Megaruptor^® 3

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			'name' => 'Megaruptor<sup>®</sup> 3',
			'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
<p></p>
<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
<ul>
<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
</ul>
</div>
<p></p>
<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
<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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			'info1' => '<h3>Excellent reproducibility and size distribution achieved with the Megaruptor 3</h3>
<center><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
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<th class="text-center" style="width: 296px; height: 55px;"></th>
<th class="text-center" style="width: 255px; height: 55px; background-color: #2b2967; color: white;">Megaruptor 3 regular</th>
<th class="text-center" style="width: 381px; height: 55px; background-color: #af3db2; color: white;">Megaruptor 3 HT with ultrafast protocol</th>
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<td style="width: 296px; height: 38px;">Run duration</td>
<td class="text-center" style="width: 255px; height: 38px;">20 min &ndash; few hours</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 5 min</td>
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<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Size</td>
<td class="text-center" style="width: 255px; height: 38px;">5 &ndash; 100 kb</td>
<td class="text-center" style="width: 381px; height: 38px;">7 &ndash; 40 kb</td>
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<td style="width: 296px; height: 38px;">Concentration</td>
<td class="text-center" style="width: 255px; height: 38px;">0 &ndash; 150 ng/&mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 50 ng/&mu;l</td>
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<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Volume</td>
<td class="text-center" style="width: 255px; height: 38px;">40 &ndash; 750 &mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">50 &ndash; 500 &mu;l</td>
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<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Speed settings</td>
<td class="text-center" style="width: 255px; height: 38px;">1 &ndash; 65</td>
<td class="text-center" style="width: 381px; height: 38px;">30 &ndash; 59</td>
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<td style="width: 296px; height: 56px;">Throughput</td>
<td class="text-center" style="width: 255px; height: 56px;">96 samples in 1 day</td>
<td class="text-center" style="width: 381px; height: 56px;">96 samples in &lt; 2h</td>
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<td class="text-center" style="width: 636px; height: 38px;" colspan="2">Multiple orifice hydrodynamic pore</td>
</tr>
<tr style="height: 32px;">
<td style="width: 296px; height: 32px;">Hardware</td>
<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
</tr>
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		'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
<p></p>
<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
<ul>
<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
</ul>
</div>
<p></p>
<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
<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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		'info1' => '<h3>Excellent reproducibility and size distribution achieved with the Megaruptor 3</h3>
<center><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
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<tbody>
<tr style="height: 55px;">
<th class="text-center" style="width: 296px; height: 55px;"></th>
<th class="text-center" style="width: 255px; height: 55px; background-color: #2b2967; color: white;">Megaruptor 3 regular</th>
<th class="text-center" style="width: 381px; height: 55px; background-color: #af3db2; color: white;">Megaruptor 3 HT with ultrafast protocol</th>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Run duration</td>
<td class="text-center" style="width: 255px; height: 38px;">20 min &ndash; few hours</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 5 min</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Size</td>
<td class="text-center" style="width: 255px; height: 38px;">5 &ndash; 100 kb</td>
<td class="text-center" style="width: 381px; height: 38px;">7 &ndash; 40 kb</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Concentration</td>
<td class="text-center" style="width: 255px; height: 38px;">0 &ndash; 150 ng/&mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 50 ng/&mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Volume</td>
<td class="text-center" style="width: 255px; height: 38px;">40 &ndash; 750 &mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">50 &ndash; 500 &mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Speed settings</td>
<td class="text-center" style="width: 255px; height: 38px;">1 &ndash; 65</td>
<td class="text-center" style="width: 381px; height: 38px;">30 &ndash; 59</td>
</tr>
<tr style="height: 56px;">
<td style="width: 296px; height: 56px;">Throughput</td>
<td class="text-center" style="width: 255px; height: 56px;">96 samples in 1 day</td>
