights that we have gained during the project. The methods and preliminary results presented herein should help other researchers attain similarly high-quality assemblies, effectively changing the landscape of insect genomics. Abstract The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture&rsquo;s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale.</p>',
			'date' => '2021-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34357286',
			'doi' => '10.3390/insects12070626',
			'modified' => '2022-08-03 16:18:33',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 35 => array(
			'id' => '4311',
			'name' => 'The American lobster genome reveals insights on longevity, neural, andimmune adaptations.',
			'authors' => 'Polinski J. M. et al. ',
			'description' => '<p>The American lobster, , is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we report a high-quality draft assembly of the genome with 25,284 predicted gene models. Analysis of the neural gene complement revealed extraordinary development of the chemosensory machinery, including a profound diversification of ligand-gated ion channels and secretory molecules. The discovery of a novel class of chimeric receptors coupling pattern recognition and neurotransmitter binding suggests a deep integration between the neural and immune systems. A robust repertoire of genes involved in innate immunity, genome stability, cell survival, chemical defense, and cuticle formation represents a diversity of defense mechanisms essential to thrive in the benthic marine environment. Together, these unique evolutionary adaptations contribute to the longevity and ecological success of this long-lived benthic predator.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34162536',
			'doi' => '10.1126/sciadv.abe8290',
			'modified' => '2022-08-03 16:19:34',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => array(
			'id' => '4316',
			'name' => 'Analysis of the Coptis chinensis genome reveals the diversification ofprotoberberine-type alkaloids.',
			'authors' => 'Liu Y. et al. ',
			'description' => '<p>Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34078898',
			'doi' => '10.1038/s41467-021-23611-0',
			'modified' => '2022-08-03 16:20:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 37 => array(
			'id' => '4348',
			'name' => 'Infectivity assessment of porcine endogenous retrovirus usinghigh-throughput sequencing technologies.',
			'authors' => 'Kono K. et al.',
			'description' => '<p>Xenogenic cell-based therapeutic products are expected to alleviate the chronic shortage of human donor organs. For example, porcine islet cell products are currently under development for the treatment of human diabetes. As porcine cells possess endogenous retrovirus (PERV), which can replicate in human cells in vitro, the potential transmission of PERV has raised concerns in the case of products that use living pig cells as raw materials. Although several PERV sequences exist in the porcine genome, not all have the ability to infect human cells. Therefore, polymerase chain reaction analysis, which amplifies a portion of the target gene, may not accurately assess the infection risk. Here, we determined porcine genome sequences and evaluated the infectivity of PERVs using high-throughput sequencing technologies. RNA sequencing was performed on both PERV-infected human cells and porcine cells, and reads mapped to PERV sequences were examined. The normalized number of the reads mapped to PERV regions was able to predict the infectivity of PERVs, indicating that it would be useful for evaluation of the PERV infection risk prior to transplantation of porcine products.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.biologicals.2021.05.001',
			'doi' => '10.1016/j.biologicals.2021.05.001',
			'modified' => '2022-08-03 16:57:04',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 38 => array(
			'id' => '4128',
			'name' => 'Chromosomal inversion polymorphisms in two sympatric ascidian lineages.',
			'authors' => 'Satou, Yutaka and Sato, Atsuko and Yasuo, Hitoyoshi and Mihirogi, Yukie andBishop, John and Fujie, Manabu and Kawamitsu, Mayumi and Hisata, Kanako andSatoh, Noriyuki',
			'description' => '<p>Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. While these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. While the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33822040',
			'doi' => '10.1093/gbe/evab068',
			'modified' => '2021-12-07 10:17:37',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4186',
			'name' => 'Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.',
			'authors' => 'Formenti G. et al.',
			'description' => '<p>BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (&gt;&thinsp;10&nbsp;kbp, PacBio or Nanopore) and short (100-300&thinsp;bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33910595',
			'doi' => '10.1186/s13059-021-02336-9',
			'modified' => '2022-01-05 15:01:11',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => array(
			'id' => '4140',
			'name' => 'Chromosomal rearrangements but no change of genes and transposable elementsrepertoires in an invasive forest-pathogenic fungus',
			'authors' => 'Demené, A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long-reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that C. parasitica genome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high quality assembled genomes, and question the role of structural variations on the invasive success of this fungal pathogen species.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1101%2F2021.03.09.434572',
			'doi' => '10.1101/2021.03.09.434572',
			'modified' => '2021-12-13 09:19:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 41 => array(
			'id' => '4191',
			'name' => 'A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.',
			'authors' => 'Liu H. et al. ',
			'description' => '<p>Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population resulting from the mating of Pekin ducks (white-shelled eggs) and mallards (green-shelled eggs). We further narrowed the candidate region to a 30-kb interval by comparing genome divergence in seven indigenous duck populations. Among the genes located in the finely mapped region, only one transcript of the ABCG2 gene (XM_013093252.2) exhibited higher uterine expression in green-shelled individuals than in white-shelled individuals, as supported by transcriptome data from four populations. ABCG2 has been reported to encode a protein that functions as a membrane transporter for biliverdin. Sanger sequencing of the whole 30-kb candidate region (Chr4: 47.41-47.44&nbsp;Mb) and a plasmid reporter assay helped to identify a single nucleotide polymorphism (Chr4: 47,418,074 G&gt;A) located in a conserved predicted promoter region whose variation may alter ABCG2 transcription activity. We provide a useful molecular marker for duck breeding and contribute data to the research on ecological evolution based on egg colour patterns among birds.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33372351',
			'doi' => '10.1111/mec.15785',
			'modified' => '2022-01-05 15:13:30',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => array(
			'id' => '4131',
			'name' => 'Genomic Characterization of VIM and MCR Co-Producers: The First TwoClinical Cases, in Italy.',
			'authors' => 'Marchetti, Vittoria Mattioni and Bitar, Ibrahim and Sarti, Mario andFogato, Elena and Scaltriti, Erika and Bracchi, Chiara and Hrabak, Jaroslavand Pongolini, Stefano and Migliavacca, Roberta',
			'description' => '<p>BACKGROUND: the co-production of carbapenemases and -genes represents a worrisome event in the treatment of infections. The aim of the study was to characterize the genomic features of two clinical complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. METHODS: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the and - type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). RESULTS: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The gene was harbored on a conjugative IncHI2 plasmid, while the determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: gene and its two component regulatory genes for increased expression on the chromosome, on non-conjugative (yet co-transferable) ColE plasmid, and on a non-conjugative IncA plasmid. CONCLUSIONS: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33418979',
			'doi' => '10.3390/diagnostics11010079',
			'modified' => '2021-12-07 10:22:20',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 43 => array(
			'id' => '4190',
			'name' => 'Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).',
			'authors' => 'Xia Z. et al.',
			'description' => '<p>Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7&thinsp;Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~1327.18&thinsp;Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33419990',
			'doi' => '10.1038/s41438-020-00455-1',
			'modified' => '2022-01-05 15:12:13',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 44 => array(
			'id' => '4205',
			'name' => 'Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.',
			'authors' => 'Suzuki Y. et al.',
			'description' => '<p>Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals characterizing rapid, haplotype-specific evolution of human centromeric arrays, while frequent single-nucleotide variants are largely conserved. We found a characteristic pattern shared among prevalent variants in human and chimpanzee. Our findings pave the way for studying sequence evolution in human and primate centromeres.</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33310858',
			'doi' => '10.1126/sciadv.abd9230',
			'modified' => '2022-01-06 15:00:50',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 45 => array(
			'id' => '4212',
			'name' => 'Efficient hybrid de novo assembly of human genomes with WENGAN.',
			'authors' => 'Di Genova A. et al. ',
			'description' => '<p>Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24-80.64&thinsp;Mb), few assembly errors (contig NGA50: 11.8-59.59&thinsp;Mb), good consensus quality (QV: 27.84-42.88) and high gene completeness (BUSCO complete: 94.6-95.2\%), while consuming low computational resources (CPU hours: 187-1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64&thinsp;Mb (NGA50: 59.59&thinsp;Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88&thinsp;Mb).</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33318652',
			'doi' => '10.1038/s41587-020-00747-w',
			'modified' => '2022-01-13 15:09:21',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 46 => array(
			'id' => '4000',
			'name' => 'Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.',
			'authors' => 'von der Heyde B, Emmanouilidou A, Mazzaferro E, Vicenzi S, Höijer I, Klingström T, Jumaa S, Dethlefsen O, Snieder H, de Geus E, Ameur A, Ingelsson E, Allalou A, Brooke HL, den Hoed M',
			'description' => '<p>A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30&nbsp;s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5&nbsp;days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25&nbsp;&micro;M ivabradine-an open channel blocker of HCNs-for 24&nbsp;h resulted in a dose-dependent higher HRV and lower heart rate at 5&nbsp;days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).</p>',
			'date' => '2020-07-16',
			'pmid' => 'http://www.pubmed.gov/32678143',
			'doi' => '10.1038/s41598-020-68567-1',
			'modified' => '2020-09-01 14:40:20',
			'created' => '2020-08-21 16:41:39',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4016',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69Escherichia coli Strain in Italy',
			'authors' => 'Mattioni, Marchetti Vittoria and Bitar, Ibrahim and Piazza, Aurora andMercato, Alessandra and Fogato, Elena and Hrabak, Jaroslav and Migliavacca,Roberta',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-15',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2020-12-16 17:36:09',
			'created' => '2020-10-12 14:54:59',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4359',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a ClinicalST69 Escherichia coli Strain in Italy',
			'authors' => 'Mattioni MV et al. ',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-01',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2022-08-03 17:12:43',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '3974',
			'name' => 'Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.',
			'authors' => 'Oulghazi S, Moumni M, Khayi S, Robic K, Sarfraz S, Lopez-Roques C, Vandecasteele C, Faure D',
			'description' => '<p>Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.</p>',
			'date' => '2020-06-13',
			'pmid' => 'http://www.pubmed.gov/32545839',
			'doi' => '10.3390/microorganisms8060895',
			'modified' => '2020-08-12 09:28:31',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '3972',
			'name' => 'Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.',
			'authors' => 'Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J',
			'description' => '<p>Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.</p>',
			'date' => '2020-06-08',
			'pmid' => 'http://www.pubmed.gov/32553272',
			'doi' => '10.1016/j.cell.2020.05.021',
			'modified' => '2020-08-12 09:27:28',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 51 => array(
			'id' => '3869',
			'name' => 'Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.',
			'authors' => 'Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J',
			'description' => '<p>Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the&nbsp;evolutionary trajectory and functional distribution&nbsp;of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S.&nbsp;epidermidis genomes from 5 healthy individuals, we found that skin S.&nbsp;epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.</p>',
			'date' => '2020-02-06',
			'pmid' => 'http://www.pubmed.gov/32004459',
			'doi' => '10.1016/j.cell.2020.01.006',
			'modified' => '2020-03-20 17:45:40',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 52 => array(
			'id' => '4247',
			'name' => 'LongQC: A Quality Control Tool for Third GenerationSequencing Long Read Data',
			'authors' => 'Fukasawa Yoshinori et al.',
			'description' => '<p>We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key statistics were optimized for long read data, and LongQC covers all major TGS platforms. LongQC processes and visualizes those statistics automatically and quickly.</p>',
			'date' => '2020-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32041730',
			'doi' => '10.1534/g3.119.400864',
			'modified' => '2022-05-24 09:03:08',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 53 => array(
			'id' => '3863',
			'name' => 'Genome Sequence of  sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.',
			'authors' => 'Anton BP, DasSarma P, Martinez FL, DasSarma SL, Al Madadha M, Roberts RJ, DasSarma S',
			'description' => '<p>An extremely halophilic archaeon, sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorporated into HaloWeb (https://halo.umbc.edu/).</p>',
			'date' => '2020-01-30',
			'pmid' => 'http://www.pubmed.gov/32001568',
			'doi' => '10.1128/MRA.01505-19.',
			'modified' => '2020-03-20 17:52:34',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 54 => array(
			'id' => '3864',
			'name' => 'The round goby genome provides insights into mechanisms that may facilitate biological invasions.',
			'authors' => 'Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S',
			'description' => '<p>BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. RESULTS: We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. CONCLUSIONS: The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.</p>',
			'date' => '2020-01-28',
			'pmid' => 'http://www.pubmed.gov/31992286',
			'doi' => '10.1186/s12915-019-0731-8',
			'modified' => '2020-03-20 17:51:48',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 55 => array(
			'id' => '3857',
			'name' => 'The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.',
			'authors' => 'Kan SL, Shen TT, Gong P, Ran JH, Wang XQ',
			'description' => '<p>BACKGROUND: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. RESULTS: Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. CONCLUSIONS: We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.</p>',
			'date' => '2020-01-20',
			'pmid' => 'http://www.pubmed.gov/31959109',
			'doi' => '10.1186/s12862-020-1582-1',
			'modified' => '2020-03-20 17:57:35',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 56 => array(
			'id' => '3858',
			'name' => 'A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).',
			'authors' => 'Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, Hiller M, Hundsdoerfer AK',
			'description' => '<p>BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged &sim;7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51&times; Pacific Biosciences long reads with an average read length of 8.9&nbsp;kb. Pacific Biosciences reads longer than 4&nbsp;kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.</p>',
			'date' => '2020-01-08',
			'pmid' => 'http://www.pubmed.gov/31972020',
			'doi' => '10.1093/gigascience/giaa001',
			'modified' => '2020-03-20 17:56:37',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 57 => array(
			'id' => '3823',
			'name' => 'Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of .',
			'authors' => 'Hovde BT, Daligault HE, Hanschen ER, Kunde YA, Johnson MB, Starkenburg SR, Johnson SL',
			'description' => '<p>The sequenced genome and the leaf transcriptome of a near relative of and was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (&lt;1 mbp) the cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified and we observed substantial diversity of genes and predicted gene products in and previously characterized toxins this suggests diverse toxin repertoires within potentially the results of rapid toxin evolution.</p>',
			'date' => '2019-11-25',
			'pmid' => 'http://www.pubmed.gov/31775284',
			'doi' => '10.3390/toxins11120691',
			'modified' => '2020-02-25 14:47:48',
			'created' => '2020-02-13 10:02:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 58 => array(
			'id' => '3813',
			'name' => 'NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.',
			'authors' => 'De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D'Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K',
			'description' => '<p>Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30&times; human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.</p>',
			'date' => '2019-11-14',
			'pmid' => 'http://www.pubmed.gov/31727106',
			'doi' => '10.1186/s13059-019-1856-3',
			'modified' => '2019-12-05 10:59:42',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 59 => array(
			'id' => '3791',
			'name' => 'Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull.',
			'authors' => 'Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL',
			'description' => '<p>Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (Pp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20&times; coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring P Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the P Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.</p>',
			'date' => '2019-10-07',
			'pmid' => 'http://www.pubmed.gov/31591551',
			'doi' => '10.1038/s41587-019-0266-0',
			'modified' => '2019-12-05 11:47:39',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 60 => array(
			'id' => '3788',
			'name' => 'Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef.',
			'authors' => 'Sekizuka T, Lee K, Kimata K, Isobe J, Kuroda M, Iyoda S, Ohnishi M, Sata T, Watahiki M',
			'description' => '<p>We present the complete genome sequence of an enterohemorrhagic O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.</p>',
			'date' => '2019-10-03',
			'pmid' => 'http://www.pubmed.gov/31582455',
			'doi' => '10.1128/MRA.00882-19.',
			'modified' => '2019-12-05 11:58:13',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 61 => array(
			'id' => '3772',
			'name' => 'Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions.',
			'authors' => 'Zhang S, Liang F, Lei C, Wu J, Fu J, Yang Q, Luo X, Yu G, Wang D, Zhang Y, Lu D, Sun X, Liang Y, Xu C',
			'description' => '<p>BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos that carry balanced inversion from those with a normal karyotype. We aim to evaluate the use of long-read sequencing in combination with haplotype linkage analysis to address this challenge. METHODS: Long-read sequencing on Oxford Nanopore platform was employed to identify the precise positions of inversion break points in four patients. Comprehensive chromosomal screening and genome-wide haplotype linkage analysis were performed based on SNP microarray. The haplotypes, including the break point regions, the whole chromosomes involved in the inversion and the corresponding homologous chromosomes, were established using informative SNPs. RESULTS: All the inversion break points were successfully identified by long-read sequencing and validated by Sanger sequencing, and on average only 13 bp differences were observed between break points inferred by long-read sequencing and Sanger sequencing. Eighteen blastocysts were biopsied and tested, in which 10 were aneuploid or unbalanced and eight were diploid with normal or balanced inversion karyotypes. Diploid embryos were transferred back to patients, the predictive results of the current methodology were consistent with fetal karyotypes of amniotic fluid or cord blood. CONCLUSIONS: Nanopore long-read sequencing is a powerful method to assay chromosomal inversions and identify exact break points. Identification of inversion break points combined with haplotype linkage analysis is an efficient strategy to distinguish embryos with normal or balanced inversion karyotypes, facilitating PGT applications.</p>',
			'date' => '2019-08-22',
			'pmid' => 'http://www.pubmed.gov/31439719',
			'doi' => '10.1136/jmedgenet-2018-105976',
			'modified' => '2019-10-02 17:08:37',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 62 => array(
			'id' => '3760',
			'name' => 'Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.',
			'authors' => 'Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, L',
			'description' => '<p>The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5&thinsp;kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions &lt;50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of &gt;15&thinsp;megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.<br /><!--50--></p>',
			'date' => '2019-08-12',
			'pmid' => 'http://www.pubmed.gov/31406327',
			'doi' => '10.1038/s41587-019-0217-9',
			'modified' => '2019-10-03 10:05:13',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 63 => array(
			'id' => '3749',
			'name' => 'Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.',
			'authors' => 'Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC',
			'description' => '<p>BACKGROUND: Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS: By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS: We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.</p>',
			'date' => '2019-07-08',
			'pmid' => 'http://www.pubmed.gov/31286858',
			'doi' => '10.1186/s12864-019-5909-5',
			'modified' => '2019-08-06 16:06:34',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 64 => array(
			'id' => '3721',
			'name' => 'Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.',
			'authors' => 'Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH',
			'description' => '<p>BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruy&egrave;re and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS: Two NWCs from Swiss Gruy&egrave;re producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS: Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.</p>',
			'date' => '2019-06-25',
			'pmid' => 'http://www.pubmed.gov/31238873',
			'doi' => '10.1186/s12866-019-1500-0',
			'modified' => '2019-07-04 18:06:26',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 65 => array(
			'id' => '3712',
			'name' => 'A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).',
			'authors' => 'Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z',
			'description' => '<p>BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential. FINDINGS: We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (&sim;211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants. CONCLUSION: This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.</p>',
			'date' => '2019-06-01',
			'pmid' => 'http://www.pubmed.gov/31216035',
			'doi' => '10.1093/gigascience/giz072',
			'modified' => '2019-07-05 14:29:16',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 66 => array(
			'id' => '3650',
			'name' => 'Genome Sequence and Methylation Patterns of  sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.',
			'authors' => 'Priya DasSarma, Anton BP, DasSarma S, Laye VJ, Guzman D, Roberts RJ, DasSarma S',
			'description' => '<p>sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Database (http://halo.umbc.edu). The polyextremophilic character and high-elevation environment make the microbe of interest for astrobiology.</p>',
			'date' => '2019-05-09',
			'pmid' => 'http://www.pubmed.gov/31072883',
			'doi' => '10.1016/j.gexplo.2004.07.001.',
			'modified' => '2019-06-07 10:11:11',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 67 => array(
			'id' => '3707',
			'name' => 'The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.',
			'authors' => 'Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C',
			'description' => '<p>Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4'-deoxyflavone synthesis in the genus&nbsp;Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30999079',
			'doi' => '10.1016/j.molp.2019.04.002',
			'modified' => '2019-07-05 14:35:57',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 68 => array(
			'id' => '3602',
			'name' => 'Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.',
			'authors' => 'Palmieri V, Dalchiele EA, Perini G, Motta A, De Spirito M, Zanoni R, Marrani AG, Papi M',
			'description' => '<p>We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoids GO-mediated oxidation of glutathione. This method offers new opportunities for the production of green biocompatible rGO and NAC-based therapies.</p>',
			'date' => '2019-03-20',
			'pmid' => 'http://www.pubmed.gov/30892320',
			'doi' => '10.1039/C9CC00429G.',
			'modified' => '2019-04-17 14:56:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 69 => array(
			'id' => '3725',
			'name' => 'The alternative reality of plant mitochondrial DNA',
			'authors' => 'Alexander Kozik, Beth A. Rowan, Dean Lavelle, Lidija Berke, M. Eric Schranz, Richard W. Michelmore, and Alan C. Christensen',
			'description' => '<p>Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative genomic arrangements (isoforms). Most mitochondrial genomes have been assembled using methods that were unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. This allowed us to characterize a comprehensive, complex set of isoforms within each species and to compare genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched linear, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement, and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms evident in our data, we inferred that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other lettuce species can be largely explained by rare recombination events that rearrange the structure. Our data demonstrate that representations of plant mitochondrial DNA as simple, genome-sized circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.</p>',
			'date' => '2019-03-01',
			'pmid' => 'https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008373',
			'doi' => '10.1101/564278.',
			'modified' => '2022-05-18 18:58:47',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 70 => array(
			'id' => '3615',
			'name' => 'Characterizing the Major Structural Variant Alleles of the Human Genome.',
			'authors' => 'Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE',
			'description' => '<p>In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30661756',
			'doi' => '10.1016/j.cell.2018.12.019',
			'modified' => '2019-04-16 13:55:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 71 => array(
			'id' => '3645',
			'name' => 'Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.',
			'authors' => 'Martínez FL, Anton BP, DasSarma P, Rajal V, Irazusta V, Roberts RJ, DasSarma S',
			'description' => '<p>Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30701250',
			'doi' => '10.1128/MRA',
			'modified' => '2019-06-07 10:15:47',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 72 => array(
			'id' => '3656',
			'name' => 'Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present  tuberculosis vaccine',
			'authors' => 'Katlyn Borgersa,Jheng-Yang Ouc, Po-Xing Zhengc, Petra Tielsa, Annelies Van Heckea, Evelyn Pletsa, Gitte Michielsena, Nele Festjensa, Nico Callewaerta, Yao-Cheng Lin',
			'description' => '<p>Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence of BCG Danish 1331 (07/270), one of the WHO reference strains for BCG vaccines. We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of this vaccine strain.</p>',
			'date' => '2018-12-26',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/31286858/',
			'doi' => '10.1101/513408.',
			'modified' => '2022-05-18 18:52:29',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 73 => array(
			'id' => '3454',
			'name' => 'SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).',
			'authors' => 'Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N',
			'description' => '<p>Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica). Findings: As part of the Genome10K (G10K) effort on generating high quality vertebrate genomes, we have assembled a highly contiguous genome assembly using Single Molecule Real-Time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from the Direct Label and Stain (DLS) technologies. As proposed by Bionano, the DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of over 25.95 Mbp. Conclusions: This high-quality genome assembly represents a valuable resource for further studies of population genetics and genomics in the barn swallow, and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.</p>',
			'date' => '2018-11-29',
			'pmid' => 'http://www.pubmed.gov/30496513',
			'doi' => '10.1093/gigascience/giy142/5202456',
			'modified' => '2019-02-15 20:35:16',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 74 => array(
			'id' => '3429',
			'name' => 'Improved reference genome of Aedes aegypti informs arbovirus vector control.',
			'authors' => 'Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gl',
			'description' => '<p>Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology&nbsp;of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.</p>',
			'date' => '2018-11-14',
			'pmid' => 'http://www.pubmed.gov/30429615',
			'doi' => '10.1038/s41586-018-0692-z',
			'modified' => '2018-12-31 11:15:00',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 75 => array(
			'id' => '3413',
			'name' => 'Whole-genome landscape of Medicago truncatula symbiotic genes.',
			'authors' => 'Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Mu',
			'description' => '<p>Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.</p>',
			'date' => '2018-11-05',
			'pmid' => 'http://www.pubmed.gov/30397259',
			'doi' => '10.1038/s41477-018-0286-7',
			'modified' => '2018-12-31 11:17:32',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 76 => array(
			'id' => '3517',
			'name' => 'Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.',
			'authors' => 'Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, ',
			'description' => '<p>Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions. However, even though genome assemblies based on long reads exhibit high contig N50s (&gt;1&thinsp;Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of &gt;5&thinsp;Mb and contain scaffolds that represent entire chromosomes or chromosome arms.</p>',
			'date' => '2018-11-02',
			'pmid' => 'http://www.pubmed.gov/30390080',
			'doi' => '10.1038/s41477-018-0289-4',
			'modified' => '2019-02-27 15:41:40',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 77 => array(
			'id' => '3441',
			'name' => 'The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.',
			'authors' => 'Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B',
			'description' => '<p>Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is&nbsp;found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H.&nbsp;axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H.&nbsp;axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of &sim;170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that&nbsp;highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.</p>',
			'date' => '2018-10-22',
			'pmid' => 'http://www.pubmed.gov/30146156',
			'doi' => '10.1016/j.cub.2018.08.023',
			'modified' => '2019-02-15 20:42:22',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 78 => array(
			'id' => '3412',
			'name' => 'Long-read sequence capture of the hemoglobin gene clusters across gadid species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes. This article is protected by copyright. All rights reserved.</p>',
			'date' => '2018-10-17',
			'pmid' => 'http://www.pubmed.org/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2018-12-31 11:19:03',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 79 => array(
			'id' => '3399',
			'name' => 'Genomic Structural Variations Within Five Continental Populations of .',
			'authors' => 'Long E, Evans C, Chaston J, Udall JA',
			'description' => '<p>Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing genes. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent diverse populations within the species. We used long-read sequencing and optical mapping technologies to identify SVs in these genomes. Among the five lines examined, we found an average of 2,928 structural variants within these genomes. These structural variations varied greatly in size and location, included many exonic regions, and could impact adaptation and genomic evolution.</p>',
			'date' => '2018-10-03',
			'pmid' => 'http://www.pubmed.gov/30111620',
			'doi' => '10.1534/g3.118.200631',
			'modified' => '2018-11-09 11:49:08',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 80 => array(
			'id' => '3403',
			'name' => 'Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.',
			'authors' => 'Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K, Zhang Q',
			'description' => '<p>Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect disease causal structural variants (SVs) from short reads sequencing technologies. Long reads sequencing can produce longer reads (typically 1000&nbsp;bp or longer), therefore offering greatly improved ability to detect SVs that may be missed by short-read sequencing. Results: Here we describe a case study, where WES identified only one heterozygous pathogenic variant for an individual suspected to have glycogen storage disease type Ia (GSD-Ia), which is an autosomal recessive disease caused by bi-allelic mutations in the gene. Through Nanopore long-read whole-genome sequencing, we identified a 7.1&nbsp;kb deletion covering two exons on the other allele, suggesting that complex structural variants (SVs) may explain a fraction of cases when the second pathogenic allele is missing from WES on recessive diseases. Both breakpoints of the deletion are within Alu elements, and we designed Sanger sequencing and quantitative PCR assays based on the breakpoints for preimplantation genetic diagnosis (PGD) for the family planning on another child. Four embryos were obtained after in vitro fertilization (IVF), and an embryo without deletion in was transplanted after PGD and was confirmed by prenatal diagnosis, postnatal diagnosis, and subsequent lack of disease symptoms after birth. Conclusions: In summary, we present one of the first examples of using long-read sequencing to identify causal yet complex SVs in exome-negative patients, which subsequently enabled successful personalized PGD.</p>',
			'date' => '2018-09-28',
			'pmid' => 'http://www.pubmed.gov/30279644',
			'doi' => '10.1186/s41065-018-0069-1',
			'modified' => '2018-11-09 11:27:02',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 81 => array(
			'id' => '3525',
			'name' => 'Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.',
			'authors' => 'Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD',
			'description' => '<p>BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences' (PacBio) and Oxford Nanopore Technologies' (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing GC repeat expansion. We also report the first long-read sequencing data characterizing the C9orf72 GC repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9. RESULTS: Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinION was a challenge for whole-genome sequencing; we were unable to attain reads covering the human C9orf72 repeat expansion using 15 flow cells. We obtained 8&times; coverage across the C9orf72 locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained &gt;&thinsp;800&times; coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual's repeat region was &gt;&thinsp;99% GC content, though we cannot rule out small interruptions. CONCLUSIONS: Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in C9orf72 expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-GC content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.</p>',
			'date' => '2018-08-21',
			'pmid' => 'http://www.pubmed.gov/30126445',
			'doi' => '10.1186/s13024-018-0274-4',
			'modified' => '2019-02-28 10:13:27',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 82 => array(
			'id' => '3524',
			'name' => 'The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.',
			'authors' => 'Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J',
			'description' => '<p>DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (&gt;94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.</p>',
			'date' => '2018-08-14',
			'pmid' => 'http://www.pubmed.gov/30108278',
			'doi' => '10.1038/s41598-018-30620-5',
			'modified' => '2019-02-28 10:12:41',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 83 => array(
			'id' => '3638',
			'name' => 'Long-read sequence capture of the haemoglobin gene clusters across codfish species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100&nbsp;kb) and MN (~200&nbsp;kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.</p>',
			'date' => '2018-08-03',
			'pmid' => 'http://www.pubmed.gov/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2019-06-07 10:24:26',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 84 => array(
			'id' => '3512',
			'name' => 'A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.',
			'authors' => 'Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Are',
			'description' => '<p>Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512&thinsp;Mb with N50 of 3.4&thinsp;Mb and 564 contigs). The length of 512&thinsp;Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.</p>',
			'date' => '2018-06-11',
			'pmid' => 'http://www.pubmed.gov/29892093',
			'doi' => '10.1038/s41477-018-0166-1',
			'modified' => '2019-02-28 10:35:49',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 85 => array(
			'id' => '3483',
			'name' => 'Overview of Next-Generation Sequencing Technologies.',
			'authors' => 'Slatko BE, Gardner AF, Ausubel FM',
			'description' => '<p>High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. &copy; 2018 by John Wiley &amp; Sons, Inc.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29851291',
			'doi' => '10.1002/cpmb.59',
			'modified' => '2019-02-14 17:07:52',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 86 => array(
			'id' => '3474',
			'name' => 'Draft genome of the Peruvian scallop Argopecten purpuratus.',
			'authors' => 'Li C, Liu X, Liu B, Ma B, Liu F, Liu G, Shi Q, Wang C',
			'description' => '<p>Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. Findings: A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. Conclusions: We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29617765',
			'doi' => '10.1093/gigascience/giy031',
			'modified' => '2019-02-15 20:33:41',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 87 => array(
			'id' => '3544',
			'name' => 'Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.',
			'authors' => 'Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F',
			'description' => '<p>BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS: In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.</p>',
			'date' => '2018-01-16',
			'pmid' => 'http://www.pubmed.gov/29338683',
			'doi' => '10.1186/s12864-017-4429-4',
			'modified' => '2019-02-28 10:58:38',
			'created' => '2019-02-27 12:54:44',
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			'id' => '3308',
			'name' => 'Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.',
			'authors' => 'Rödelsperger C. et al.',
			'description' => '<p>The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P.&nbsp;pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P.&nbsp;pacificus. Despite widespread conservation of synteny between P.&nbsp;pacificus and C.&nbsp;elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C.&nbsp;elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P.&nbsp;pacificus.</p>',
			'date' => '2017-10-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045848',
			'doi' => '',
			'modified' => '2018-01-04 10:15:03',
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			'id' => '3279',
			'name' => 'De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads',
			'authors' => 'Korlach J. et al.',
			'description' => '<p>Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.</p>',
			'date' => '2017-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29020750',
			'doi' => '',
			'modified' => '2017-10-16 10:27:47',
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			'name' => 'DNA fragmentation and quality control analysis ',
			'authors' => 'Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian',
			'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
<p><strong>Introduction</strong></p>
<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
<p><strong>Results</strong></p>
<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
<p><strong>Conclusion</strong></p>
<p>Unbiased DNA fragmentation with the Diagenode One, the Bioruptor<sup>&reg;</sup>&nbsp;Pico, or the Megaruptor<sup>&reg;</sup>&nbsp;for short- or long-read sequencing combined with sizing on the Fragment Analyzer<sup>&trade;</sup>&nbsp;delivers an efficient workflow solution for preparing and analyzing libraries with even distribution and representation of the genome.</p>
<p></p>',
			'date' => '2016-09-29',
			'pmid' => 'http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.f.397.html',
			'doi' => '',
			'modified' => '2016-10-20 16:37:08',
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			'description' => '<p>Established in March 15<span>th </span><span>2000, DNA Link, Inc. has developed as one of the leading full genomic service provider with its extensive 17 years of experience. DNA Link has been involved in numerous genomic researches including many national projects, and contributed to the expansion of the genomic industry. </span></p>
<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p>',
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<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p><cite>Hyeyoon, Jang - Lab Manager - Seoul, Korea</cite></blockquote>
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<p><span><strong><span style="text-decoration: underline;">Note</span>:&nbsp;</strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a><span>&nbsp;</span><span>are sold separately.</span></span></p>',
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	'description' => '<p>Several methods exist today for shearing genomic DNA, but few are reliable for generating DNA fragments &gt;50 kb necessary for assembly of many microbial, human, plant and animal genomes <em>de novo</em>. Pacific Biosciences highly recommends the Megaruptor<sup>TM</sup> System for shearing genomic DNA to large fragments for long-read sequencing in the Sequel&reg; System.</p>',
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	'type' => 'Application note',
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	'name' => 'DNA fragmentation and quality control analysis ',
	'authors' => 'Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian',
	'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
<p><strong>Introduction</strong></p>
<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
<p><strong>Results</strong></p>
<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
<p><strong>Conclusion</strong></p>
<p>Unbiased DNA fragmentation with the Diagenode One, the Bioruptor<sup>&reg;</sup>&nbsp;Pico, or the Megaruptor<sup>&reg;</sup>&nbsp;for short- or long-read sequencing combined with sizing on the Fragment Analyzer<sup>&trade;</sup>&nbsp;delivers an efficient workflow solution for preparing and analyzing libraries with even distribution and representation of the genome.</p>
<p></p>',
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	'pmid' => 'http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.f.397.html',
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Notice (8): Undefined variable: campaign_id [APP/View/Products/view.ctp, line 755]
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			'name' => '次世代シーケンシング',
			'description' => '<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2 style="font-size: 22px;">DNA断片化、ライブラリー調製、自動化：NGSのワンストップショップ</h2>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-12 medium-12 large-12 columns">