<td class="text-center" style="width: 381px; height: 56px;">96 samples in &lt; 2h</td>
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<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Shearing disposables</td>
<td class="text-center" style="width: 636px; height: 38px;" colspan="2">Multiple orifice hydrodynamic pore</td>
</tr>
<tr style="height: 32px;">
<td style="width: 296px; height: 32px;">Hardware</td>
<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
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			'name' => 'Megaruptor 3 Shearing Kit',
			'description' => '<p>The Megaruptor 3 shearing kitには、すぐに使えるHydropore-SyringeとHydro Tubesの合計16サンプルが含まれています。 Shearing kitはMegaruptor&reg;3（B06010003）と併用するよう特別設計になっており、<strong>5 kbから100 kb以上</strong>の範囲で再現性のあるDNA断片を生成が可能です。</p>
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<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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			'name' => 'Megaruptor 3 DNAFluid+ Kit',
			'description' => '<h2 style="text-align: left;">The DNAFluid+ Kit for viscous DNA</h2>
<p><span style="font-weight: 400;">The DNAFluid+ Kit for viscous DNA&nbsp; eliminates the challenges of using </span><b>highly viscous extracted DNA samples </b><span style="font-weight: 400;">for any downstream steps and QC. The</span><span style="font-weight: 400;">&nbsp;</span><b><i>DNAFluid+ Kit </i></b><span style="font-weight: 400;">consists of proprietary "<span>Hydropore-Syringe" and "Hydro Tube"&nbsp;</span>shearing accessories that reduce the viscosity of DNA by pre-conditioning&nbsp;high molecular weight DNA prior to shearing on the </span><b><i>Megaruptor 3. </i></b><span style="font-weight: 400;">This combination of the DNAFluid+ Kit and the Megaruptor 3 together achieve effective, automated homogenization of highly viscous DNA samples while keeping the integrity of the DNA and full control of the DNA size prior to any downstream applications.&nbsp;</span></p>
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			'info1' => '<h3>Validation data: DNAFluid+ Kit for viscous DNA</h3>
<p><span>Validation of the DNA Fluid+ Kit on viscous samples is shown below. HMW DNA was extracted from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit. First, the sample was pre-sheared using the DNA Fluid+ Kit (speed 59) and then diluted to 50 ng/uL and sheared using the Long Hydropore (speed 31) on the Megaruptor 3 system. PacBio HiFi sequencing was performed on the sheared DNA using a 30 hr movie, SMRTbell Express Template Prep Kit 2.0, Binding Kit 2.0, and Sequel II Sequencing Kit 2.0, and Circulomics SRE XS size selection. These results show that Circulomics SRE XS is a good substitute for gel-based size selection and that the DNAFluid+ works well to pre-condition DNA for Long Hydropore shearing without clogging.</span></p>
<h2 class="card-title text-lg">DNA Fluid+ Kit effectively pre-conditions HMW DNA to allow consistent shearing across samples of varying viscosity.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid1.png" /></p>
<p><span>Fig.1. The Femto Pulse traces show fragment size distributions of: 1) native HMW DNA isolated from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit (black curve), 2) after pre-shearing with the Diagenode DNA Fluid+ Kit (blue curve) and 3) after shearing to ~18 kb with the Diagenode Long Hydropore using Megaruptor3 (red curve). Pre-shearing the HMW DNA enables more consistent shearing performance across samples of varying viscosity.</span></p>
<h2 class="card-title text-lg">Excellent read length distribution of sequencing results using DNA treated with DNA Fluid+ Kit.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid2.png" width="600" height="449" /></p>
<p class="text-xs">Fig. 2. After shearing the gDNA that was pre-conditioned with the Diagenode DNA Fluid+ Kit, HiFi read length distribution of GM12878 SMRTbell library shows excellent read length distribution. Sequencing was performed on the PacBio Sequel II system.</p>
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<p>Sterile Hydropores, Syringes, and Hydro Tubes 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>
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			'meta_title' => 'Megaruptor DNAFluid+ kit',
			'meta_keywords' => 'homogenization, viscous, HMW, DNA',
			'meta_description' => 'Megaruptor DNAFluid+  kit',
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			'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
<p><span style="font-weight: 400;">The new 12 sample&nbsp;capacity&nbsp;is optimal for use prior to library preparation on the <a href="https://www.pacb.com/revio/">PacBio Revio</a>, matching the new system's higher throughput and increased&nbsp;efficiency on time.&nbsp;</span></p>
<p>See video on how to use your 12 sample cassette:</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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<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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			'name' => 'Complete Genome Sequence of Lacticaseibacillus rhamnosus DM065,Isolated from the Human Oral Cavity.',
			'authors' => 'Park  Do-Young et al.',