<h4>1. 断片化装置を選択してください：150 bp〜75 kbの範囲でDNAを断片化します。</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-pico-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/bioruptor_pico.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/megaruptor2-1-unit"><img src="https://www.diagenode.com/img/product/shearing_technologies/B06010001_megaruptor2.jpg" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/bioruptor-one-sonication-device"><img src="https://www.diagenode.com/img/product/shearing_technologies/br-one-profil.png" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns">5&mu;lまで断片化：150 bp〜2 kb<br />NGS DNAライブラリー調製およびFFPE核酸抽出に最適で、</td>
<td class="small-4 medium-4 large-4 columns">2 kb〜75 kbの範囲をできます。<br />メイトペアライブラリー調製および長いフラグメントDNAシーケンシングに最適で、この軽量デスクトップデバイスで</td>
<td class="small-4 medium-4 large-4 columns">20または50&mu;lの断片化が可能です。</td>
</tr>
</tbody>
</table>
<table class="small-12 medium-12 large-12 columns">
<tbody>
<tr>
<th class="small-8 medium-8 large-8 columns">
<h4>2. 最適化されたライブラリー調整キットを選択してください。</h4>
</th>
<th class="small-4 medium-4 large-4 columns">
<h4>3. ライブラリー前処理自動化を選択して、比類のないデータ再現性を実感</h4>
</th>
</tr>
<tr style="background-color: #ffffff;">
<td class="small-12 medium-12 large-12 columns"></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns"><a href="../p/microplex-library-preparation-kit-v2-x12-12-indices-12-rxns"><img src="https://www.diagenode.com/img/product/kits/microPlex_library_preparation.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/ideal-library-preparation-kit-x24-incl-index-primer-set-1-24-rxns"><img src="https://www.diagenode.com/img/product/kits/box_kit.jpg" style="display: block; margin-left: auto; margin-right: auto;" height="173" width="250" /></a></td>
<td class="small-4 medium-4 large-4 columns"><a href="../p/sx-8g-ip-star-compact-automated-system-1-unit"><img src="https://www.diagenode.com/img/product/automation/B03000002%20_ipstar_compact.png" style="display: block; margin-left: auto; margin-right: auto;" /></a></td>
</tr>
<tr>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">50pgの低入力：MicroPlex Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">5ng以上：iDeal&nbsp;Library Preparation Kit</td>
<td class="small-4 medium-4 large-4 columns" style="text-align: center;">Achieve great NGS data easily</td>
</tr>
</tbody>
</table>
</div>
</div>
<blockquote>
<div class="row">
<div class="small-12 medium-12 large-12 columns"><span class="label" style="margin-bottom: 16px; margin-left: -22px; font-size: 15px;">DiagenodeがNGS研究にぴったりなプロバイダーである理由</span>
<p>Diagenodeは15年以上もエピジェネティクス研究に専念、専門としています。 ChIP研究クロマチン用のユニークな断片化システムの開発から始まり、 専門知識を活かし、5&mu;lのせん断体積まで可能で、NGS DNAライブラリーの調製に最適な最先端DNA断片化装置の開発にたどり着きました。 我々は以来、ChIP-seq、Methyl-seq、NGSライブラリー調製用キットを研究開発し、業界をリードする免疫沈降研究と同様に、ライブラリー調製を自動化および完結させる独自の自動化システムを開発にも成功しました。</p>
<ul>
<li>信頼されるせん断装置</li>
<li>様々なインプットからのライブラリ作成キット</li>
<li>独自の自動化デバイス</li>
</ul>
</div>
</div>
</blockquote>
<div class="row">
<div class="small-12 columns">
<ul class="accordion" data-accordion="">
<li class="accordion-navigation"><a href="#panel1a">次世代シーケンシングへの理解とその専門知識</a>
<div id="panel1a" class="content">
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<p><strong>次世代シーケンシング (NGS)</strong> ）は、著しいスケールとハイスループットでシーケンシングを行い、1日に数十億もの塩基生成を可能にします。 NGSのハイスループットは迅速でありながら正確で、再現性のあるデータセットを実現し、さらにシーケンシング費用を削減します。 NGSは、ゲノムシーケンシング、ゲノム再シーケンシング、デノボシーケンシング、トランスクリプトームシーケンシング、その他にDNA-タンパク質相互作用の検出やエピゲノムなどを示します。 指数関数的に増加するシーケンシングデータの需要は、計算分析の障害や解釈、データストレージなどの課題を解決します。</p>
<p>アプリケーションおよび出発物質に応じて、数百万から数十億の鋳型DNA分子を大規模に並行してシーケンシングすることが可能です。その為に、異なる化学物質を使用するいくつかの市販のNGSプラットフォームを利用することができます。 NGSプラットフォームの種類によっては、事前準備とライブラリー作成が必要です。</p>
<p>NGSにとっても、特にデータ処理と分析に関した大きな課題はあります。第3世代技術はゲノミクス研究にさらに革命を起こすであろうと大きく期待されています。</p>
</div>
</div>
<div class="row">
<div class="small-6 medium-6 large-6 columns">
<p><strong>NGS アプリケーション</strong></p>
<ul>
<li>全ゲノム配列決定</li>
<li>デノボシーケンシング</li>
<li>標的配列</li>
<li>Exomeシーケンシング</li>
<li>トランスクリプトーム配列決定</li>
<li>ゲノム配列決定</li>
<li>ミトコンドリア配列決定</li>
<li>DNA-タンパク質相互作用（ChIP-seq</li>
<li>バリアント検出</li>
<li>ゲノム仕上げ</li>
</ul>
</div>
<div class="small-6 medium-6 large-6 columns">
<p><strong>研究分野におけるNGS:</strong></p>
<ul>
<li>腫瘍学</li>
<li>リプロダクティブ・ヘルス</li>
<li>法医学ゲノミクス</li>
<li>アグリゲノミックス</li>
<li>複雑な病気</li>
<li>微生物ゲノミクス</li>
<li>食品・環境ゲノミクス</li>
<li>創薬ゲノミクス - パーソナライズド・メディカル</li>
</ul>
</div>
<div class="small-12 medium-12 large-12 columns">
<p><strong>NGSの用語</strong></p>
<dl>
<dt>リード（読み取り）</dt>
<dd>この装置から得られた連続した単一のストレッチ</dd>
<dt>断片リード</dt>
<dd>フラグメントライブラリからの読み込み。 シーケンシングプラットフォームに応じて、読み取りは通常約100〜300bp。</dd>
<dt>断片ペアエンドリード</dt>
<dd>断片ライブラリーからDNA断片の各末端2つの読み取り。</dd>
<dt>メイトペアリード</dt>
<dd>大きなDNA断片（通常は予め定義されたサイズ範囲）の各末端から2つの読み取り。</dd>
<dt>カバレッジ（例）</dt>
<dd>30&times;適用範囲とは、参照ゲノム中の各塩基対が平均30回の読み取りを示す。</dd>
</dl>
</div>
</div>
<div class="row">
<div class="small-12 medium-12 large-12 columns">
<h2>NGSプラットフォーム</h2>
<h3><a href="http://www.illumina.com" target="_blank">イルミナ</a></h3>
<p>イルミナは、クローン的に増幅された鋳型DNA（クラスター）上に位置する、蛍光標識された可逆的鎖ターミネーターヌクレオチドを用いた配列別合成技術を使用。 DNAクラスターは、ガラスフローセルの表面上に固定化され、 ワークフローは、4つのヌクレオチド（それぞれ異なる蛍光色素で標識された）の組み込み、4色イメージング、色素や末端基の切断、取り込み、イメージングなどを繰り返します。フローセルは大規模な並列配列決定を受ける。 この方法により、単一蛍光標識されたヌクレオチドの制御添加によるモノヌクレオチドのエラーを回避する可能性があります。 読み取りの長さは、通常約100〜150 bpです。</p>
<h3><a href="http://www.lifetechnologies.com" target="_blank">イオン トレント</a></h3>
<p>イオントレントは、半導体技術チップを用いて、合成中にヌクレオチドを取り込む際に放出されたプロトンを検出します。 これは、イオン球粒子と呼ばれるビーズの表面にエマルションPCR（emPCR）を使用し、リンクされた特定のアダプターを用いてDNA断片を増幅します。 各ビーズは1種類のDNA断片で覆われていて、異なるDNA断片を有するビーズは次いで、チップの陽子感知ウェル内に配置されます。 チップには一度に4つのヌクレオチドのうちの1つが浸水し、このプロセスは異なるヌクレオチドで15秒ごとに繰り返されます。 配列決定の間に4つの塩基の各々が1つずつ導入されます、組み込みの場合はプロトンが放出され、電圧信号が取り込みに比例して検出されます。.</p>
<h3><a href="http://www.pacificbiosciences.com" target="_blank">パシフィック バイオサイエンス</a></h3>
<p>パシフィックバイオサイエンスでは、20kbを超える塩基対の読み取りも、単一分子リアルタイム（SMRT）シーケンシングによる構造および細胞タイプの変化を観察することができます。 このプラットフォームでは、超長鎖二本鎖DNA（dsDNA）断片が、Megaruptor（登録商標）のようなDiagenode装置を用いたランダムシアリングまたは目的の標的領域の増幅によって生成されます。 SMRTbellライブラリーは、ユニバーサルヘアピンアダプターをDNA断片の各末端に連結することによって生成します。 サイズ選択条件による洗浄ステップの後、配列決定プライマーをSMRTbellテンプレートにアニーリングし、鋳型DNAに結合したDNAポリメラーゼを含む配列決定を、蛍光標識ヌクレオチドの存在下で開始。 各塩基が取り込まれると、異なる蛍光のパルスをリアルタイムで検出します。</p>
<h3><a href="https://nanoporetech.com" target="_blank">オックスフォード ナノポア</a></h3>
<p>Oxford Nanoporeは、単一のDNA分子配列決定に基づく技術を開発します。その技術により生物学的分子、すなわちDNAが一群の電気抵抗性高分子膜として位置するナノスケールの孔（ナノ細孔）またはその近くを通過し、イオン電流が変化します。 この変化に関する情報は、例えば4つのヌクレオチド（AまたはG r CまたはT）ならびに修飾されたヌクレオチドすべてを区別することによって分子情報に訳されます。 シーケンシングミニオンデバイスのフローセルは、数百個のナノポアチャネルのセンサアレイを含みます。 DNAサンプルは、Diagenode社のMegaruptor（登録商標）を用いてランダムシアリングによって生成され得る超長鎖DNAフラグメントが必要です。</p>
<h3><a href="http://www.lifetechnologies.com/be/en/home/life-science/sequencing/next-generation-sequencing/solid-next-generation-sequencing.html" target="_blank">SOLiD</a></h3>
<p>SOLiDは、ユニークな化学作用により、何千という個々のDNA分子の同時配列決定を可能にします。 それは、アダプター対ライブラリーのフラグメントが適切で、せん断されたゲノムDNAへのアダプターのライゲーションによるライブラリー作製から始まります。 次のステップでは、エマルジョンPCR（emPCR）を実施して、ビーズの表面上の個々の鋳型DNA分子をクローン的に増幅。 emPCRでは、個々の鋳型DNAをPCR試薬と混合し、水中油型エマルジョン内の疎水性シェルで囲まれた水性液滴内のプライマーコートビーズを、配列決定のためにロードするスライドガラスの表面にランダムに付着。 この技術は、シークエンシングプライマーへのライゲーションで競合する4つの蛍光標識されたジ塩基プローブのセットを使用します。</p>
<h3><a href="http://454.com/products/technology.asp" target="_blank">454</a></h3>
<p>454は、大規模並列パイロシーケンシングを利用しています。 始めに全ゲノムDNAまたは標的遺伝子断片の300〜800bp断片のライブラリー調製します。 次に、DNAフラグメントへのアダプターの付着および単一のDNA鎖の分離。 その後アダプターに連結されたDNAフラグメントをエマルジョンベースのクローン増幅（emPCR）で処理し、DNAライブラリーフラグメントをミクロンサイズのビーズ上に配置します。 各DNA結合ビーズを光ファイバーチップ上のウェルに入れ、器具に挿入します。 4つのDNAヌクレオチドは、配列決定操作中に固定された順序で連続して加えられ、並行して配列決定されます。</p>
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<div class="small-12 medium-12 large-12 columns">In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size (depending on the sequencing platform) to enable sensitive and reliable NGS results. The <strong>Bioruptor</strong><sup>&reg;</sup> <strong>Pico</strong> and the <strong>Megaruptor</strong><sup>&reg;</sup> provide superior sample yields, fragment size, and consistency, which are essential for Next-Generation Sequencing workflows. Follow our guidelines and find the good parameters for your expected DNA size: <a href="https://pybrevet.typeform.com/to/o8cQfM">DNA shearing with the Bioruptor<sup>&reg;</sup></a>.</div>
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<div class="small-5 medium-5 large-5 columns"><small><strong>Programmable DNA size distribution and high reproducibility with Bioruptor<sup>&reg;</sup> Pico using 0.65 (panel A) or 0.1 ml (panel B) microtubes</strong>. <b>Panel A:</b> 200 bp after 13 cycles (13 sec ON/OFF) using 100 &micro;l volume. Average size: 204; CV%:1.89%). <b>Panel B:</b> 200 bp after 20 cycles (30 sec ON/OFF) using 10 &micro;l volume. (Average size: 215 bp; CV%: 6.6%). <b>Panel A &amp; B:</b> peak electropherogram view. <b>Panel C &amp; D:</b> virtual gel view.</small></div>
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<p><br /><br /></p>
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<div class="small-10 medium-10 large-10 columns text-center end small-offset-1"><img src="https://www.diagenode.com/img/applications/megaruptor-short-frag.jpg" /></div>
<div class="small-12 medium-12 large-12 columns"><small><strong> Reproducible and narrow DNA size distribution with Megaruptor&reg; using short fragment size Hydropores Validation using two different DNA sources and two different methods of analysis. A:</strong> Shearing of lambda phage genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different speed settings and analyzed on 1% agarose gel. <strong>B:</strong> Bioanalyzer profiles of human genomic DNA (20 ng/&mu;l; 150 &mu;l/sample) sheared at different software settings of 2 and 5 kb. Three independent experiments were run for each setting. (Agilent DNA 12000 kit was used for separation and fragment sizing).</small></div>
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<div class="small-4 medium-4 large-4 columns text-center"><img src="https://www.diagenode.com/img/applications/megaruptor-long-frag.jpg" /></div>
<div class="small-8 medium-8 large-8 columns"><small><strong> Demonstrated shearing to fragment sizes between 15 kb and 75 kb with Megaruptor&reg; using long fragment size Hydropores. &nbsp;</strong>Image shows DNA size distribution of human genomic DNA sheared with long fragment Hydropores. DNA was analyzed by pulsed field gel electrophoresis (PFGE) in 1% agarose gel and a mean size of smears was estimated using Image Lab 4.1 software.<br /> * indicates unsheared DNA </small></div>
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<h3><strong>Your partner in long-read sequencing</strong></h3>
<p>Sequencing technologies have revolutionized genomics and biology researches. Long read sequencing enables researchers to access a more comprehensive view of genomes with higher accuracy. However, one of the most critical aspects of optimal library preparation is the quality of the DNA to be sequenced. The DNA must first be effectively and consistently sheared into the appropriate fragment size. The Megaruptor gives state-of-art shearing performance providing optimal long-read sequencing using <strong>PacBio&reg; and Oxford Nanopore<sup>TM</sup>technologies.</strong></p>
<p><strong></strong></p>
<center><a href="https://www.diagenode.com/p/megaruptor-cassette-12" class="tiny details button">CHECK OUT THE NEW 12-SAMPLE CASSETTE. RUN 50% MORE SAMPLES ON YOUR MEGARUPTOR 3!</a></center>
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<p><a href="https://www.diagenode.com/en/documents/pacbio-megaruptor-application-note"><img src="https://www.diagenode.com/img/banners/pacbio-mega-banner.png" /></a></p>
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<h4 style="font-size: 22px;"><a href="https://www.diagenode.com/en/p/megaruptor-3">Click here to discover our latest innovation</a></h4>
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<p><span>We have designed the Megaruptor</span>&reg;&nbsp;<span>2 using our highest level of knowledge in shearing so that it exceeds your expectations. This device will serve your research needs for many years and will provide the best experience with long DNA molecules preparation. </span></p>
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<p><span>The Megaruptor</span><span>&reg; </span><span>2 was designed to provide researchers with a simple, automated, and reproducible device for the fragmentation of DNA in the range of 3 kb - 75 kb </span><span>(contact us for the 3 kb setting)</span><span>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly interface allows for two samples to be processed sequentially without additional user input and without cross-contamination. Just set the desired parameters and the automated system takes care of the rest. Clogging issues are eliminated in this design. </span></p>
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			'description' => '<p><span>The Megaruptor</span><span>&reg; </span><span>provides a simple, robust, and straight forward method for reproducible DNA shearing to obtain ultra-large DNA fragments. The system has been easily integrated into our workflow for long range sequencing of single molecules using the RSII platform from Pacific Biosciences</span><span>&reg;</span><span>. The obtained dense distribution of fragment sizes after shearing and the low content of non-sheared as well as short fragments was beneficial for the performance of the whole library preparation process. </span></p>',
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			'description' => '<p>Wageningen University has a strong background in plant genome sequencing including contributions to the Arabidopsis, potato and tomato genome research as partner of various international consortia. The sequencing facility of Wageningen University operates several 2nd and 3rd generation sequencing platforms including a Pacbio RS-II. The rapid developments of this third generation sequencing resulting in continuously increased read length requires a reliable DNA fragmentation into large molecules. The benefit of these large DNA molecules is their ability to span repetitive sequences which appeared to be crucial for de-novo reconstruction of large and complex genomes. To stay ahead of new developments intended for sequencing library preparations we tested the Megaruptor<span>&reg; </span>from Diagenode for optimizing our library preparation procedure targeting very large DNA molecules used for Pacbio sequencing.For this purpose we used the Megaruptor<span>&reg; </span>using large hydropores, evaluating target fragmentation size, fragment range, reproducibility and the ease in usage.</p>',
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			'description' => '<p>The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate DNA damage sites across a genome enable an understanding of the consequences of DNA damage as well as how damage is repaired, which can have key diagnostic and therapeutic implications. Importantly, advancements in technology have enabled the development of high-throughput sequencing-based DNA damage detection methods. These methods require DNA enrichment or amplification steps that limit the ability to quantitate the DNA damage sites. Further, each of these methods is typically tailored to detect only a specific type of damage. RAre DAmage and Repair (RADAR) sequencing is a DNA sequencing workflow that overcomes these limitations and enables detection and quantitation of DNA damage sites in any organism on a genome-wide scale. RADAR-seq works by replacing DNA damage sites with a patch of modified bases that can be directly detected by Pacific Biosciences Single-Molecule Real Time sequencing. Here, we present three protocols that enable detection of thymine dimers and ribonucleotides in bacterial and archaeal genomes. Basic Protocol 1 enables construction of a reference genome required for RADAR-seq analyses. Basic Protocol 2 describes how to locate, quantitate, and compare thymine dimer levels in Escherichia coli exposed to varying amounts of UV light. Basic Protocol 3 describes how to locate, quantitate, and compare ribonucleotide levels in wild-type and &Delta;RNaseH2 Thermococcus kodakarensis. Importantly, all three protocols provide in-depth steps for data analysis. Together they serve as proof-of-principle experiments that will allow users to adapt the protocols to locate and quantitate a wide variety of DNA damage sites in any organism. &copy; 2022 New England Biolabs. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Constructing a reference genome utilizing SMRT sequencing Basic Protocol 2: Mapping and quantitating genomic thymine dimer formation in untreated versus UV-irradiated E. coli using RADAR-seq Basic Protocol 3: Mapping and quantitating genomic ribonucleotide incorporation in wildtype versus &Delta;RNaseH2 T. kodakarensis using RADAR-seq.</p>',
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			'description' => '<p>Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.</p>',
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			'doi' => '10.1371/journal.pgen.1010479',
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			'description' => '<p>Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36369227',
			'doi' => '10.1038/s41597-022-01762-z',
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			'description' => '<p>The kinetoplastids are unicellular flagellates that derive their name from the &lsquo;kinetoplast&rsquo;, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein products of this mitochondrial genome are encoded as cryptogenes; their transcripts require editing to generate an open reading frame. This happens through RNA editing, whereby small regulatory guide (g)RNAs direct the proper insertion and deletion of one or more uridines at each editing site within specific transcript regions. An accurate perspective of the kDNA expansion and evolution of their unique uridine insertion/deletion editing across kinetoplastids has been difficult to achieve. Here, we resolved the kDNA structure and editing patterns in the early-branching kinetoplastid Trypanoplasma borreli and compare them with those of the well-studied trypanosomatids. We find that its kDNA consists of circular molecules of about 42 kb that harbor the rRNA and protein-coding genes, and 17 different contigs of approximately 70 kb carrying an average of 23 putative gRNA loci per contig. These contigs may be linear molecules, as they contain repetitive termini. Our analysis uncovered a putative gRNA population with unique length and sequence parameters that is massive relative to the editing needs of this parasite. We validated or determined the sequence identity of four edited mRNAs, including one coding for ATP synthase 6 that was previously thought to be missing. We utilized computational methods to show that the T. borreli transcriptome includes a substantial number of transcripts with inconsistent editing patterns, apparently products of non-canonical editing. This species utilizes the most extensive uridine deletion compared to other studied kinetoplastids to enforce amino acid conservation of cryptogene products, although insertions still remain more frequent. Finally, in three tested mitochondrial transcriptomes of kinetoplastids, uridine deletions are more common in the raw mitochondrial reads than aligned to the fully edited, translationally competent mRNAs. We conclude that the organization of kDNA across known kinetoplastids represents variations on partitioned coding and repetitive regions of circular molecules encoding mRNAs and rRNAs, while gRNA loci are positioned on a highly unstable population of molecules that differ in relative abundance across strains. Likewise, while all kinetoplastids possess conserved machinery performing RNA editing of the uridine insertion/deletion type, its output parameters are species-specific.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.csbj.2022.11.023',
			'doi' => '10.1016/j.csbj.2022.11.023',
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			'name' => 'Evaluation of the pathogenesis of non-typical strain with α-hemolysin,Vibrio parahaemolyticus 353, isolated from Chinese seafood throughcomparative genome and transcriptome analysis.',
			'authors' => 'Zha  Fei et al.',
			'description' => '<p>Vibrio parahaemolyticus outbreaks frequently occur, causing gastrointestinal sickness owing to the consumption of aquatic foods by various virulence factors; however, the mechanism of pathogenesis is still unknown. In this study, a non-typical strain of V. parahaemolyticus, named VP353, was isolated from shrimp in China. Its comparative genome and transcriptome after infection with Caco-2 cells were examined to illustrate the mechanisms of its pathogenesis. VP353 was a tdh-trh- strain but uncommonly manifested robust cytotoxicity towards Caco-2 cells. Compared with the standard strain RIMD2210633, VP353 harbored alpha-hemolysins (hlyA, hlyB, hlyC, and hlyD) was first reported in V. parahaemolyticus and showed high diversity in the T3SS2 gene cluster. Moreover, the expression of flagella, T2SS, quorum sensing-related genes, hlyA, hlyC were up-regulated, and hlyB, hlyD were down-regulated. In summary, our results demonstrate that some novel virulence factors contribute to the pathogenesis of V. parahaemolyticus infection.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36437125',
			'doi' => '10.1016/j.marpolbul.2022.114276',
			'modified' => '2023-03-07 08:55:16',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4476',
			'name' => 'Rapid and comprehensive diagnostic method for repeat expansion diseasesusing nanopore sequencing.',
			'authors' => 'Miyatake  S. et al.',
			'description' => '<p>We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer using the adaptive sampling option, in which software-based target assignment is available without prior sample enrichment, and built an analysis pipeline that prioritized the disease-causing loci. Twenty-two patients with various neurological and neuromuscular diseases, including 12 with genetically diagnosed repeat expansion diseases and 10 manifesting cerebellar ataxia, but without genetic diagnosis, were analyzed. We first sequenced the 12 molecularly diagnosed patients and accurately confirmed expanded repeats in all with uniform depth of coverage across the loci. Next, we applied our method and a conventional method to 10 molecularly undiagnosed patients. Our method corrected inaccurate diagnoses of two patients by the conventional method. Our method is superior to conventional diagnostic methods in terms of speed, accuracy, and comprehensiveness.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36289212',
			'doi' => '10.1038/s41525-022-00331-y',
			'modified' => '2022-11-18 12:21:42',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4478',
			'name' => 'Characterization of somatic structural variations in 528 Chineseindividuals with Esophageal squamous cell carcinoma.',
			'authors' => 'Cui   H. et al.',