			'description' => '<p>The 3.0-Mb complete genome of Lacticaseibacillus rhamnosus strain DM065, which was isolated from the oral cavity of healthy volunteers in South Korea, was sequenced using a combination of PacBio and Illumina technologies. The genome consists of one circular chromosome and two plasmids and lacks antimicrobial resistance genes.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36321910',
			'doi' => '10.1128/mra.00899-22',
			'modified' => '2022-11-18 12:27:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4655',
			'name' => 'The genome sequence of the malaria mosquito, Anopheles funestus,Giles, 1900',
			'authors' => 'Ayala  Diego et al.',
			'description' => '<p>We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18445.1',
			'doi' => '10.12688/wellcomeopenres.18445.1',
			'modified' => '2023-03-07 08:54:22',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4475',
			'name' => 'Semi-automated assembly of high-quality diploid human reference genomes.',
			'authors' => 'Jarvis  Erich D et al.',
			'description' => '<p>The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within &plusmn;1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36261518',
			'doi' => '10.1038/s41586-022-05325-5',
			'modified' => '2022-11-18 12:20:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4477',
			'name' => 'Integration of Hi-C with short and long-read genome sequencingreveals the structure of germline rearranged genomes.',
			'authors' => 'Schöpflin  R.et al.',
			'description' => '<p>Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in &gt;300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100&thinsp;kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200&thinsp;kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36309531',
			'doi' => '10.1038/s41467-022-34053-7',
			'modified' => '2022-11-18 12:22:31',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4485',
			'name' => 'The genome sequence of the orange-tip butterfly, Anthocharis cardamines(Linnaeus, 1758)',
			'authors' => 'Ebdon  S. et al.',
			'description' => '<p>We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74\%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18117.1',
			'doi' => '10.12688/wellcomeopenres.18117.1',
			'modified' => '2022-11-18 12:32:05',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4486',
			'name' => 'The genome sequence of the satellite, Eupsilia transversa (Hufnagel,1766)',
			'authors' => 'Crowley  L. et al.',
			'description' => '<p>We present a genome assembly from an individual female Eupsilia transversa (the satellite; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 467 megabases in span. The entire assembly (100\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,065 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18105.1',
			'doi' => '10.12688/wellcomeopenres.18105.1',
			'modified' => '2022-11-18 12:32:51',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4487',
			'name' => 'The genome sequence of the common yellow swallowtail, Papilio machaon(Linnaeus, 1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual female Papilio machaon (the common yellow swallowtail; Arthropoda; Insecta; Lepidoptera; Papilionidae). The genome sequence is 252 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 31 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,323 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18119.1',
			'doi' => '10.12688/wellcomeopenres.18119.1',
			'modified' => '2022-11-18 12:33:33',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4489',
			'name' => 'The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual male Erebia ligea (Arran brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 506 megabases in span. The majority (99.92\%) of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.2 kilobases in length.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18115.1',
			'doi' => '10.12688/wellcomeopenres.18115.1',
			'modified' => '2022-11-18 12:36:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4500',
			'name' => 'Complete Genome Sequence of  Strain DM083 Isolated from HumanTongue Coating.',
			'authors' => 'Park  Do-Young  et al.',
			'description' => '<p>We isolated Lactiplantibacillus plantarum DM083 from the human tongue coating to establish a strain library for oral probiotics. It has a single circular 3,197,299 bp chromosome with a guanine-cytosine (GC) content of 44.6\% without plasmids. Importantly, the genome is devoid of the antimicrobial resistance gene, satisfying the minimum safety requirement for probiotics.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36165646',
			'doi' => '10.1128/mra.00675-22',
			'modified' => '2022-11-21 10:32:09',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4501',
			'name' => 'The genome sequence of the yellow-legged clearwing, Synanthedonvespiformis (Linnaeus, 1761)',
			'authors' => 'Boyes  Douglas and Lees  David',
			'description' => '<p>We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100\% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length. Keywords</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18109.1',
			'doi' => '10.12688/wellcomeopenres.18109.1',
			'modified' => '2022-11-21 10:32:47',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4503',
			'name' => 'The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763)',
			'authors' => 'Boyes  Douglas and Boyes  Clare',
			'description' => '<p>We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18103.1',
			'doi' => '10.12688/wellcomeopenres.18103.1',
			'modified' => '2022-11-21 10:35:00',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4504',
			'name' => 'The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808)',
			'authors' => 'Boyes  Douglas and Gibbs  Melanie',
			'description' => '<p>We present a genome assembly from an individual female Mythimna impura (smoky wainscot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 949 megabases in span. The majority of the assembly (98.39\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,441 protein coding genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18104.1',
			'doi' => '10.12688/wellcomeopenres.18104.1',
			'modified' => '2022-11-21 10:35:36',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4509',
			'name' => 'Comparative analyses of Theobroma cacao and T. grandiflorummitogenomes reveal conserved gene content embedded within complex andplastic structures.',
			'authors' => 'de Abreu  Vinicius A C et al.',
			'description' => '<p>Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and comparative analyses. The two most known species in Theobroma L. (Malvaceae s.l.) genus are T. cacao, and T. grandiflorum. Besides the economic value, both species also show considerable biotechnology potential due to their other derived products, thus, aggregating additional economic value for the agroindustry. Here, we assembled and compared the mtDNA of Theobroma cacao and T. grandiflorum to generate a new genomics resource and unravel evolutionary trends. Graph-based analyses revealed that both mtDNA exhibit multiple alternative arrangements, confirming the dynamism commonly observed in plant mtDNA. The disentangled assembly graph revealed potential predominant circular molecules. The master circle molecules span 543,794&nbsp;bp for T. cacao and 501,598&nbsp;bp for T. grandiflorum, showing 98.9\% of average sequence identity. Both mtDNA contains the same set of 39 plant mitochondrial genes, commonly found in other rosid mitogenomes. The main features are a duplicated copy of atp4, the absence of rpl6, rps2, rps8, and rps11, and the presence of two chimeric open-reading frames. Moreover, we detected few ptDNA integrations mainly represented by tRNAs, and no viral sequences were detected. Phylogenomics analyses indicate Theobroma spp. are nested in Malvaceae family. The main mtDNA differences are related to distinct structural rearrangements and exclusive regions associated with relics of Transposable Elements, supporting the hypothesis of dynamic mitochondrial genome maintenance and divergent evolutionary paths and pressures after species differentiation.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36150535',
			'doi' => '10.1016/j.gene.2022.146904',
			'modified' => '2022-11-21 10:36:50',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4505',
			'name' => 'The genome sequence of the wall brown, Lasiommata megera (Linnaeus,1767)',
			'authors' => 'Lohse  Konrad and Wright  Charlotte',
			'description' => '<p>We present a genome assembly from an individual female Lasiommata megera (the wall brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 488 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 30 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18106.1',
			'doi' => '10.12688/wellcomeopenres.18106.1',
			'modified' => '2023-02-17 08:54:13',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4507',
			'name' => 'The genome sequence of the sallow kitten, Furcula furcula (Clerck,1759)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100\%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18112.1',
			'doi' => '10.12688/wellcomeopenres.18112.1',
			'modified' => '2023-02-17 08:55:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4508',
			'name' => 'The genome sequence of the peacock moth, Macaria notata (Linnaeus,1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18108.1',
			'doi' => '10.12688/wellcomeopenres.18108.1',
			'modified' => '2023-02-17 08:56:15',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4513',
			'name' => 'Plant species-specific basecaller improves actual accuracy of nanoporesequencing',
			'authors' => 'Ferguson  Scott et al.',
			'description' => '<p>Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specific basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specific basecaller models. We also evaluate accuracy gains from ONT&rsquo;s improved flowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1919465%2Fv1',
			'doi' => '10.21203/rs.3.rs-1919465/v1',
			'modified' => '2023-02-17 08:57:19',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => 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) 21 => array(
			'id' => '4450',
			'name' => 'The leaf beetle Chelymorpha alternans propagates a plant pathogen inexchange for pupal protection.',
			'authors' => 'Berasategui  Aileen et al.',