			'description' => '<p>Esophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations' mechanisms and biological functions. SVs show multi-mode distributions in size, indicating distinct mutational processes. We develop a tool and define five types of complex rearrangements with templated insertions. We highlight a type of fold-back inversion, which is associated with poor outcomes. Distinct rearrangement signatures demonstrate variable genomic metrics such as replicating time, spatial proximity, and chromatin accessibility. Specifically, fold-back inversion tends to occur near the centrosome; TD-c2 (Tandem duplication-cluster2) is significantly enriched in chromatin-accessibility and early-replication region compared to other signatures. Analyses of TD-c2 signature reveal 9 TD hotspots, of which we identify a hotspot consisting of a super-enhancer of PTHLH. We confirm the oncogenic effect of the PTHLH gene and its interaction with enhancers through functional experiments. Finally, extrachromosomal circular DNAs (ecDNAs) are present in 14\% of ESCCs and have strong selective advantages to driver genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36272974',
			'doi' => '10.1038/s41467-022-33994-3',
			'modified' => '2022-11-18 12:23:21',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4483',
			'name' => 'The Capparis spinosa var. herbacea genome provides the first genomicinstrument for a diversity and evolution study of the Capparaceae family.',
			'authors' => 'Wang  Lei et al.',
			'description' => '<p>BACKGROUND: The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited because of the lack of its reference genome. FINDINGS: We sequenced and assembled the Capparis spinosa var. herbacea (Willd.) genome using data obtained from the combination of PacBio circular consensus sequencing and high-throughput chromosome conformation capture. The final genome assembly was approximately 274.53 Mb (contig N50 length of 9.36 Mb, scaffold N50 of 15.15 Mb), 99.23\% of which was assigned to 21 chromosomes. In the whole-genome sequence, tandem repeats accounted for 19.28\%, and transposable element sequences accounted for 43.98\%. The proportion of tandem repeats in the C. spinosa var. herbacea genome was much higher than the average of 8.55\% in plant genomes. A total of 21,577 protein-coding genes were predicted, with 98.82\% being functionally annotated. The result of species divergence times showed that C. spinosa var. herbacea and Tarenaya hassleriana separated from a common ancestor 43.31 million years ago. CONCLUSIONS: This study reported a high-quality reference genome assembly and genome features for the Capparaceae family. The assembled C. spinosa var. herbacea genome might provide a system for studying the diversity, speciation, and evolution of this family and serve as an important resource for understanding the mechanism of drought and high-temperature resistance.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36310248',
			'doi' => '10.1093/gigascience/giac106',
			'modified' => '2022-11-18 12:30:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4484',
			'name' => 'Genomic Characterization and Antimicrobial Susceptibility ofDromedary-Associated  from the Horn of Africa.',
			'authors' => 'Akarsu  H. et al.',
			'description' => '<p>Members of the family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized strains from apparently healthy and diseased camels ( = 84) and cattle ( = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by (K), /, /, /, , , , and , respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the and families, reported here for the first time for certain species of . All strains contained at least one intact prophage sequence, mainly belonging to the family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct clades and species. Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226992',
			'doi' => '10.1128/aem.01146-22',
			'modified' => '2022-11-18 12:31:20',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4418',
			'name' => 'Complete Genome Sequences of the Soil Oxalotrophic BacteriumCupriavidus oxalaticus Strain Ox1 and Its DerivedmCherry-Tagged Strain.',
			'authors' => 'Palmieri  Fabio et al. ',
			'description' => '<p>Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69&thinsp;Mb, with a GC content of 66.9\%. The genome sequence of Ox1 contains a complete operon for the degradation and assimilation of oxalate.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35924938',
			'doi' => '10.1128/mra.00181-22',
			'modified' => '2022-09-27 14:42:06',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4442',
			'name' => 'The improved genome of the nematode Parapristionchus giblindavisiprovides insights into lineage-specific gene family evolution.',
			'authors' => 'Röseler  W. et al. ',
			'description' => '<p>Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricted genes. To trace back the evolution of such new or rapidly evolving genes, a robust phylogenomic framework is indispensable. Here, we present an improved version of the genome of Parapristionchus giblindavisi which is the only known member of the sister group of Pristionchus. Relative to the previous short read assembly, the new genome is based on long reads and displays higher levels of contiguity, completeness, and correctness. Specifically, the number of contigs dropped from over 7303 to 735 resulting in an N50 increase from 112&thinsp;kb to 791&thinsp;kb. We made use of the new genome to revisit the evolution of multiple gene families. This revealed Pristionchus-specific expansions of several environmentally responsive gene families and a Pristionchus-specific loss of the de novo purine biosynthesis pathway. Focusing on the evolution of sulfatases and sulfotransferases, which control the mouth form plasticity in P. pacificus, reveals differences in copy number and genomic configurations between the genera Pristionchus and Parapristionchus. Altogether, this demonstrates the utility of the P. giblindavisi genome to date and polarize lineage-specific patterns.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35980151',
			'doi' => '10.1093/g3journal/jkac215',
			'modified' => '2022-10-14 16:33:33',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4443',
			'name' => 'The chromosome-level genome of Gypsophila paniculata reveals themolecular mechanism of floral development and ethylene insensitivity',
			'authors' => 'Fan  Li et al. ',
			'description' => '<p>Gypsophila paniculata, belonging to the Caryophyllaceae of the Caryophyllales, is one of the worldwide famous cut flowers. It is commonly used as dried flowers, whereas the underlying mechanism of flower senescence has not yet been addressed. Here, we present a chromosome-scale genome assembly for G. paniculata with a total size of 749.58 Mb. Whole-genome duplication signatures unveil two major duplication events in its evolutionary history, an ancient one occurring before the divergence of Caryophyllaceae and a more recent one shared with Dianthus caryophyllus. The integrative analyses combining genomic and transcriptomic data reveal the mechanisms regulating floral development and ethylene response of G. paniculata. The reduction of AGAMOUS expression probably caused by sequence polymorphism and the mutation in miR172 binding site of PETALOSA are associated with the double flower formation in G. paniculata. The low expression of ERS (ETHYLENE RESPONSE SENSOR) and the reduction of downstream ERF (ETHYLENE RESPONSE FACTOR) gene copy number collectively lead to the ethylene insensitivity of G. paniculata, affecting flower senescence and making it capable of making dried flowers. This study provides a cornerstone for understanding the underlying principles governing floral development and flower senescence, which could accelerate the molecular breeding of the Caryophyllaceae species.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac176/6674669',
			'doi' => '10.1093/hr/uhac176',
			'modified' => '2022-10-14 16:34:34',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4445',
			'name' => 'Patients with biallelic GGC repeat expansions in NOTCH2NLCexhibiting a typical neuronal intranuclear inclusion disease phenotype.',
			'authors' => 'Kameyama  Shinichi et al.',
			'description' => '<p>We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of the entire NOTCH2NLC GGC repeat expansion and DNA methylation were comprehensively evaluated using fluorescent amplicon length PCR (AL-PCR), Southern blotting and targeted long-read sequencing, and detailed genetic/epigenetic and clinical features were described. In AL-PCR, we could not recognize the wild-type allele in both patients. Targeted long-read sequencing revealed that one patient harbored a homozygous repeat expansion. The other patient harbored compound heterozygous repeat expansions. The GGC repeats and the nearest CpG island were hypomethylated in all expanded alleles in both patients. Both patients harboring the biallelic GGC repeat expansion showed a typical dementia-dominant NIID phenotype. In conclusion, the biallelic GGC repeat expansion in two typical NIID patients indicated that NOTCH2NLC-related diseases could be completely dominant.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36041634',
			'doi' => '10.1016/j.ygeno.2022.110469',
			'modified' => '2022-10-21 09:28:25',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4453',
			'name' => 'A haplotype resolved chromosomal level avocado genome allows analysis ofnovel avocado genes',
			'authors' => 'Onkar N. et al. ',
			'description' => '<p>Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado cultivar Hass, which represents 80\% of the world&rsquo;s avocado consumption. The DNA contigs produced from Pacific Biosciences HiFi reads were further assembled using a previously published version of the genome supported by a genetic map. The total assembly was 913 Mb with a contig N50 of 84 Mb. Contigs assigned to the 12 chromosomes represented 874 Mb and covered 98.8\% of benchmarked single-copy genes from embryophytes. Annotation of protein coding sequences identified 48&thinsp;915 avocado genes of which 39&thinsp;207 could be ascribed functions. The genome contained 62.6\% repeat elements. Specific biosynthetic pathways of interest in the genome were investigated. The analysis suggested that the predominant pathway of heptose biosynthesis in avocado may be through sedoheptulose 1,7 bisphosphate rather than via alternative routes. Endoglucanase genes were high in number, consistent with avocado using cellulase for fruit ripening. The avocado genome appeared to have a limited number of translocations between homeologous chromosomes, despite having undergone multiple genome duplication events. Proteome clustering with related species permitted identification of genes unique to avocado and other members of the Lauraceae family, as well as genes unique to species diverged near or prior to the divergence of monocots and eudicots. This genome provides a tool to support future advances in the development of elite avocado varieties with higher yields and fruit quality.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://academic.oup.com/hr/advance-article/doi/10.1093/hr/uhac157/6652665',
			'doi' => 'https://doi.org/10.1093/hr/uhac157',
			'modified' => '2022-10-21 09:36:02',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4432',
			'name' => 'Identification of Laportea bulbifera using the Complete ChloroplastGenome as a Super-Barcode',
			'authors' => 'Wang  Wenting et al.',
			'description' => '<p>Laportea bulbifera, a Miao medicine grown in karst areas, has exerts a unique curative effect on skin itching in the elderly, with an annual sales of &gt; 100 million Yuan. Owing to the shortage of resources and large morphological variations in L. bulbifera, it is difficult to identify the species correctly using only traditional methods, which seriously affects the safety of drug usage for patients. This study obtained the complete high-quality L. bulbifera chloroplast (cp) genome, using second- and third-generation highthroughput sequencing. The cp genome was 149,911 bp in length, with a typical quadripartite structure. A total of 127 genes were annotated, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. There was an inverted small single copy (SSC) structure in the L. bulbifera cp genome, one large-scale rearrangement of ~ 39 kb excised in the SSC and IR regions. The complete cp genome sequence used as a super-barcode and the highly variable regions (ycf1, matK, and ndhD), especially matK, can be used as specific barcodes to accurately distinguish L. bulbifera from counterfeits and closely related species. This study is important for the identification of L. bulbifera and lays a theoretical foundation for elucidating the phylogenetic relationship of the species</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1793400%2Fv1',
			'doi' => '10.21203/rs.3.rs-1793400/v1',
			'modified' => '2022-09-28 09:10:15',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4435',
			'name' => 'Oxford Nanopore R10.4 long-read sequencing enables the generation ofnear-finished bacterial genomes from pure cultures and metagenomes withoutshort-read or reference polishing.',
			'authors' => 'Sereika  Mantas et al.',
			'description' => '<p>Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35789207',
			'doi' => '10.1038/s41592-022-01539-7',
			'modified' => '2022-09-28 09:21:29',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4462',
			'name' => 'Complete Genome Sequences of Multidrug-Resistant Campylobactercoli Strains YH501, YH503, and YH504, from Retail Chicken.',
			'authors' => 'He  Yiping et al.',
			'description' => '<p>Campylobacter coli is an important foodborne pathogen that can cause inflammation of the intestine and diarrhea in humans. The complete genomes, including megaplasmids, of C. coli strains YH501, YH503, and YH504 from retail chicken were sequenced and assembled. Whole-genome analysis revealed a number of virulence and antibiotic resistance genes, suggesting significant potential for these poultry-originating isolates to cause human disease.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35862903',
			'doi' => '10.1128/mra.00237-22',
			'modified' => '2022-10-21 09:48:05',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4463',
			'name' => 'High-Quality Genome Assembly of Nannochloris desiccata 2437 andIts Associated Bacterial Community.',
			'authors' => 'Sanders  Claire K et al.',
			'description' => '<p>High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assembled in 29 contigs.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35770994',
			'doi' => '10.1128/mra.00710-21',
			'modified' => '2022-10-21 09:48:45',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4461',
			'name' => 'Long-read Oxford nanopore sequencing reveals a de novo case of complexchromosomal rearrangement involving chromosomes 2, 7, and 13.',
			'authors' => 'Xing  Lingling et al.',
			'description' => '<p>BACKGROUND: Complex chromosomal rearrangements (CCRs) are associated with high reproductive risk, infertility, abnormalities in offspring, and recurrent miscarriage in women. It is essential to accurately characterize apparently balanced chromosome rearrangements in unaffected individuals. METHODS: A CCR young couple who suffered two spontaneous abortions and underwent labor induction due to fetal chromosomal abnormalities was studied using long-read sequencing(LRS), single-nucleotide polymorphism (SNP) array, G-banding karyotype analysis (550-band resolution), and Sanger sequencing. RESULTS: SNP analysis of the amniotic fluid cells during the third pregnancy revealed a 9.9-Mb duplication at 7q21.11q21.2 and a 24.8-Mb heterozygous deletion at 13q21.1q31.1. The unaffected female partner was a carrier of a three-way CCR [46,XX,? ins(7;13)(q21.1;q21.1q22)t(2;13)(p23;q22)]. Subsequent LRS analysis revealed the exact breakpoint locations on the derivative chromosomes and the specific method of chromosome rearrangement, indicating that the CCR carrier was a more complex structural rearrangement comprising five breakpoints. Furthermore, LRS detected an inserted fragment of chromosome 13 in chromosome 7. CONCLUSIONS: LRS is effective for analyzing the complex structural variations of the human genome and may be used to clarify the specific CCRs for effective genetic counseling and appropriate intervention.</p>',
			'date' => '2022-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35758276',
			'doi' => '10.1002/mgg3.2011',
			'modified' => '2022-10-21 09:47:15',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4361',
			'name' => 'Accumulation of endosymbiont genomes in an insect autosome followed byendosymbiont replacement.',
			'authors' => 'Tvedte  Eric S. et al. ',
			'description' => '<p>Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT). A prominent source of LGT is Wolbachia, a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells. The DNA transfer from the Wolbachia endosymbiont wAna to Drosophila ananassae is extensive and has been localized to chromosome 4, contributing to chromosome expansion in this lineage. As has happened frequently with claims of bacteria-to-eukaryote LGT, the contribution of wAna transfers to the expanded size of D.&nbsp;ananassae chromosome 4 has been specifically contested owing to an assembly where Wolbachia sequences were classified as contaminants and removed. Here, long-read sequencing with DNA from a Wolbachia-cured line enabled assembly of 4.9 Mbp of nuclear Wolbachia transfers (nuwts) in D.&nbsp;ananassae and a 24-kbp nuclear mitochondrial transfer. The nuwts are &lt;8,000 years old in at least two locations in chromosome 4 with at least one whole-genome integration followed by rapid extensive duplication of most of the genome with regions that have up to 10 copies. The genes in nuwts are accumulating small indels and mobile element insertions. Among the highly duplicated genes are cifA and cifB, two genes associated with Wolbachia-mediated Drosophila cytoplasmic incompatibility. The wAna strain that was the source of nuwts was subsequently replaced by a different wAna endosymbiont. Direct RNA Nanopore sequencing of Wolbachia-cured lines identified nuwt transcripts, including spliced transcripts, but functionality, if any, remains elusive.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35671755',
			'doi' => '10.1016/j.cub.2022.05.024',
			'modified' => '2022-08-04 15:47:25',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => array(
			'id' => '4363',
			'name' => 'DNA Hypermethylation and a Specific Methylation Spectrum on theX Chromosome in Turner Syndrome as Determined by NanoporeSequencing',
			'authors' => 'Fan  Xin et al.',
			'description' => '<p>The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio-WES) were used for the first time to investigate TS. Results: Thirteen TS (45X0) patients and eight controls were enrolled. Trio-WES analysis did not find any pathogenetic or likely pathogenic variants except X chromosome (chrX) deletion. The average methylation levels and patterns of chrX in 45X0 and 46XY were similar, and significantly higher than in 46XX (p = 2.22 &times; 10&minus;16). Both hyper-methylation and hypo-methylation were detected in the CpG island (CGI), CGI_shore, promoter, genebody, and PAR1-region, while in the transposon element inactivation regions of the chrX and hypermethylation were predominant. A total of 125 differentially methylated genes were identified in 45X0 compared to 46XX, including 8 and 117 hypermethylated and hypomethylated genes, respectively, with the enrichment terms of mitophagy, regulation of DNA-binding transcription factor activity, etc. Conclusions: The results suggest that the methylation profile in patients with TS might be determined by the number of X chromosomes; the patterns of methylation in TS were precisely associated with the maintenance of genomic stability and improvement of gene expression. Differentially methylated genes/pathways might reveal the potential epigenetic modulation and lead to better understanding of TS.</p>',
			'date' => '2022-05-01',
			'pmid' => 'https://doi.org/10.3390%2Fjpm12060872',
			'doi' => '10.3390/jpm12060872',
			'modified' => '2022-08-04 15:49:32',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 21 => array(
			'id' => '4530',
			'name' => 'The genome sequence of Anoplius nigerrimus (Scopoli, 1763), a spiderwasp',
			'authors' => 'Falk  Steven and Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual Anoplius nigerrimus (Arthropoda; Insecta; Hymenoptera; Pompilidae) of unknown sex. The genome sequence is 624 megabases in span. In total, 45.75\% of the assembly is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 17.5 kilobases in length.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17814.1',
			'doi' => '10.12688/wellcomeopenres.17814.1',
			'modified' => '2023-02-17 08:59:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4522',
			'name' => 'Familial long-read sequencing increases yield of de novo mutations.',
			'authors' => 'Noyes  Michelle D et al.',
			'description' => '<p>Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20\% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5\% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41&nbsp;&times; 10 substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by &gt;25\% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35290762',
			'doi' => '10.1016/j.ajhg.2022.02.014',
			'modified' => '2023-02-17 09:01:49',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4525',
			'name' => 'Transposon activity, local duplications and propagation of structuralvariants across haplotypes drive the evolution of the Drosophila S2cell line.',
			'authors' => 'Lewerentz  Jacob et al.',
			'description' => '<p>BACKGROUND: Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked short- and long-read sequencing to perform haplotype-level reconstruction of the genome of a Drosophila melanogaster cell line (S2-DRSC) with a complex genome structure. RESULTS: Using a custom implementation (that is designed to use ultra-long reads in complex genomes with nested rearrangements) to call structural variants (SVs), we found that the most common SV was repetitive sequence insertion or deletion (&gt;&thinsp;80\% of SVs), with Gypsy retrotransposon insertions dominating. The second most common SV was local sequence duplication. SNPs and other SVs were rarer, but several large chromosomal translocations and mitochondrial genome insertions were observed. Haplotypes were highly similar at the nucleotide level but structurally very different. Insertion SVs existed at various haplotype frequencies and were unlinked on chromosomes, demonstrating that haplotypes have different structures and suggesting the existence of a mechanism that allows SVs to propagate across haplotypes. Finally, using public short-read data, we found that transposable element insertions and local duplications are common in other D. melanogaster cell lines. CONCLUSIONS: The S2-DRSC cell line evolved through retrotransposon activity and vast local sequence duplications, that we hypothesize were the products of DNA re-replication events. Additionally, mutations can propagate across haplotypes (possibly explained by mitotic recombination), which enables fine-tuning of mutational impact and prevents accumulation of deleterious events, an inherent problem of clonal reproduction. We conclude that traditional linear homozygous genome representation conceals the complexity when dealing with rearranged and heterozygous clonal cells.</p>',