			'description' => '<p>Many insects rely on microbial protection in the early stages of their development. However, in contrast to symbiont-mediated defense of eggs and young instars, the role of microbes in safeguarding pupae remains relatively unexplored, despite the susceptibility of the immobile stage to antagonistic challenges. Here, we outline the importance of symbiosis in ensuring pupal protection by describing a mutualistic partnership between the ascomycete Fusarium oxysporum and Chelymorpha alternans, a leaf beetle. The symbiont rapidly proliferates at the onset of pupation, extensively and conspicuously coating C.&nbsp;alternans during metamorphosis. The fungus confers defense against predation as symbiont elimination results in reduced pupal survivorship. In exchange, eclosing beetles vector F.&nbsp;oxysporum to their host plants, resulting in a systemic infection. By causing wilt disease, the fungus retained its phytopathogenic capacity in light of its symbiosis with C.&nbsp;alternans. Despite possessing a relatively reduced genome, F.&nbsp;oxysporum encodes metabolic pathways that reflect its dual lifestyle as a plant pathogen and a defensive insect symbiont. These include virulence factors underlying plant colonization, along with mycotoxins that may contribute to the defensive biochemistry of the insect host. Collectively, our findings shed light on a mutualism predicated on pupal protection of an herbivorous beetle in exchange for symbiont dissemination and propagation.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35987210',
			'doi' => '10.1016/j.cub.2022.07.065',
			'modified' => '2022-10-21 09:29:09',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4431',
			'name' => 'The genome sequence of the hawthorn shieldbug, Acanthosomahaemorrhoidale (Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Mulley  John',
			'description' => '<p>We present a genome assembly from an individual male Acanthosoma haemorrhoidale (hawthorn shieldbug; Arthropoda; Insecta; Hemiptera; Acanthosomatidae). The genome sequence is 866 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 7 chromosomal pseudomolecules with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 18.9 kilobases in length.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17926.1',
			'doi' => '10.12688/wellcomeopenres.17926.1',
			'modified' => '2022-09-28 09:09:34',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4433',
			'name' => 'The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87\%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://wellcomeopenresearch.org/articles/7-189',
			'doi' => '10.12688/wellcomeopenres.17925.1',
			'modified' => '2022-09-28 09:13:35',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4518',
			'name' => 'Equilibrated evolution of the mixed auto-/allopolyploidhaplotype-resolved genome of the invasive hexaploid Prussian carp.',
			'authors' => 'Kuhl  Heiner et al.',
			'description' => '<p>Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35835759',
			'doi' => '10.1038/s41467-022-31515-w',
			'modified' => '2023-02-17 08:58:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4372',
			'name' => 'Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing',
			'authors' => 'Yang  X. et al.',
			'description' => '<p>The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (haplotype 1 (H1): 3.1 Gb, haplotype 2 (H2): 2.9 Gb). The continuity (H1: contig N50 = 28.2 Mb, H2: contig N50 = 25.9 Mb) and completeness (BUSCO: H1 = 94.9\%, H2 = 93.5\%) are substantially better than those of other Chinese genomes, for example, HX1, NH1.0, and YH2.0. By comparing HJ genome with GRCh38, we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2, respectively. In addition, we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2, respectively. Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.fmre.2022.02.005',
			'doi' => '10.1016/j.fmre.2022.02.005',
			'modified' => '2022-08-04 16:11:38',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4523',
			'name' => 'Complete Genome Sequence of Herpes Simplex Virus 2 StrainG.',
			'authors' => 'Chang  Weizhong et al.',
			'description' => '<p>Herpes simplex virus type (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the '&alpha;' sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the '&alpha;' sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35336943',
			'doi' => '10.3390/v14030536',
			'modified' => '2023-02-17 09:03:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4464',
			'name' => 'The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900',
			'authors' => 'Macadam  Craig et al. ',
			'description' => '<p>We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79\%) is scaffolded into 12 chromosomal pseudomolecules, with the X sex chromosome assembled. The X chromosome was found at half coverage, but no Y chromosome was found. The mitochondrial genome was assembled, and is 16.0 kb in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17684.1',
			'doi' => '10.12688/wellcomeopenres.17684.1',
			'modified' => '2022-10-21 09:51:18',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4465',
			'name' => 'The genome sequence of the furry-claspered furrow bee, Lasioglossumlativentre (Schenck, 1853)',
			'authors' => 'Falk  Steven and Monks  Joseph',
			'description' => '<p>We present a genome assembly from an individual male Lasioglossum lativentre (the furry-claspered furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 479 megabases in span. The majority of the assembly (75.22\%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome was also assembled, and is 15.3 kilobases in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17706.1',
			'doi' => '10.12688/wellcomeopenres.17706.1',
			'modified' => '2022-10-21 09:51:46',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => 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) 30 => array(
			'id' => '4369',
			'name' => 'The genome sequence of a parasitoid wasp,  Forster, 1771.',
			'authors' => 'Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual female (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64\%) is scaffolded into 12 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 10,622 protein coding genes.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419493',
			'doi' => '10.12688/wellcomeopenres.17683.1',
			'modified' => '2022-08-04 16:21:40',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4506',
			'name' => 'The genome sequence of the brimstone moth, Opisthograptis luteolata(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas and Phillips  Dominic',
			'description' => '<p>We present a genome assembly from an individual male (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226159',
			'doi' => '10.12688/wellcomeopenres.18101.1',
			'modified' => '2023-02-17 08:59:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4529',
			'name' => 'The genome sequence of Gymnosoma rotundatum (Linnaeus, 1758), aparasitoid ladybird fly',
			'authors' => 'Smith  Matthew',
			'description' => '<p>We present a genome assembly from an individual male (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 779 megabases in span. The majority of the assembly (97.07\%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419492',
			'doi' => '10.12688/wellcomeopenres.17782.1',
			'modified' => '2023-02-17 09:00:46',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4256',
			'name' => 'Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca).',
			'authors' => 'Huang Yi et al.',
			'description' => '<p>Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2\%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.</p>',
			'date' => '2021-11-01',
			'pmid' => 'https://doi.org/10.1093%2Fjhered%2Fesab071',
			'doi' => '10.1093/jhered/esab071',
			'modified' => '2022-05-20 09:47:15',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => 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) 35 => array(
			'id' => '4308',
			'name' => 'De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus).',
			'authors' => 'Pickett, Brandon D and Glass, Jessica R and Ridge, PerryG and Kauwe, John S K',
			'description' => '<p>The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95\% complete, and the genome is comprised of 16.9\% repetitive elements. The assembly was annotated with 33.1&thinsp;K protein-coding genes, 71.4\% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://doi.org/10.1093%2Fg3journal%2Fjkab229',
			'doi' => '10.1093/g3journal/jkab229',
			'modified' => '2022-06-20 09:08:51',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => 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) 37 => 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) 38 => array(
			'id' => '4123',
			'name' => 'Familial thrombocytopenia due to a complex structural variant resulting ina WAC-ANKRD26 fusion transcript.',
			'authors' => 'Wahlster, Lara and Verboon, Jeffrey M and Ludwig, Leif S and Black, Susan Cand Luo, Wendy and Garg, Kopal and Voit, Richard A and Collins, Ryan L andGarimella, Kiran and Costello, Maura and Chao, Katherine R and Goodrich,Julia K and DiTroia, Stephanie ',
			'description' => '<p>Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleotide variants that prevent silencing of ANKRD26 expression during hematopoietic differentiation. Short-read whole-exome and genome sequencing approaches were unable to identify a causal variant in this family. Using long-read whole-genome sequencing, a large complex structural variant involving a paired-duplication inversion was identified. Through functional studies, we show that this structural variant results in a pathogenic gain-of-function WAC-ANKRD26 fusion transcript. Our findings illustrate how complex structural variants that may be missed by conventional genome sequencing approaches can cause human disease.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33857290',
			'doi' => '10.1084/jem.20210444',
			'modified' => '2021-12-07 09:58:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4134',
			'name' => 'PCIP-seq: simultaneous sequencing of integrated viral genomes and theirinsertion sites with long reads.',
			'authors' => 'Artesi, M. et al.',
			'description' => '<p>The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33823910',
			'doi' => '10.1186/s13059-021-02307-0',
			'modified' => '2021-12-10 17:12:45',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => 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) 41 => array(
			'id' => '4122',
			'name' => 'Comparison of long read sequencing technologies in interrogating bacteriaand fly genomes.',
			'authors' => 'Tvedte, Eric S and Gasser, Mark and Sparklin, Benjamin C and Michalski,Jane and Hjelmen, Carl E and Johnston, J Spencer and Zhao, Xuechu andBromley, Robin and Tallon, Luke J and Sadzewicz, Lisa and Rasko, David Aand Hotopp, Julie C Dunning',