			'date' => '2022-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35392795',
			'doi' => '10.1186/s12864-022-08472-1',
			'modified' => '2023-02-17 09:02:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4466',
			'name' => 'Phylogenomics and Comparative Genomics Highlight SpecificGenetic Features in  Species.',
			'authors' => 'Sun  Yi-Fei et al.',
			'description' => '<p>The species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic analyses to better understand the genetic blueprint of this fungal lineage. We investigated seven genomes, including three new genomes, , , and . The size of the newly sequenced genomes ranged from 60.34 to 84.27 Mb and they encoded 15,007 to 20,460 genes. A total of 58 species, including 40 white-rot fungi, 11 brown-rot fungi, four ectomycorrhizal fungi, one endophyte fungus, and two pathogens in Basidiomycota, were used for phylogenomic analyses based on 143 single-copy genes. It confirmed that species belong to the core polyporoid clade. Comparing to the other selected species, the genomes of the species encoded a larger set of genes involved in terpene metabolism and coding for secreted proteins (CAZymes, lipases, proteases and SSPs). Of note, has the largest genome size with no obvious genome wide duplication, but showed transposable elements (TEs) expansion and the largest set of terpene gene clusters, suggesting a high ability to produce terpenoids for medicinal treatment. also encoded the largest set of proteins containing domains for cytochrome P450s, heterokaryon incompatibility and major facilitator families. Besides, the size of secretome is the largest, including CAZymes (AA9, GH18, A01A), proteases G01, and lipases GGGX, which may enhance the catabolism of cell wall carbohydrates, proteins, and fats during hosts colonization. The current genomic resource will be used to develop further biotechnology and medicinal applications, together with ecological studies of the species.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35330313',
			'doi' => '10.3390/jof8030311',
			'modified' => '2022-10-21 09:50:01',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4366',
			'name' => 'Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes',
			'authors' => 'Rabanal  Fernando A. and Gräff  Maike and Lanz  Christa andFritschi  Katrin and Llaca  Victor and Lang  Michelle andCarbonell-Bejerano  Pablo and Henderson  Ian and Weigel Detlef',
			'description' => '<p><span>Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant&nbsp;</span><em>Arabidopsis thaliana</em><span>, other than the reference accession Col-0, all other accessions<span>&nbsp;</span></span><em>de novo</em><span><span>&nbsp;</span>assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of &gt;85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two<span>&nbsp;</span></span><em>A. thaliana</em><span><span>&nbsp;</span>accessions.</span></p>',
			'date' => '2022-02-15',
			'pmid' => 'https://doi.org/10.1101%2F2022.02.15.480579',
			'doi' => '10.1101/2022.02.15.480579',
			'modified' => '2022-08-04 16:02:44',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4362',
			'name' => 'Chromosomal rearrangements with stable repertoires of genes andtransposable elements in an invasive forest-pathogenic fungus',
			'authors' => 'Demené A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in detail for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de novo whole-genome assembly obtained from a new method of DNA extraction and long-reads sequencing Nanopore technology obtained from a Japanese isolate sampled in the native area of the species. The comparison with a recently published reference genome revealed stable gene and transposable elements (TEs) repertoires. We also showed that the C. parasitica genome is lowly compartmentalized, with a poor association between TEs and genes, such as those potentially involved in host interactions (i.e., genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high-quality assembled genomes, and questions the role of structural variations in the invasive success of this fungal pathogen species.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.biorxiv.org/content/10.1101/2021.03.09.434572v5',
			'doi' => '/',
			'modified' => '2022-08-04 15:48:42',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4374',
			'name' => 'Genomic characterisation of three GES-producing Enterobacteralesisolated in the Czech Republic.',
			'authors' => 'Finianos  M. et al.',
			'description' => '<p>OBJECTIVES: The aim of the study is to characterise the genomic features of three GES-producing Enterobacterales isolates from Czech hospitals. METHODS: In 2020, during a routine screening of the hospital's surfaces in Prague General Hospital, two strains (CZ862 and CZ863) that belonged to the Enterobacter cloacae complex were found to be bla positive. Another bla positive strain identified as Klebsiella oxytoca was recovered from a patient hospitalised in Pilsen. Antibiotic susceptibility profiling was done with broth microdilution assay. Conjugation/transformation experiments were performed on all three strains. Genomic DNA of the three isolates was subjected to whole genome sequencing using PacBio platform. RESULTS: Multilocus sequence types typing of CZ862 and CZ863 identified the strains as ST837 and a novel ST (ST1622). Both bla harbouring plasmids showed high sequence similarity and complete query coverage (100\% and 99.98\%) with pEcl-35771cz. Both plasmids had two copies of bla instead of one copy as found in pEcl-35771cz. The clinical isolate CZ598 belonged to ST180. The plasmid harboured bla gene, cat and aac(6')-lb and the novel variant bla No similar sequences were observed, suggesting a novel plasmid. CONCLUSION: The detection of the two bla-positive plasmids in the same hospital environment, the first report after 3 years, suggests a hidden source. This highlights the importance of the hidden sources and evolution of such plasmids on the route of spreading into clinical settings. Also, the detection of the new bla, which is thought in this case to be associated with carbapenem resistance, imposes a health risk if disseminated, limiting therapeutic options.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35231657',
			'doi' => '10.1016/j.jgar.2022.02.016',
			'modified' => '2022-08-04 16:18:16',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4254',
			'name' => 'Improved chromosome-level genome assembly of the Glanville fritillarybutterfly () integrating Pacific Biosciences long reads and ahigh-density linkage map',
			'authors' => 'Smolander Olli-Pekka et al.',
			'description' => '<p>Abstract Background The Glanville fritillary (Melitaea cinxia) butterfly is a model system for metapopulation dynamics research in fragmented landscapes. Here, we provide a chromosome-level assembly of the butterfly's genome produced from Pacific Biosciences sequencing of a pool of males, combined with a linkage map from population crosses. Results The final assembly size of 484 Mb is an increase of 94 Mb on the previously published genome. Estimation of the completeness of the genome with BUSCO indicates that the genome contains 92&ndash;94\% of the BUSCO genes in complete and single copies. We predicted 14,810 genes using the MAKER pipeline and manually curated 1,232 of these gene models. Conclusions The genome and its annotated gene models are a valuable resource for future comparative genomics, molecular biology, transcriptome, and genetics studies on this species.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35022701',
			'doi' => '10.1093/gigascience/giab097',
			'modified' => '2022-05-20 09:45:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => array(
			'id' => '4284',
			'name' => 'PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs,and methylation.',
			'authors' => 'Mahmoud Medhat et al.',
			'description' => '<p>Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehensive insight into the sample and thus enables novel findings in biology or medicine. PRINCESS is a structured workflow that takes raw sequence reads and generates a fully phased SNV, SV, and methylation call set within a few hours. PRINCESS achieves high accuracy and long phasing even on low coverage datasets and can resolve repetitive, complex medical relevant genes that often escape detection. PRINCESS is publicly available at https://github.com/MeHelmy/princess under the MIT license.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34521442',
			'doi' => '10.1186/s13059-021-02486-w',
			'modified' => '2022-05-24 09:07:16',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 30 => array(
			'id' => '4286',
			'name' => 'Establishing community reference samples, data and call sets forbenchmarking cancer mutation detection using whole-genome sequencing.',
			'authors' => 'Fang Li Tai et al.',
			'description' => '<p>The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor-normal genomic DNA (gDNA) samples derived from a breast cancer cell line-which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations-and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with &gt;2,000-fold coverage, spanning 82\% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking 'tumor-only' or 'matched tumor-normal' analyses.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34504347',
			'doi' => '10.1038/s41587-021-00993-6',
			'modified' => '2022-05-24 09:09:41',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4291',
			'name' => 'LeafGo: Leaf to Genome, a quick workflow to produce high-quality denovo plant genomes using long-read sequencing technology.',
			'authors' => 'Driguez Patrick et al.',
			'description' => '<p>Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from tissue and produces genomes with modest laboratory and bioinformatic resources in approximately 7 days and using one long-read sequencing technology. LeafGo is optimized with ten different plant species, three of which are used to generate high-quality chromosome-level assemblies without any scaffolding technologies. Finally, we report the diploid genomes of Eucalyptus rudis and E. camaldulensis and the allotetraploid genome of Arachis hypogaea.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34479618',
			'doi' => '10.1186/s13059-021-02475-z',
			'modified' => '2022-05-24 09:16:42',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4310',
			'name' => 'Targeted long-read sequencing identifies missing disease-causingvariation.',
			'authors' => 'Miller Danny E et al.',
			'description' => '<p>Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.ajhg.2021.06.006',
			'doi' => '10.1016/j.ajhg.2021.06.006',
			'modified' => '2022-06-22 09:26:54',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4342',
			'name' => 'Evidence of an epidemic spread of KPC-producing  in Czech hospitals',
			'authors' => 'Kraftova Lucie et al.',
			'description' => '<p>The aim of the present study is to describe the ongoing spread of the KPC-producing strains, which is evolving to an epidemic in Czech hospitals. During the period of 2018&ndash;2019, a total of 108 KPC-producing Enterobacterales were recovered from 20 hospitals. Analysis of long-read sequencing data revealed the presence of several types of blaKPC-carrying plasmids; 19 out of 25 blaKPC-carrying plasmids could be assigned to R (n&thinsp;=&thinsp;12), N (n&thinsp;=&thinsp;5), C (n&thinsp;=&thinsp;1) and P6 (n&thinsp;=&thinsp;1) incompatibility (Inc) groups. Five of the remaining blaKPC-carrying plasmids were multireplicon, while one plasmid couldn&rsquo;t be typed. Additionally, phylogenetic analysis confirmed the spread of blaKPC-carrying plasmids among different clones of diverse Enterobacterales species. Our findings demonstrated that the increased prevalence of KPC-producing isolates was due to plasmids spreading among different species. In some districts, the local dissemination of IncR and IncN plasmids was observed. Additionally, the ongoing evolution of blaKPC-carrying plasmids, through genetic rearrangements, favours the preservation and further dissemination of these mobile genetic elements. Therefore, the situation should be monitored, and immediate infection control should be implemented in hospitals reporting KPC-producing strains.</p>',
			'date' => '2021-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34344951',
			'doi' => '10.1038/s41598-021-95285-z',
			'modified' => '2022-06-22 09:33:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => array(
			'id' => '4309',
			'name' => 'The USDA-ARS Ag100Pest Initiative: High-Quality GenomeAssemblies for Agricultural Pest Arthropod Research',
			'authors' => 'Childers  A.K. et al.',
			'description' => '<p>Simple Summary High-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technical challenge of isolating the necessary quantity and quality of DNA from many species. Sequencing methods have now improved such that many insect genomes can be sequenced and assembled at scale. We created the Ag100Pest Initiative to propel agricultural research forward by assembling reference-quality genomes of important arthropod pest species. Here, we describe the Ag100Pest Initiative&rsquo;s processes and experimental procedures. We show that the Ag100Pest Initiative will greatly expand the diversity of publicly available arthropod genome assemblies. We also demonstrate the high quality of preliminary contig assemblies. We share arthropod-specific technical details and insights that we have gained during the project. The methods and preliminary results presented herein should help other researchers attain similarly high-quality assemblies, effectively changing the landscape of insect genomics. Abstract The phylum Arthropoda includes species crucial for ecosystem stability, soil health, crop production, and others that present obstacles to crop and animal agriculture. The United States Department of Agriculture&rsquo;s Agricultural Research Service initiated the Ag100Pest Initiative to generate reference genome assemblies of arthropods that are (or may become) pests to agricultural production and global food security. We describe the project goals, process, status, and future. The first three years of the project were focused on species selection, specimen collection, and the construction of lab and bioinformatics pipelines for the efficient production of assemblies at scale. Contig-level assemblies of 47 species are presented, all of which were generated from single specimens. Lessons learned and optimizations leading to the current pipeline are discussed. The project name implies a target of 100 species, but the efficiencies gained during the project have supported an expansion of the original goal and a total of 158 species are currently in the pipeline. We anticipate that the processes described in the paper will help other arthropod research groups or other consortia considering genome assembly at scale.</p>',
			'date' => '2021-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34357286',
			'doi' => '10.3390/insects12070626',
			'modified' => '2022-08-03 16:18:33',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 35 => array(
			'id' => '4311',
			'name' => 'The American lobster genome reveals insights on longevity, neural, andimmune adaptations.',
			'authors' => 'Polinski J. M. et al. ',
			'description' => '<p>The American lobster, , is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we report a high-quality draft assembly of the genome with 25,284 predicted gene models. Analysis of the neural gene complement revealed extraordinary development of the chemosensory machinery, including a profound diversification of ligand-gated ion channels and secretory molecules. The discovery of a novel class of chimeric receptors coupling pattern recognition and neurotransmitter binding suggests a deep integration between the neural and immune systems. A robust repertoire of genes involved in innate immunity, genome stability, cell survival, chemical defense, and cuticle formation represents a diversity of defense mechanisms essential to thrive in the benthic marine environment. Together, these unique evolutionary adaptations contribute to the longevity and ecological success of this long-lived benthic predator.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34162536',
			'doi' => '10.1126/sciadv.abe8290',
			'modified' => '2022-08-03 16:19:34',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => array(
			'id' => '4316',
			'name' => 'Analysis of the Coptis chinensis genome reveals the diversification ofprotoberberine-type alkaloids.',
			'authors' => 'Liu Y. et al. ',
			'description' => '<p>Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotation of C. chinensis. Phylogenetic and comparative genomic analyses reveal the phylogenetic placement of this species and identify a single round of ancient whole-genome duplication (WGD) shared by the Ranunculaceae. We characterize genes involved in the biosynthesis of protoberberine-type alkaloids in C. chinensis. In particular, local genomic tandem duplications contribute to member amplification of a Ranunculales clade-specific gene family of the cytochrome P450 (CYP) 719. The functional versatility of a key CYP719 gene that encodes the (S)-canadine synthase enzyme involved in the berberine biosynthesis pathway may play critical roles in the diversification of other berberine-related alkaloids in C. chinensis. Our study provides insights into the genomic landscape of early-diverging eudicots and provides a valuable model genome for genetic and applied studies of Ranunculales.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/34078898',
			'doi' => '10.1038/s41467-021-23611-0',
			'modified' => '2022-08-03 16:20:31',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 37 => array(
			'id' => '4348',
			'name' => 'Infectivity assessment of porcine endogenous retrovirus usinghigh-throughput sequencing technologies.',
			'authors' => 'Kono K. et al.',
			'description' => '<p>Xenogenic cell-based therapeutic products are expected to alleviate the chronic shortage of human donor organs. For example, porcine islet cell products are currently under development for the treatment of human diabetes. As porcine cells possess endogenous retrovirus (PERV), which can replicate in human cells in vitro, the potential transmission of PERV has raised concerns in the case of products that use living pig cells as raw materials. Although several PERV sequences exist in the porcine genome, not all have the ability to infect human cells. Therefore, polymerase chain reaction analysis, which amplifies a portion of the target gene, may not accurately assess the infection risk. Here, we determined porcine genome sequences and evaluated the infectivity of PERVs using high-throughput sequencing technologies. RNA sequencing was performed on both PERV-infected human cells and porcine cells, and reads mapped to PERV sequences were examined. The normalized number of the reads mapped to PERV regions was able to predict the infectivity of PERVs, indicating that it would be useful for evaluation of the PERV infection risk prior to transplantation of porcine products.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.biologicals.2021.05.001',
			'doi' => '10.1016/j.biologicals.2021.05.001',
			'modified' => '2022-08-03 16:57:04',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 38 => array(
			'id' => '4128',
			'name' => 'Chromosomal inversion polymorphisms in two sympatric ascidian lineages.',
			'authors' => 'Satou, Yutaka and Sato, Atsuko and Yasuo, Hitoyoshi and Mihirogi, Yukie andBishop, John and Fujie, Manabu and Kawamitsu, Mayumi and Hisata, Kanako andSatoh, Noriyuki',
			'description' => '<p>Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential cause for chromosomal speciation. There are two closely related, partially sympatric lineages of ascidians in the genus Ciona, which we call type-A and type-B animals in the present study. While these invertebrate chordates are largely isolated reproductively, hybrids can be found in wild populations, suggesting incomplete prezygotic barriers. Although the genome of type-A animals has been decoded and widely used, the genome for type-B animals has not been decoded at the chromosomal level. In the present study, we sequenced the genomes of two type-B individuals from different sides of the English Channel (in the zone of sympatry with type-A individuals) and compared them at the chromosomal level with the type-A genome. While the overall structures were well conserved between type A and type B, chromosomal alignments revealed many inversions differentiating these two types of Ciona; it is probable that the frequent inversions have contributed to separation between these two lineages. In addition, comparisons of the genomes between the two type-B individuals revealed that type B had high rates of inversion polymorphisms and nucleotide polymorphisms, and thus type B might be in the process of differentiation into multiple new types or species. Our results suggest an important role of inversions in chromosomal speciation of these broadcasting spawners.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33822040',
			'doi' => '10.1093/gbe/evab068',
			'modified' => '2021-12-07 10:17:37',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4186',
			'name' => 'Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.',
			'authors' => 'Formenti G. et al.',
			'description' => '<p>BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (&gt;&thinsp;10&nbsp;kbp, PacBio or Nanopore) and short (100-300&thinsp;bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33910595',
			'doi' => '10.1186/s13059-021-02336-9',
			'modified' => '2022-01-05 15:01:11',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => array(
			'id' => '4140',
			'name' => 'Chromosomal rearrangements but no change of genes and transposable elementsrepertoires in an invasive forest-pathogenic fungus',
			'authors' => 'Demené, A. et al.',
			'description' => '<p>Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adapt to new environments. Cryphonectria parasitica, causing the Chestnut blight disease, is an invasive fungal pathogen species associated with several recent host shifts during its successive introductions from Asia to North America and Europe. Previous cytological karyotyping and genomic studies suggested several chromosomal rearrangements which remains to be described in details for this species. A serious limitation for valid genome comparisons is the access to robust genome assemblies that usually contain genomic regions of low complexity. We present a new de-novo whole-genome assembly obtained from a high quality DNA extraction and long-reads sequencing Nanopore technology obtained from an isolate sampled in the native Japanese area of the species. The comparison with a recently published reference genome showed no significant variations in gene and transposable elements (TEs) repertoires. We also showed that C. parasitica genome is lowly compartmentalized, with a poor association between TEs and some specific genes, such as those potentially involved in host interactions (i.e. genes coding for small secreted proteins or for secondary metabolites). This genome comparison, however, detected several large chromosomal rearrangements that may have important consequences in gene regulations and sexual mating in this invasive species. This study opens the way for more comparisons of high quality assembled genomes, and question the role of structural variations on the invasive success of this fungal pathogen species.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://doi.org/10.1101%2F2021.03.09.434572',
			'doi' => '10.1101/2021.03.09.434572',
			'modified' => '2021-12-13 09:19:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 41 => array(
			'id' => '4191',
			'name' => 'A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.',
			'authors' => 'Liu H. et al. ',
			'description' => '<p>Avian egg coloration is shaped by natural selection, but its genetic basis remains unclear. Here, we used genome-wide association analysis and identity by descent to finely map green egg colour to a 179-kb region of Chr4 based on the resequencing of 352 ducks (Anas platyrhynchos) from a segregating population resulting from the mating of Pekin ducks (white-shelled eggs) and mallards (green-shelled eggs). We further narrowed the candidate region to a 30-kb interval by comparing genome divergence in seven indigenous duck populations. Among the genes located in the finely mapped region, only one transcript of the ABCG2 gene (XM_013093252.2) exhibited higher uterine expression in green-shelled individuals than in white-shelled individuals, as supported by transcriptome data from four populations. ABCG2 has been reported to encode a protein that functions as a membrane transporter for biliverdin. Sanger sequencing of the whole 30-kb candidate region (Chr4: 47.41-47.44&nbsp;Mb) and a plasmid reporter assay helped to identify a single nucleotide polymorphism (Chr4: 47,418,074 G&gt;A) located in a conserved predicted promoter region whose variation may alter ABCG2 transcription activity. We provide a useful molecular marker for duck breeding and contribute data to the research on ecological evolution based on egg colour patterns among birds.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33372351',
			'doi' => '10.1111/mec.15785',
			'modified' => '2022-01-05 15:13:30',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => array(
			'id' => '4131',
			'name' => 'Genomic Characterization of VIM and MCR Co-Producers: The First TwoClinical Cases, in Italy.',
			'authors' => 'Marchetti, Vittoria Mattioni and Bitar, Ibrahim and Sarti, Mario andFogato, Elena and Scaltriti, Erika and Bracchi, Chiara and Hrabak, Jaroslavand Pongolini, Stefano and Migliavacca, Roberta',
			'description' => '<p>BACKGROUND: the co-production of carbapenemases and -genes represents a worrisome event in the treatment of infections. The aim of the study was to characterize the genomic features of two clinical complex (ECC) isolates, co-producing VIM and MCR enzymes, in Italy. METHODS: species identification and antibiotic susceptibility profiling were performed using MALDI-TOF and broth microdilution methods, respectively. Transferability of the and - type genes was verified through conjugation experiment. Extracted DNA was sequenced using long reads sequencing technology on the Sequel I platform (PacBio). RESULTS: the first isolate showed clinical resistance against ertapenem yet was colistin susceptible (EUCAST 2020 breakpoints). The gene was harbored on a conjugative IncHI2 plasmid, while the determinant was harbored on a conjugative IncN plasmid. The second isolate, resistant to both carbapenems and colistin, harbored: gene and its two component regulatory genes for increased expression on the chromosome, on non-conjugative (yet co-transferable) ColE plasmid, and on a non-conjugative IncA plasmid. CONCLUSIONS: to our knowledge, this is the first report of co-production of VIM and MCR in ECC isolates in Italy.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33418979',
			'doi' => '10.3390/diagnostics11010079',
			'modified' => '2021-12-07 10:22:20',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 43 => array(
			'id' => '4190',
			'name' => 'Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).',
			'authors' => 'Xia Z. et al.',
			'description' => '<p>Passion fruit (Passiflora edulis Sims) is an economically valuable fruit that is cultivated in tropical and subtropical regions of the world. Here, we report an ~1341.7&thinsp;Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~1327.18&thinsp;Mb) of the assembly assigned to nine pseudochromosomes. The genome includes 23,171 protein-coding genes, and most of the assembled sequences are repetitive sequences, with long-terminal repeats (LTRs) being the most abundant. Phylogenetic analysis revealed that passion fruit diverged after Brassicaceae and before Euphorbiaceae. Ks analysis showed that two whole-genome duplication events occurred in passion fruit at 65 MYA and 12 MYA, which may have contributed to its large genome size. An integrated analysis of genomic, transcriptomic, and metabolomic data showed that 'alpha-linolenic acid metabolism', 'metabolic pathways', and 'secondary metabolic pathways' were the main pathways involved in the synthesis of important volatile organic compounds (VOCs) in passion fruit, and this analysis identified some candidate genes, including GDP-fucose Transporter 1-like, Tetratricopeptide repeat protein 33, protein NETWORKED 4B isoform X1, and Golgin Subfamily A member 6-like protein 22. In addition, we identified 13 important gene families in fatty acid pathways and eight important gene families in terpene pathways. Gene family analysis showed that the ACX, ADH, ALDH, and HPL gene families, especially ACX13/14/15/20, ADH13/26/33, ALDH1/4/21, and HPL4/6, were the key genes for ester synthesis, while the TPS gene family, especially PeTPS2/3/4/24, was the key gene family for terpene synthesis. This work provides insights into genome evolution and flavor trait biology and offers valuable resources for the improved cultivation of passion fruit.</p>',
			'date' => '2021-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33419990',
			'doi' => '10.1038/s41438-020-00455-1',
			'modified' => '2022-01-05 15:12:13',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 44 => array(
			'id' => '4205',
			'name' => 'Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.',
			'authors' => 'Suzuki Y. et al.',
			'description' => '<p>Our understanding of centromere sequence variation across human populations is limited by its extremely long nested repeat structures called higher-order repeats that are challenging to sequence. Here, we analyzed chromosomes 11, 17, and X using long-read sequencing data for 36 individuals from diverse populations including a Han Chinese trio and 21 Japanese. We revealed substantial structural diversity with many previously unidentified variant higher-order repeats specific to individuals characterizing rapid, haplotype-specific evolution of human centromeric arrays, while frequent single-nucleotide variants are largely conserved. We found a characteristic pattern shared among prevalent variants in human and chimpanzee. Our findings pave the way for studying sequence evolution in human and primate centromeres.</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33310858',
			'doi' => '10.1126/sciadv.abd9230',
			'modified' => '2022-01-06 15:00:50',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 45 => array(
			'id' => '4212',
			'name' => 'Efficient hybrid de novo assembly of human genomes with WENGAN.',
			'authors' => 'Di Genova A. et al. ',
			'description' => '<p>Generating accurate genome assemblies of large, repeat-rich human genomes has proved difficult using only long, error-prone reads, and most human genomes assembled from long reads add accurate short reads to polish the consensus sequence. Here we report an algorithm for hybrid assembly, WENGAN, that provides very high quality at low computational cost. We demonstrate de novo assembly of four human genomes using a combination of sequencing data generated on ONT PromethION, PacBio Sequel, Illumina and MGI technology. WENGAN implements efficient algorithms to improve assembly contiguity as well as consensus quality. The resulting genome assemblies have high contiguity (contig NG50: 17.24-80.64&thinsp;Mb), few assembly errors (contig NGA50: 11.8-59.59&thinsp;Mb), good consensus quality (QV: 27.84-42.88) and high gene completeness (BUSCO complete: 94.6-95.2\%), while consuming low computational resources (CPU hours: 187-1,200). In particular, the WENGAN assembly of the haploid CHM13 sample achieved a contig NG50 of 80.64&thinsp;Mb (NGA50: 59.59&thinsp;Mb), which surpasses the contiguity of the current human reference genome (GRCh38 contig NG50: 57.88&thinsp;Mb).</p>',
			'date' => '2020-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33318652',
			'doi' => '10.1038/s41587-020-00747-w',
			'modified' => '2022-01-13 15:09:21',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 46 => array(
			'id' => '4000',
			'name' => 'Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.',
			'authors' => 'von der Heyde B, Emmanouilidou A, Mazzaferro E, Vicenzi S, Höijer I, Klingström T, Jumaa S, Dethlefsen O, Snieder H, de Geus E, Ameur A, Ingelsson E, Allalou A, Brooke HL, den Hoed M',
			'description' => '<p>A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline to systematically characterize candidate genes for HRV in live zebrafish embryos. Nine zebrafish orthologues of six human candidate genes were targeted simultaneously in eggs from fish that transgenically express GFP on smooth muscle cells (Tg[acta2:GFP]), to visualize the beating heart. An automated analysis of repeated 30&nbsp;s recordings of beating atria in 381 live, intact zebrafish embryos at 2 and 5&nbsp;days post-fertilization highlighted genes that influence HRV (hcn4 and si:dkey-65j6.2 [KIAA1755]); heart rate (rgs6 and hcn4); and the risk of sinoatrial pauses and arrests (hcn4). Exposure to 10 or 25&nbsp;&micro;M ivabradine-an open channel blocker of HCNs-for 24&nbsp;h resulted in a dose-dependent higher HRV and lower heart rate at 5&nbsp;days post-fertilization. Hence, our screen confirmed the role of established genes for heart rate and rhythm (RGS6 and HCN4); showed that ivabradine reduces heart rate and increases HRV in zebrafish embryos, as it does in humans; and highlighted a novel gene that plays a role in HRV (KIAA1755).</p>',
			'date' => '2020-07-16',
			'pmid' => 'http://www.pubmed.gov/32678143',
			'doi' => '10.1038/s41598-020-68567-1',
			'modified' => '2020-09-01 14:40:20',
			'created' => '2020-08-21 16:41:39',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4016',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69Escherichia coli Strain in Italy',
			'authors' => 'Mattioni, Marchetti Vittoria and Bitar, Ibrahim and Piazza, Aurora andMercato, Alessandra and Fogato, Elena and Hrabak, Jaroslav and Migliavacca,Roberta',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-15',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2020-12-16 17:36:09',
			'created' => '2020-10-12 14:54:59',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4359',
			'name' => 'Genomic Insight of VIM-harboring IncA Plasmid from a ClinicalST69 Escherichia coli Strain in Italy',
			'authors' => 'Mattioni MV et al. ',
			'description' => '<p>Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 Escherichia coli strain from an Italian Long-Term Care Facility (LTCF) inpatient. Methods: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the blaVIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using &ldquo;Microbial Assembly&rdquo;. Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. Results: Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (aac(6&prime;)-Ib4, ant(3&Prime;)-Ia, aph(3&Prime;)-Ib, aph(3&prime;)-XV, aph(6)-Id), beta-lactam resistance (blaSHV-12, blaVIM-1), macrolides resistance (mph(A)), phenicol resistance (catB2), quinolones resistance (qnrS1), sulphonamide resistance (sul1, sul2), and trimethoprim resistance (dfrA14), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. Conclusions: The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the blaVIM-1 gene in Italy.</p>',
			'date' => '2020-07-01',
			'pmid' => 'https://www.mdpi.com/2076-2607/8/8/1232/htm',
			'doi' => '10.3390/microorganisms8081232',
			'modified' => '2022-08-03 17:12:43',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '3974',
			'name' => 'Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.',
			'authors' => 'Oulghazi S, Moumni M, Khayi S, Robic K, Sarfraz S, Lopez-Roques C, Vandecasteele C, Faure D',
			'description' => '<p>Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato fields recently. To this end, samplings were conducted in three major potato growing areas over a three-year period (2015-2017). Pathogens were characterized by sequence determination of both the gene marker and genomes using Illumina and Oxford Nanopore technologies. We isolated 119 pathogens belonging to (19%), (3%), (5%), (56%) and (17%). Their taxonomic assignation was confirmed by draft genome analyses of 10 representative strains of the collected species. were isolated from a unique area where a wide species diversity of pectinolytic pathogens was observed. In tuber rotting assays, isolates were more aggressive than Pectobacterium isolates. The complete genome sequence of LAR.16.03.LID was obtained and compared with other genomes from public databases. Overall, this study highlighted the ecological context from which some Dickeya and Pectobacterium species emerged in Morocco, and reported the first complete genome of a strain isolated in Morocco that will be suitable for further epidemiological studies.</p>',
			'date' => '2020-06-13',
			'pmid' => 'http://www.pubmed.gov/32545839',
			'doi' => '10.3390/microorganisms8060895',
			'modified' => '2020-08-12 09:28:31',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '3972',
			'name' => 'Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.',
			'authors' => 'Alonge M, Wang X, Benoit M, Soyk S, Pereira L, Zhang L, Suresh H, Ramakrishnan S, Maumus F, Ciren D, Levy Y, Harel TH, Shalev-Schlosser G, Amsellem Z, Razifard H, Caicedo AL, Tieman DM, Klee H, Kirsche M, Aganezov S, Ranallo-Benavidez TR, Lemmon ZH, Kim J',
			'description' => '<p>Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in 100 diverse tomato lines. This panSV genome, along with 14 new reference assemblies, revealed large-scale intermixing of diverse genotypes, as well as thousands of SVs intersecting genes and cis-regulatory regions. Hundreds of SV-gene pairs exhibit subtle and significant expression changes, which could broadly influence quantitative trait variation. By combining quantitative genetics with genome editing, we show how multiple SVs that changed gene dosage and expression levels modified fruit flavor, size, and production. In the last example, higher order epistasis among four SVs affecting three related transcription factors allowed introduction of an important harvesting trait in modern tomato. Our findings highlight the underexplored role of SVs in genotype-to-phenotype relationships and their widespread importance and utility in crop improvement.</p>',
			'date' => '2020-06-08',
			'pmid' => 'http://www.pubmed.gov/32553272',
			'doi' => '10.1016/j.cell.2020.05.021',
			'modified' => '2020-08-12 09:27:28',
			'created' => '2020-08-10 12:12:25',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 51 => array(
			'id' => '3869',
			'name' => 'Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.',
			'authors' => 'Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J',
			'description' => '<p>Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the&nbsp;evolutionary trajectory and functional distribution&nbsp;of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S.&nbsp;epidermidis genomes from 5 healthy individuals, we found that skin S.&nbsp;epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.</p>',
			'date' => '2020-02-06',
			'pmid' => 'http://www.pubmed.gov/32004459',
			'doi' => '10.1016/j.cell.2020.01.006',
			'modified' => '2020-03-20 17:45:40',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 52 => array(
			'id' => '4247',
			'name' => 'LongQC: A Quality Control Tool for Third GenerationSequencing Long Read Data',
			'authors' => 'Fukasawa Yoshinori et al.',
			'description' => '<p>We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key statistics were optimized for long read data, and LongQC covers all major TGS platforms. LongQC processes and visualizes those statistics automatically and quickly.</p>',
			'date' => '2020-02-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32041730',
			'doi' => '10.1534/g3.119.400864',
			'modified' => '2022-05-24 09:03:08',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 53 => array(
			'id' => '3863',
			'name' => 'Genome Sequence of  sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.',
			'authors' => 'Anton BP, DasSarma P, Martinez FL, DasSarma SL, Al Madadha M, Roberts RJ, DasSarma S',
			'description' => '<p>An extremely halophilic archaeon, sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorporated into HaloWeb (https://halo.umbc.edu/).</p>',
			'date' => '2020-01-30',
			'pmid' => 'http://www.pubmed.gov/32001568',
			'doi' => '10.1128/MRA.01505-19.',
			'modified' => '2020-03-20 17:52:34',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 54 => array(
			'id' => '3864',
			'name' => 'The round goby genome provides insights into mechanisms that may facilitate biological invasions.',
			'authors' => 'Adrian-Kalchhauser I, Blomberg A, Larsson T, Musilova Z, Peart CR, Pippel M, Solbakken MH, Suurväli J, Walser JC, Wilson JY, Alm Rosenblad M, Burguera D, Gutnik S, Michiels N, Töpel M, Pankov K, Schloissnig S, Winkler S',
			'description' => '<p>BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales and present promising case studies to understand factors involved the impressive ability of some species to colonize novel environments. We seize the unique opportunity presented by the round goby invasion to study genomic substrates potentially involved in colonization success. RESULTS: We report a highly contiguous long-read-based genome and analyze gene families that we hypothesize to relate to the ability of these fish to deal with novel environments. The analyses provide novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns of epigenetic regulators, and the presence of osmoregulatory genes that may have contributed to the round goby's capacity to invade cold and salty waters. A recurring theme across all analyzed gene families is gene expansions. CONCLUSIONS: The expanded innate immune system of round goby may potentially contribute to its ability to colonize novel areas. Since other gene families also feature copy number expansions in the round goby, and since other Gobiidae also feature fascinating environmental adaptations and are excellent colonizers, further long-read genome approaches across the goby family may reveal whether gene copy number expansions are more generally related to the ability to conquer new habitats in Gobiidae or in fish.</p>',
			'date' => '2020-01-28',
			'pmid' => 'http://www.pubmed.gov/31992286',
			'doi' => '10.1186/s12915-019-0731-8',
			'modified' => '2020-03-20 17:51:48',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 55 => array(
			'id' => '3857',
			'name' => 'The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.',
			'authors' => 'Kan SL, Shen TT, Gong P, Ran JH, Wang XQ',
			'description' => '<p>BACKGROUND: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. RESULTS: Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. CONCLUSIONS: We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.</p>',
			'date' => '2020-01-20',
			'pmid' => 'http://www.pubmed.gov/31959109',
			'doi' => '10.1186/s12862-020-1582-1',
			'modified' => '2020-03-20 17:57:35',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 56 => array(
			'id' => '3858',
			'name' => 'A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).',
			'authors' => 'Pippel M, Jebb D, Patzold F, Winkler S, Vogel H, Myers G, Hiller M, Hundsdoerfer AK',
			'description' => '<p>BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged &sim;7.5 million years ago, making this rather young genus an interesting system to study a wide range of questions including the process of speciation, ecological adaptation, and adaptive radiation. RESULTS: Here we present a high-quality genome assembly of the bat hawkmoth Hyles vespertilio, the first reference genome of a member of the Hyles genus. We generated 51&times; Pacific Biosciences long reads with an average read length of 8.9&nbsp;kb. Pacific Biosciences reads longer than 4&nbsp;kb were assembled into contigs, resulting in a 651.4-Mb assembly consisting of 530 contigs with an N50 value of 7.5 Mb. The circular mitochondrial contig has a length of 15,303 bp. The H. vespertilio genome is very repeat-rich and exhibits a higher repeat content (50.3%) than other Bombycoidea species such as Bombyx mori (45.7%) and Manduca sexta (27.5%). We developed a comprehensive gene annotation workflow to obtain consensus gene models from different evidence including gene projections, protein homology, transcriptome data, and ab initio predictions. The resulting gene annotation is highly complete with 94.5% of BUSCO genes being completely present, which is higher than the BUSCO completeness of the B. mori (92.2%) and M. sexta (90%) annotations. CONCLUSIONS: Our gene annotation strategy has general applicability to other genomes, and the H. vespertilio genome provides a valuable molecular resource to study a range of questions in this genus, including phylogeny, incomplete lineage sorting, speciation, and hybridization. A genome browser displaying the genome, alignments, and annotations is available at https://genome-public.pks.mpg.de/cgi-bin/hgTracks?db=HLhylVes1.</p>',
			'date' => '2020-01-08',
			'pmid' => 'http://www.pubmed.gov/31972020',
			'doi' => '10.1093/gigascience/giaa001',
			'modified' => '2020-03-20 17:56:37',
			'created' => '2020-03-13 13:45:54',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 57 => array(
			'id' => '3823',
			'name' => 'Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of .',
			'authors' => 'Hovde BT, Daligault HE, Hanschen ER, Kunde YA, Johnson MB, Starkenburg SR, Johnson SL',
			'description' => '<p>The sequenced genome and the leaf transcriptome of a near relative of and was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that contain genes with abrin-like, pulchellin-like, and agglutinin-like homology, with full-length transcripts detected in leaf tissue for 9 of the 26 coding regions. All of the toxin-like genes were identified within only five isolated regions of the genome, with each region containing 1 to 16 gene variants within each genomic region (&lt;1 mbp) the cultivar sequenced here contains genes which encode for proteins that are homologous to certain abrin and prepropulchellin genes previously identified and we observed substantial diversity of genes and predicted gene products in and previously characterized toxins this suggests diverse toxin repertoires within potentially the results of rapid toxin evolution.</p>',
			'date' => '2019-11-25',
			'pmid' => 'http://www.pubmed.gov/31775284',
			'doi' => '10.3390/toxins11120691',
			'modified' => '2020-02-25 14:47:48',
			'created' => '2020-02-13 10:02:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 58 => array(
			'id' => '3813',
			'name' => 'NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.',
			'authors' => 'De Roeck A, De Coster W, Bossaerts L, Cacace R, De Pooter T, Van Dongen J, D'Hert S, De Rijk P, Strazisar M, Van Broeckhoven C, Sleegers K',
			'description' => '<p>Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30&times; human genome coverage and enables accurate assessment of tandem repeats including the 10,000-bp Alzheimer's disease-associated ABCA7 VNTR. The Guppy "flip-flop" base caller and tandem-genotypes tandem repeat caller are efficient for large-scale tandem repeat assessment, but base calling and alignment challenges persist. We present NanoSatellite, which analyzes tandem repeats directly on electric current data and improves calling of GC-rich tandem repeats, expanded alleles, and motif interruptions.</p>',
			'date' => '2019-11-14',
			'pmid' => 'http://www.pubmed.gov/31727106',
			'doi' => '10.1186/s13059-019-1856-3',
			'modified' => '2019-12-05 10:59:42',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 59 => array(
			'id' => '3791',
			'name' => 'Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull.',
			'authors' => 'Young AE, Mansour TA, McNabb BR, Owen JR, Trott JF, Brown CT, Van Eenennaam AL',
			'description' => '<p>Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P Celtic POLLED allele, with horned cows (pp) and obtained six heterozygous (Pp) polled calves. The calves had no horns and were otherwise healthy and phenotypically unremarkable. We conducted whole-genome sequencing of all animals using an Illumina HiSeq4000 to achieve ~20&times; coverage. Bioinformatics analyses revealed the bull was a compound heterozygote, carrying one naturally occurring P Celtic POLLED allele and an allele containing an additional introgression of the homology-directed repair donor plasmid along with the P Celtic allele. These alleles segregated in the offspring of this bull, and inheritance of either allele produced polled calves. No other unintended genomic alterations were observed. These data can be used to inform conversations in the scientific community, with regulatory authorities and with the public around 'intentional genomic alterations' and future regulatory actions regarding genome-edited animals.</p>',
			'date' => '2019-10-07',
			'pmid' => 'http://www.pubmed.gov/31591551',
			'doi' => '10.1038/s41587-019-0266-0',
			'modified' => '2019-12-05 11:47:39',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 60 => array(
			'id' => '3788',
			'name' => 'Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef.',
			'authors' => 'Sekizuka T, Lee K, Kimata K, Isobe J, Kuroda M, Iyoda S, Ohnishi M, Sata T, Watahiki M',
			'description' => '<p>We present the complete genome sequence of an enterohemorrhagic O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.</p>',
			'date' => '2019-10-03',
			'pmid' => 'http://www.pubmed.gov/31582455',
			'doi' => '10.1128/MRA.00882-19.',
			'modified' => '2019-12-05 11:58:13',
			'created' => '2019-12-02 15:25:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 61 => array(
			'id' => '3772',
			'name' => 'Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions.',
			'authors' => 'Zhang S, Liang F, Lei C, Wu J, Fu J, Yang Q, Luo X, Yu G, Wang D, Zhang Y, Lu D, Sun X, Liang Y, Xu C',
			'description' => '<p>BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos that carry balanced inversion from those with a normal karyotype. We aim to evaluate the use of long-read sequencing in combination with haplotype linkage analysis to address this challenge. METHODS: Long-read sequencing on Oxford Nanopore platform was employed to identify the precise positions of inversion break points in four patients. Comprehensive chromosomal screening and genome-wide haplotype linkage analysis were performed based on SNP microarray. The haplotypes, including the break point regions, the whole chromosomes involved in the inversion and the corresponding homologous chromosomes, were established using informative SNPs. RESULTS: All the inversion break points were successfully identified by long-read sequencing and validated by Sanger sequencing, and on average only 13 bp differences were observed between break points inferred by long-read sequencing and Sanger sequencing. Eighteen blastocysts were biopsied and tested, in which 10 were aneuploid or unbalanced and eight were diploid with normal or balanced inversion karyotypes. Diploid embryos were transferred back to patients, the predictive results of the current methodology were consistent with fetal karyotypes of amniotic fluid or cord blood. CONCLUSIONS: Nanopore long-read sequencing is a powerful method to assay chromosomal inversions and identify exact break points. Identification of inversion break points combined with haplotype linkage analysis is an efficient strategy to distinguish embryos with normal or balanced inversion karyotypes, facilitating PGT applications.</p>',
			'date' => '2019-08-22',
			'pmid' => 'http://www.pubmed.gov/31439719',
			'doi' => '10.1136/jmedgenet-2018-105976',
			'modified' => '2019-10-02 17:08:37',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 62 => array(
			'id' => '3760',
			'name' => 'Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.',
			'authors' => 'Wenger AM, Peluso P, Rowell WJ, Chang PC, Hall RJ, Concepcion GT, Ebler J, Fungtammasan A, Kolesnikov A, Olson ND, Töpfer A, Alonge M, Mahmoud M, Qian Y, Chin CS, Phillippy AM, Schatz MC, Myers G, DePristo MA, Ruan J, Marschall T, Sedlazeck FJ, Zook JM, L',
			'description' => '<p>The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequencing (PacBio) and generate highly accurate (99.8%) long high-fidelity (HiFi) reads with an average length of 13.5&thinsp;kilobases (kb). We applied our approach to sequence the well-characterized human HG002/NA24385 genome and obtained precision and recall rates of at least 99.91% for single-nucleotide variants (SNVs), 95.98% for insertions and deletions &lt;50 bp (indels) and 95.99% for structural variants. Our CCS method matches or exceeds the ability of short-read sequencing to detect small variants and structural variants. We estimate that 2,434 discordances are correctable mistakes in the 'genome in a bottle' (GIAB) benchmark set. Nearly all (99.64%) variants can be phased into haplotypes, further improving variant detection. De novo genome assembly using CCS reads alone produced a contiguous and accurate genome with a contig N50 of &gt;15&thinsp;megabases (Mb) and concordance of 99.997%, substantially outperforming assembly with less-accurate long reads.<br /><!--50--></p>',
			'date' => '2019-08-12',
			'pmid' => 'http://www.pubmed.gov/31406327',
			'doi' => '10.1038/s41587-019-0217-9',
			'modified' => '2019-10-03 10:05:13',
			'created' => '2019-10-02 16:16:55',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 63 => array(
			'id' => '3749',
			'name' => 'Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.',
			'authors' => 'Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC',
			'description' => '<p>BACKGROUND: Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS: By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS: We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.</p>',
			'date' => '2019-07-08',
			'pmid' => 'http://www.pubmed.gov/31286858',
			'doi' => '10.1186/s12864-019-5909-5',
			'modified' => '2019-08-06 16:06:34',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 64 => array(
			'id' => '3721',
			'name' => 'Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.',
			'authors' => 'Somerville V, Lutz S, Schmid M, Frei D, Moser A, Irmler S, Frey JE, Ahrens CH',
			'description' => '<p>BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial strain is in most cases straightforward, more informative data about co-existing bacteria as well as synergistic and antagonistic effects can be obtained from a direct analysis of microbial communities. However, the complexity of metagenomic samples represents a major challenge. While third generation sequencing technologies have been suggested to enable finished metagenome-assembled genomes, to our knowledge, the complete genome assembly of all dominant strains in a microbiome sample has not been demonstrated. Natural whey starter cultures (NWCs) are used in cheese production and represent low-complexity microbiomes. Previous studies of Swiss Gruy&egrave;re and selected Italian hard cheeses, mostly based on amplicon metagenomics, concurred that three species generally pre-dominate: Streptococcus thermophilus, Lactobacillus helveticus and Lactobacillus delbrueckii. RESULTS: Two NWCs from Swiss Gruy&egrave;re producers were subjected to whole metagenome shotgun sequencing using the Pacific Biosciences Sequel and Illumina MiSeq platforms. In addition, longer Oxford Nanopore Technologies MinION reads had to be generated for one to resolve repeat regions. Thereby, we achieved the complete assembly of all dominant bacterial genomes from these low-complexity NWCs, which was corroborated by a 16S rRNA amplicon survey. Moreover, two distinct L. helveticus strains were successfully co-assembled from the same sample. Besides bacterial chromosomes, we could also assemble several bacterial plasmids and phages and a corresponding prophage. Biologically relevant insights were uncovered by linking the plasmids and phages to their respective host genomes using DNA methylation motifs on the plasmids and by matching prokaryotic CRISPR spacers with the corresponding protospacers on the phages. These results could only be achieved by employing long-read sequencing data able to span intragenomic as well as intergenomic repeats. CONCLUSIONS: Here, we demonstrate the feasibility of complete de novo genome assembly of all dominant strains from low-complexity NWCs based on whole metagenomics shotgun sequencing data. This allowed to gain novel biological insights and is a fundamental basis for subsequent systems-wide omics analyses, functional profiling and phenotype to genotype analysis of specific microbial communities.</p>',
			'date' => '2019-06-25',
			'pmid' => 'http://www.pubmed.gov/31238873',
			'doi' => '10.1186/s12866-019-1500-0',
			'modified' => '2019-07-04 18:06:26',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 65 => array(
			'id' => '3712',
			'name' => 'A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).',
			'authors' => 'Li Q, Li H, Huang W, Xu Y, Zhou Q, Wang S, Ruan J, Huang S, Zhang Z',
			'description' => '<p>BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-coverage short Illumina sequences have been used to assemble draft cucumber genomes, but the incompleteness and low quality of these genomes limit their use in comparative genomics and genetic research. A high-quality and complete cucumber genome assembly is therefore essential. FINDINGS: We assembled single-molecule real-time (SMRT) long reads to generate an improved cucumber reference genome. This version contains 174 contigs with a total length of 226.2 Mb and an N50 of 8.9 Mb, and provides 29.0 Mb more sequence data than previous versions. Using 10X Genomics and high-throughput chromosome conformation capture (Hi-C) data, 89 contigs (&sim;211.0 Mb) were directly linked into 7 pseudo-chromosome sequences. The newly assembled regions show much higher guanine-cytosine or adenine-thymine content than found previously, which is likely to have been inaccessible to Illumina sequencing. The new assembly contains 1,374 full-length long terminal retrotransposons and 1,078 novel genes including 239 tandemly duplicated genes. For example, we found 4 tandemly duplicated tyrosylprotein sulfotransferases, in contrast to the single copy of the gene found previously and in most other plants. CONCLUSION: This high-quality genome presents novel features of the cucumber genome and will serve as a valuable resource for genetic research in cucumber and plant comparative genomics.</p>',
			'date' => '2019-06-01',
			'pmid' => 'http://www.pubmed.gov/31216035',
			'doi' => '10.1093/gigascience/giz072',
			'modified' => '2019-07-05 14:29:16',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 66 => array(
			'id' => '3650',
			'name' => 'Genome Sequence and Methylation Patterns of  sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.',
			'authors' => 'Priya DasSarma, Anton BP, DasSarma S, Laye VJ, Guzman D, Roberts RJ, DasSarma S',
			'description' => '<p>sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Database (http://halo.umbc.edu). The polyextremophilic character and high-elevation environment make the microbe of interest for astrobiology.</p>',
			'date' => '2019-05-09',
			'pmid' => 'http://www.pubmed.gov/31072883',
			'doi' => '10.1016/j.gexplo.2004.07.001.',
			'modified' => '2019-06-07 10:11:11',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 67 => array(
			'id' => '3707',
			'name' => 'The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.',
			'authors' => 'Zhao Q, Yang J, Cui MY, Liu J, Fang Y, Yan M, Qiu W, Shang H, Xu Z, Yidiresi R, Weng JK, Pluskal T, Vigouroux M, Steuernagel B, Wei Y, Yang L, Hu Y, Chen XY, Martin C',
			'description' => '<p>Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4'-deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4'-deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo- and subfunctionalizations were involved in the evolution of 4'-deoxyflavone synthesis in the genus&nbsp;Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.</p>',
			'date' => '2019-04-15',
			'pmid' => 'http://www.pubmed.gov/30999079',
			'doi' => '10.1016/j.molp.2019.04.002',
			'modified' => '2019-07-05 14:35:57',
			'created' => '2019-07-04 10:42:34',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 68 => array(
			'id' => '3602',
			'name' => 'Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.',
			'authors' => 'Palmieri V, Dalchiele EA, Perini G, Motta A, De Spirito M, Zanoni R, Marrani AG, Papi M',
			'description' => '<p>We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoids GO-mediated oxidation of glutathione. This method offers new opportunities for the production of green biocompatible rGO and NAC-based therapies.</p>',
			'date' => '2019-03-20',
			'pmid' => 'http://www.pubmed.gov/30892320',
			'doi' => '10.1039/C9CC00429G.',
			'modified' => '2019-04-17 14:56:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 69 => array(
			'id' => '3725',
			'name' => 'The alternative reality of plant mitochondrial DNA',
			'authors' => 'Alexander Kozik, Beth A. Rowan, Dean Lavelle, Lidija Berke, M. Eric Schranz, Richard W. Michelmore, and Alan C. Christensen',
			'description' => '<p>Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondrial genomes have one or more pairs of large repeats that can act as sites for inter- or intramolecular recombination, leading to multiple alternative genomic arrangements (isoforms). Most mitochondrial genomes have been assembled using methods that were unable to capture the complete spectrum of isoforms within a species, leading to an incomplete inference of their structure and recombinational activity. To document and investigate underlying reasons for structural diversity in plant mitochondrial DNA, we used long-read (PacBio) and short-read (Illumina) sequencing data to assemble and compare mitochondrial genomes of domesticated (Lactuca sativa) and wild (L. saligna and L. serriola) lettuce species. This allowed us to characterize a comprehensive, complex set of isoforms within each species and to compare genome structures between species. Physical analysis of L. sativa mtDNA molecules by fluorescence microscopy revealed a variety of linear, branched linear, and circular structures. The mitochondrial genomes for L. sativa and L. serriola were identical in sequence and arrangement, and differed substantially from L. saligna, indicating that the mitochondrial genome structure did not change during domestication. From the isoforms evident in our data, we inferred that recombination occurs at repeats of all sizes at variable frequencies. The differences in genome structure between L. saligna and the two other lettuce species can be largely explained by rare recombination events that rearrange the structure. Our data demonstrate that representations of plant mitochondrial DNA as simple, genome-sized circular molecules are not accurate descriptions of their true nature and that in reality plant mitochondrial DNA is a complex, dynamic mixture of forms.</p>',
			'date' => '2019-03-01',
			'pmid' => 'https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008373',
			'doi' => '10.1101/564278.',
			'modified' => '2022-05-18 18:58:47',
			'created' => '2019-07-31 13:35:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 70 => array(
			'id' => '3615',
			'name' => 'Characterizing the Major Structural Variant Alleles of the Human Genome.',
			'authors' => 'Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE',
			'description' => '<p>In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30661756',
			'doi' => '10.1016/j.cell.2018.12.019',
			'modified' => '2019-04-16 13:55:52',
			'created' => '2019-04-16 12:25:30',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 71 => array(
			'id' => '3645',
			'name' => 'Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.',
			'authors' => 'Martínez FL, Anton BP, DasSarma P, Rajal V, Irazusta V, Roberts RJ, DasSarma S',
			'description' => '<p>Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-time sequencing.</p>',
			'date' => '2019-01-24',
			'pmid' => 'http://www.pubmed.gov/30701250',
			'doi' => '10.1128/MRA',
			'modified' => '2019-06-07 10:15:47',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 72 => array(
			'id' => '3656',
			'name' => 'Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present  tuberculosis vaccine',
			'authors' => 'Katlyn Borgersa,Jheng-Yang Ouc, Po-Xing Zhengc, Petra Tielsa, Annelies Van Heckea, Evelyn Pletsa, Gitte Michielsena, Nele Festjensa, Nico Callewaerta, Yao-Cheng Lin',
			'description' => '<p>Mycobacterium bovis bacillus Calmette-Gu&eacute;rin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence of BCG Danish 1331 (07/270), one of the WHO reference strains for BCG vaccines. We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of this vaccine strain.</p>',
			'date' => '2018-12-26',
			'pmid' => 'https://pubmed.ncbi.nlm.nih.gov/31286858/',
			'doi' => '10.1101/513408.',
			'modified' => '2022-05-18 18:52:29',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 73 => array(
			'id' => '3454',
			'name' => 'SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).',
			'authors' => 'Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N',
			'description' => '<p>Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference genome assembly for the European subspecies (H. r. rustica). Findings: As part of the Genome10K (G10K) effort on generating high quality vertebrate genomes, we have assembled a highly contiguous genome assembly using Single Molecule Real-Time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived both from the Nick, Label, Repair and Stain and from the Direct Label and Stain (DLS) technologies. As proposed by Bionano, the DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of over 25.95 Mbp. Conclusions: This high-quality genome assembly represents a valuable resource for further studies of population genetics and genomics in the barn swallow, and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.</p>',
			'date' => '2018-11-29',
			'pmid' => 'http://www.pubmed.gov/30496513',
			'doi' => '10.1093/gigascience/giy142/5202456',
			'modified' => '2019-02-15 20:35:16',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 74 => array(
			'id' => '3429',
			'name' => 'Improved reference genome of Aedes aegypti informs arbovirus vector control.',
			'authors' => 'Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gl',
			'description' => '<p>Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology&nbsp;of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector.</p>',
			'date' => '2018-11-14',
			'pmid' => 'http://www.pubmed.gov/30429615',
			'doi' => '10.1038/s41586-018-0692-z',
			'modified' => '2018-12-31 11:15:00',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 75 => array(
			'id' => '3413',
			'name' => 'Whole-genome landscape of Medicago truncatula symbiotic genes.',
			'authors' => 'Pecrix Y, Staton SE, Sallet E, Lelandais-Brière C, Moreau S, Carrère S, Blein T, Jardinaud MF, Latrasse D, Zouine M, Zahm M, Kreplak J, Mayjonade B, Satgé C, Perez M, Cauet S, Marande W, Chantry-Darmon C, Lopez-Roques C, Bouchez O, Bérard A, Debellé F, Mu',
			'description' => '<p>Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacBio sequencing has led to a substantially improved genome assembly of Medicago truncatula A17, a legume model species notable for endosymbiosis studies, and has enabled the identification of genome rearrangements between genotypes at a near-base-pair resolution. Annotation of the new M. truncatula genome sequence has allowed for a thorough analysis of transposable elements and their dynamics, as well as the identification of new players involved in symbiotic nodule development, in particular 1,037 upregulated long non-coding RNAs (lncRNAs). We have also discovered that a substantial proportion (~35% and 38%, respectively) of the genes upregulated in nodules or expressed in the nodule differentiation zone colocalize in genomic clusters (270 and 211, respectively), here termed symbiotic islands. These islands contain numerous expressed lncRNA genes and display differentially both DNA methylation and histone marks. Epigenetic regulations and lncRNAs are therefore attractive candidate elements for the orchestration of symbiotic gene expression in the M. truncatula genome.</p>',
			'date' => '2018-11-05',
			'pmid' => 'http://www.pubmed.gov/30397259',
			'doi' => '10.1038/s41477-018-0286-7',
			'modified' => '2018-12-31 11:17:32',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 76 => array(
			'id' => '3517',
			'name' => 'Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.',
			'authors' => 'Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, ',
			'description' => '<p>Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions. However, even though genome assemblies based on long reads exhibit high contig N50s (&gt;1&thinsp;Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of &gt;5&thinsp;Mb and contain scaffolds that represent entire chromosomes or chromosome arms.</p>',
			'date' => '2018-11-02',
			'pmid' => 'http://www.pubmed.gov/30390080',
			'doi' => '10.1038/s41477-018-0289-4',
			'modified' => '2019-02-27 15:41:40',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 77 => array(
			'id' => '3441',
			'name' => 'The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.',
			'authors' => 'Gautier M, Yamaguchi J, Foucaud J, Loiseau A, Ausset A, Facon B, Gschloessl B, Lagnel J, Loire E, Parrinello H, Severac D, Lopez-Roques C, Donnadieu C, Manno M, Berges H, Gharbi K, Lawson-Handley L, Zang LS, Vogel H, Estoup A, Prud'homme B',
			'description' => '<p>Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of dark, i.e., melanic, forms displaying discrete color patterns is&nbsp;found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and red patches on adult elytra varies wildly within species, forming strikingly different complex color patterns [7, 8]. In the harlequin ladybird, Harmonia axyridis, more than 200 distinct color forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus [9, 10]. Here, we combined whole-genome sequencing, population-based genome-wide association studies, gene expression, and functional analyses to establish that the transcription factor Pannier controls melanic pattern polymorphism in H.&nbsp;axyridis. We show that pannier is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra and thus determines the distinct color patterns in H.&nbsp;axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of &sim;170 kb in the cis-regulatory regions of pannier, with a 50 kb inversion between color forms. This most likely helps maintain the distinct alleles found in natural populations. Thus, we propose that&nbsp;highly variable discrete color forms can arise in natural populations through cis-regulatory allelic variation of a single gene.</p>',
			'date' => '2018-10-22',
			'pmid' => 'http://www.pubmed.gov/30146156',
			'doi' => '10.1016/j.cub.2018.08.023',
			'modified' => '2019-02-15 20:42:22',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 78 => array(
			'id' => '3412',
			'name' => 'Long-read sequence capture of the hemoglobin gene clusters across gadid species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the hemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100kb) and MN (~200kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes. This article is protected by copyright. All rights reserved.</p>',
			'date' => '2018-10-17',
			'pmid' => 'http://www.pubmed.org/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2018-12-31 11:19:03',
			'created' => '2018-12-04 09:51:07',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 79 => array(
			'id' => '3399',
			'name' => 'Genomic Structural Variations Within Five Continental Populations of .',
			'authors' => 'Long E, Evans C, Chaston J, Udall JA',
			'description' => '<p>Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations containing genes. Large structural variations represent a significant amount of the genetic diversity within a population. We used a global sampling of (Ithaca, Zimbabwe, Beijing, Tasmania, and Netherlands) to represent diverse populations within the species. We used long-read sequencing and optical mapping technologies to identify SVs in these genomes. Among the five lines examined, we found an average of 2,928 structural variants within these genomes. These structural variations varied greatly in size and location, included many exonic regions, and could impact adaptation and genomic evolution.</p>',
			'date' => '2018-10-03',
			'pmid' => 'http://www.pubmed.gov/30111620',
			'doi' => '10.1534/g3.118.200631',
			'modified' => '2018-11-09 11:49:08',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 80 => array(
			'id' => '3403',
			'name' => 'Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.',
			'authors' => 'Miao H, Zhou J, Yang Q, Liang F, Wang D, Ma N, Gao B, Du J, Lin G, Wang K, Zhang Q',
			'description' => '<p>Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and genetic counseling. One possible reason is the limited ability to detect disease causal structural variants (SVs) from short reads sequencing technologies. Long reads sequencing can produce longer reads (typically 1000&nbsp;bp or longer), therefore offering greatly improved ability to detect SVs that may be missed by short-read sequencing. Results: Here we describe a case study, where WES identified only one heterozygous pathogenic variant for an individual suspected to have glycogen storage disease type Ia (GSD-Ia), which is an autosomal recessive disease caused by bi-allelic mutations in the gene. Through Nanopore long-read whole-genome sequencing, we identified a 7.1&nbsp;kb deletion covering two exons on the other allele, suggesting that complex structural variants (SVs) may explain a fraction of cases when the second pathogenic allele is missing from WES on recessive diseases. Both breakpoints of the deletion are within Alu elements, and we designed Sanger sequencing and quantitative PCR assays based on the breakpoints for preimplantation genetic diagnosis (PGD) for the family planning on another child. Four embryos were obtained after in vitro fertilization (IVF), and an embryo without deletion in was transplanted after PGD and was confirmed by prenatal diagnosis, postnatal diagnosis, and subsequent lack of disease symptoms after birth. Conclusions: In summary, we present one of the first examples of using long-read sequencing to identify causal yet complex SVs in exome-negative patients, which subsequently enabled successful personalized PGD.</p>',
			'date' => '2018-09-28',
			'pmid' => 'http://www.pubmed.gov/30279644',
			'doi' => '10.1186/s41065-018-0069-1',
			'modified' => '2018-11-09 11:27:02',
			'created' => '2018-11-08 12:59:45',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 81 => array(
			'id' => '3525',
			'name' => 'Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.',
			'authors' => 'Ebbert MTW, Farrugia SL, Sens JP, Jansen-West K, Gendron TF, Prudencio M, McLaughlin IJ, Bowman B, Seetin M, DeJesus-Hernandez M, Jackson J, Brown PH, Dickson DW, van Blitterswijk M, Rademakers R, Petrucelli L, Fryer JD',
			'description' => '<p>BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences' (PacBio) and Oxford Nanopore Technologies' (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing GC repeat expansion. We also report the first long-read sequencing data characterizing the C9orf72 GC repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9. RESULTS: Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinION was a challenge for whole-genome sequencing; we were unable to attain reads covering the human C9orf72 repeat expansion using 15 flow cells. We obtained 8&times; coverage across the C9orf72 locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained &gt;&thinsp;800&times; coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual's repeat region was &gt;&thinsp;99% GC content, though we cannot rule out small interruptions. CONCLUSIONS: Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies in C9orf72 expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-GC content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.</p>',
			'date' => '2018-08-21',
			'pmid' => 'http://www.pubmed.gov/30126445',
			'doi' => '10.1186/s13024-018-0274-4',
			'modified' => '2019-02-28 10:13:27',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 82 => array(
			'id' => '3524',
			'name' => 'The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.',
			'authors' => 'Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J',
			'description' => '<p>DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (&gt;94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.</p>',
			'date' => '2018-08-14',
			'pmid' => 'http://www.pubmed.gov/30108278',
			'doi' => '10.1038/s41598-018-30620-5',
			'modified' => '2019-02-28 10:12:41',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
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		),
		(int) 83 => array(
			'id' => '3638',
			'name' => 'Long-read sequence capture of the haemoglobin gene clusters across codfish species.',
			'authors' => 'Hoff SNK, Baalsrud HT, Tooming-Klunderud A, Skage M, Richmond T, Obernosterer G, Shirzadi R, Tørresen OK, Jakobsen KS, Jentoft S',
			'description' => '<p>Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long-read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom-made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100&nbsp;kb) and MN (~200&nbsp;kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage-specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long-read capture as a versatile approach for comparative genomic studies by generation of a cross-species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.</p>',
			'date' => '2018-08-03',
			'pmid' => 'http://www.pubmed.gov/30329222',
			'doi' => '10.1111/1755-0998.12955',
			'modified' => '2019-06-07 10:24:26',
			'created' => '2019-06-06 12:11:18',
			'ProductsPublication' => array(
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		(int) 84 => array(
			'id' => '3512',
			'name' => 'A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.',
			'authors' => 'Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Are',
			'description' => '<p>Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512&thinsp;Mb with N50 of 3.4&thinsp;Mb and 564 contigs). The length of 512&thinsp;Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.</p>',
			'date' => '2018-06-11',
			'pmid' => 'http://www.pubmed.gov/29892093',
			'doi' => '10.1038/s41477-018-0166-1',
			'modified' => '2019-02-28 10:35:49',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
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		),
		(int) 85 => array(
			'id' => '3483',
			'name' => 'Overview of Next-Generation Sequencing Technologies.',
			'authors' => 'Slatko BE, Gardner AF, Ausubel FM',
			'description' => '<p>High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. &copy; 2018 by John Wiley &amp; Sons, Inc.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29851291',
			'doi' => '10.1002/cpmb.59',
			'modified' => '2019-02-14 17:07:52',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
				[maximum depth reached]
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		(int) 86 => array(
			'id' => '3474',
			'name' => 'Draft genome of the Peruvian scallop Argopecten purpuratus.',
			'authors' => 'Li C, Liu X, Liu B, Ma B, Liu F, Liu G, Shi Q, Wang C',
			'description' => '<p>Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 to 10 years. Therefore, researchers have been using it to develop hybrid vigor. Here, we performed whole genome sequencing, assembly, and gene annotation of the Peruvian scallop, with an important aim to develop genomic resources for genetic breeding in scallops. Findings: A total of 463.19-Gb raw DNA reads were sequenced. A draft genome assembly of 724.78 Mb was generated (accounting for 81.87% of the estimated genome size of 885.29 Mb), with a contig N50 size of 80.11 kb and a scaffold N50 size of 1.02 Mb. Repeat sequences were calculated to reach 33.74% of the whole genome, and 26,256 protein-coding genes and 3,057 noncoding RNAs were predicted from the assembly. Conclusions: We generated a high-quality draft genome assembly of the Peruvian scallop, which will provide a solid resource for further genetic breeding and for the analysis of the evolutionary history of this economically important scallop.</p>',
			'date' => '2018-04-01',
			'pmid' => 'http://www.pubmed.gov/29617765',
			'doi' => '10.1093/gigascience/giy031',
			'modified' => '2019-02-15 20:33:41',
			'created' => '2019-02-14 15:01:22',
			'ProductsPublication' => array(
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		),
		(int) 87 => array(
			'id' => '3544',
			'name' => 'Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.',
			'authors' => 'Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F',
			'description' => '<p>BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS: We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS: In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.</p>',
			'date' => '2018-01-16',
			'pmid' => 'http://www.pubmed.gov/29338683',
			'doi' => '10.1186/s12864-017-4429-4',
			'modified' => '2019-02-28 10:58:38',
			'created' => '2019-02-27 12:54:44',
			'ProductsPublication' => array(
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			)
		),
		(int) 88 => array(
			'id' => '3308',
			'name' => 'Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.',
			'authors' => 'Rödelsperger C. et al.',
			'description' => '<p>The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling various developmental processes, its high degree of fragmentation complicated virtually all genomic analyses. Here, we present a de novo genome assembly from single-molecule, long-read sequencing data consisting of 135 P.&nbsp;pacificus contigs. When combined with a genetic linkage map, 99% of the assembly could be ordered and oriented into six chromosomes. This allowed us to robustly characterize chromosomal patterns of gene density, repeat content, nucleotide diversity, linkage disequilibrium, and macrosynteny in P.&nbsp;pacificus. Despite widespread conservation of synteny between P.&nbsp;pacificus and C.&nbsp;elegans, we identified one major translocation from an autosome to the sex chromosome in the lineage leading to C.&nbsp;elegans. This highlights the potential of the chromosome-scale assembly for future genomic studies of P.&nbsp;pacificus.</p>',
			'date' => '2017-10-17',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29045848',
			'doi' => '',
			'modified' => '2018-01-04 10:15:03',
			'created' => '2018-01-04 10:15:03',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 89 => array(
			'id' => '3279',
			'name' => 'De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads',
			'authors' => 'Korlach J. et al.',
			'description' => '<p>Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional cloning efforts for the correct sequences. A promising solution is long-read sequencing. Here we tested PacBio-based long-read sequencing and diploid assembly for potential improvements to the Sanger-based intermediate-read zebra finch reference and Illumina-based short-read Anna's hummingbird reference, 2 vocal learning avian species widely studied in neuroscience and genomics. With DNA of the same individuals used to generate the reference genomes, we generated diploid assemblies with the FALCON-Unzip assembler, resulting in contigs with no gaps in the megabase range, representing 150-fold and 200-fold improvements over the current zebra finch and hummingbird references, respectively. These long-read and phased assemblies corrected and resolved what we discovered to be numerous misassemblies in the references, including missing sequences in gaps, erroneous sequences flanking gaps, base call errors in difficult-to-sequence regions, complex repeat structure errors, and allelic differences between the 2 haplotypes. These improvements were validated by single long-genome and transcriptome reads and resulted for the first time in completely resolved protein-coding genes widely studied in neuroscience and specialized in vocal learning species. These findings demonstrate the impact of long reads, sequencing of previously difficult-to-sequence regions, and phasing of haplotypes on generating the high-quality assemblies necessary for understanding gene structure, function, and evolution.</p>',
			'date' => '2017-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29020750',
			'doi' => '',
			'modified' => '2017-10-16 10:27:47',
			'created' => '2017-10-16 10:27:47',
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		),
		(int) 90 => array(
			'id' => '3041',
			'name' => 'DNA fragmentation and quality control analysis ',
			'authors' => 'Wassim Lakhal, Irina Panteleeva, Sharon Squazzo, Rini Saxena, Jerome Kroonen, Steve Siembieda, Markus Tilmes & Jonathan Hagopian',
			'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
<p><strong>Introduction</strong></p>
<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
<p><strong>Results</strong></p>
<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
<p><strong>Conclusion</strong></p>
<p>Unbiased DNA fragmentation with the Diagenode One, the Bioruptor<sup>&reg;</sup>&nbsp;Pico, or the Megaruptor<sup>&reg;</sup>&nbsp;for short- or long-read sequencing combined with sizing on the Fragment Analyzer<sup>&trade;</sup>&nbsp;delivers an efficient workflow solution for preparing and analyzing libraries with even distribution and representation of the genome.</p>
<p></p>',
			'date' => '2016-09-29',
			'pmid' => 'http://www.nature.com/nmeth/journal/v13/n10/full/nmeth.f.397.html',
			'doi' => '',
			'modified' => '2016-10-20 16:37:08',
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			'id' => '64',
			'name' => 'DNA Link Megaruptor',
			'description' => '<p>Established in March 15<span>th </span><span>2000, DNA Link, Inc. has developed as one of the leading full genomic service provider with its extensive 17 years of experience. DNA Link has been involved in numerous genomic researches including many national projects, and contributed to the expansion of the genomic industry. </span></p>
<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p>',
			'author' => 'Hyeyoon, Jang - Lab Manager - Seoul, Korea',
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			'id' => '58',
			'name' => 'MPIDB_Megaruptor 2',
			'description' => '<p><span>The system performance was very good. High molecular weight DNA of different plants (Arabidopsis Alm, Hops polaris and wine Villard Blanc) was isolated and diluted to 50ng/&micro;l or 70ng/&micro;l. We aimed for fragment length 30kb at the volume 150&micro;l.</span><br /><span>We achieved good results and we will continue with bead purification and library preps for PacBio sequencing. &nbsp;I like the user friendly interface of the Megaruptor<sup>&reg;</sup>&nbsp;2. Just two parameters had to be specified: volume of each sample and desired mean fragment size. The processed DNA has a narrow size distribution at around 30kb.</span></p>',
			'author' => 'Christa Lanz and Julia Hildebrandt, Max Planck Institute for Developmental Biology, Tübingen, Germany',
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$testimonials = '<blockquote><p><span>The system performance was very good. High molecular weight DNA of different plants (Arabidopsis Alm, Hops polaris and wine Villard Blanc) was isolated and diluted to 50ng/&micro;l or 70ng/&micro;l. We aimed for fragment length 30kb at the volume 150&micro;l.</span><br /><span>We achieved good results and we will continue with bead purification and library preps for PacBio sequencing. &nbsp;I like the user friendly interface of the Megaruptor<sup>&reg;</sup>&nbsp;2. Just two parameters had to be specified: volume of each sample and desired mean fragment size. The processed DNA has a narrow size distribution at around 30kb.</span></p><cite>Christa Lanz and Julia Hildebrandt, Max Planck Institute for Developmental Biology, Tübingen, Germany</cite></blockquote>
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<p>On one hand, DNA Link was the very first company to introduce the RS II system from Pacific Bioscience in Asia, and has been approved as one of the eight global certified service providers for PacBio. Since 2012, DNA Link has been providing quality results that&nbsp;are controlled under strict criteria and successfully assisted numerous research projects.</p>
<p>PacBio platforms&rsquo; strongest upside is that it generates the longest reads among all&nbsp;sequencing platforms, and constructing long-read libraries using high molecular weight DNA is the most crucial part of utilizing the platforms. Within the PacBio library preparation process, shearing the DNA molecules accordingly to the library size is the initial step for a successful library construction. Sufficient library yield can be obtained only if the DNA molecules are sheared within the targeted size.</p>
<p>DNA Link has been using the Megaruptor instrument from Diagenode for this shearing process, as it is easy to use and has less contamination risk for using disposable&nbsp;hydropores, which contributes to the overall efficiency of the laboratory logistics.</p>
<p><a href="https://www.nature.com/nmeth/journal/v13/n10/pdf/nmeth.f.397.pdf">Read our new Nature Methods publication about the Megaruptor 2 and best NGS library preparation practices</a></p><cite>Hyeyoon, Jang - Lab Manager - Seoul, Korea</cite></blockquote>
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<p><span><strong><span style="text-decoration: underline;">Note</span>:&nbsp;</strong><a href="https://www.diagenode.com/en/p/hydro-tubes-50-pc">Hydro Tubes (C30010018)</a><span>&nbsp;</span><span>are sold separately.</span></span></p>',
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	'description' => '<p>Several methods exist today for shearing genomic DNA, but few are reliable for generating DNA fragments &gt;50 kb necessary for assembly of many microbial, human, plant and animal genomes <em>de novo</em>. Pacific Biosciences highly recommends the Megaruptor<sup>TM</sup> System for shearing genomic DNA to large fragments for long-read sequencing in the Sequel&reg; System.</p>',
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	'description' => '<p><b></b>Optimal&nbsp;data generation using NGS platforms relies on a few sample-preparation prerequisites, namely, precise DNA fragmentation, size-range analysis, and smear quantification. The Diagenode One, Bioruptor<sup>&reg;</sup>, Megaruptor<sup>&reg;</sup>, and Fragment Analyzer<sup>&trade;</sup>&nbsp;by Advanced Analytical ensure that these first critical steps generate quality results.</p>
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<p>NGS technologies have revolutionized genomics research. Optimal DNA shearing, sizing, and quantification during library construction are critical to generate high-quality sequencing data. DNA must be efficiently sheared to an appropriate and consistent fragment size (depending on the sequencing platform) and accurately analyzed to measure distributions and molarity concentrations. The combined use of Diagenode's shearing instruments with Advanced Analytical's Fragment Analyzer<sup>&trade;</sup>&nbsp;can optimize small-fragment (100 bp&ndash;1 kb) and long-fragment (2&ndash;75 kb) NGS library preparation workflows.</p>
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<p>1. Precisely shear, size, and quantify DNA down to 100 bp for short-read sequencing.</p>
<p>2. Accurately shear, size, and quantify DNA up to 50 kb for long-read sequencing.</p>
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