			'description' => '<p>The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33768248',
			'doi' => '10.1093/g3journal/jkab083',
			'modified' => '2021-12-07 09:57:33',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => 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) 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' => '4037',
			'name' => 'Complete Genome Sequence of  sp. Strain Nx66, Isolated from WatersContaminated with Petrochemicals in El Saf-Saf Valley, Algeria.',
			'authors' => 'Chéraiti, Nardjess and Plewniak, Frédéric and Tighidet, Salima andSayeh, Amalia and Gil, Lisa and Malherbe, Ludivine and Memmi, Yosr andZilliox, Laurence and Vandecasteele, Céline and Boyer, Pierre andLopez-Roques, Céline and Jaulhac, Benoît and Bensou',
			'description' => '<p>sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 &times; 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42&thinsp;Mb and one plasmid of 34.22&thinsp;kb.</p>',
			'date' => '2020-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29457705',
			'doi' => '10.1128/MRA.01130-20',
			'modified' => '2021-02-18 17:13:56',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4043',
			'name' => 'Contrasting signatures of genomic divergence during sympatric speciation.',
			'authors' => 'Kautt, Andreas F and Kratochwil, Claudius F and Nater, Alexander andMachado-Schiaffino, Gonzalo and Olave, Melisa and Henning, Frederico andTorres-Dowdall, Julián and Härer, Andreas and Hulsey, C Darrin andFranchini, Paolo and Pippel, Martin and Myers,',
			'description' => '<p>The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33116308',
			'doi' => '10.1038/s41586-020-2845-0',
			'modified' => '2021-02-19 13:51:04',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4066',
			'name' => 'Genome structure and content of the rice root-knot nematode ().',
			'authors' => 'Phan, Ngan Thi and Orjuela, Julie and Danchin, Etienne G J and Klopp,Christophe and Perfus-Barbeoch, Laetitia and Kozlowski, Djampa K andKoutsovoulos, Georgios D and Lopez-Roques, Céline and Bouchez, Olivier andZahm, Margot and Besnard, Guillaume and B',
			'description' => '<p>Discovered in the 1960s, is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294&nbsp;kb, totaling 41.5&nbsp;Mb). The completeness scores of our assembly are among the highest currently published for genomes. We predicted 10,284 protein-coding genes spanning 75.5\% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61\% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of .&nbsp; and its closest relatives.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33144944',
			'doi' => '10.1002/ece3.6680',
			'modified' => '2021-02-19 17:46:50',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '4074',
			'name' => 'Repeat expansions confer WRN dependence in microsatellite-unstablecancers.',
			'authors' => 'van Wietmarschen, Niek and Sridharan, Sriram and Nathan, William J andTubbs, Anthony and Chan, Edmond M and Callen, Elsa and Wu, Wei and Belinky,Frida and Tripathi, Veenu and Wong, Nancy and Foster, Kyla and Noorbakhsh,Javad and Garimella, Kiran and Cr',
			'description' => '<p>The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32999459',
			'doi' => '10.1038/s41586-020-2769-8',
			'modified' => '2021-02-19 18:07:45',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '4081',
			'name' => 'Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient withe14a3 BCR-ABL1 transcript using Nanopore sequencing.',
			'authors' => 'Zhao, Hu and Chen, Yuan and Shen, Chanjuan and Li, Lingshu and Li, Qingzhaoand Tan, Kui and Huang, Huang and Hu, Guoyu',
			'description' => '<p>BACKGROUND: The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations. Here, we present a CML patient with e14a3 BCR-ABL1 transcript and t(9;22;12) variant Philadelphia (Ph) chromosome. METHODS: Cytogenetic analysis and fluorescence in situ hybridization (FISH) was performed to identify the chromosomal aberrations and gene fusions. Rare fusion transcript was verified by a reverse transcription-polymerase chain reaction (RT-PCR). Breakpoints were characterized and validated using Oxford Nanopore Technologies (ONT) (Oxford, UK) and Sanger sequencing, respectively. RESULTS: The karyotype showed the translocation t(9;22;12)(q34;q11.2;q24) [20] and FISH indicated 40\% positive BCR-ABL1 fusion signals. The RT-PCR suggested e14a3 type fusion transcript. The ONT sequencing analysis identified specific positions of translocation breakpoints: chr22:23633040-chr9:133729579, chr12:121567595-chr22:24701405, which were confirmed using Sanger sequencing. The patient achieved molecular remission 3 months after imatinib therapy. CONCLUSIONS: The present study indicates Nanopore sequencing as a valid strategy, which can characterize breakpoints precisely in special clinical cases with atypical structural variations. CML patients with e14a3 transcripts may have good clinical course in the tyrosine kinase inhibitor era, as reviewed here.</p>',
			'date' => '2020-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32949441',
			'doi' => '10.1002/jgm.3276',
			'modified' => '2021-03-15 16:56:36',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 51 => array(
			'id' => '4059',
			'name' => 'Interruption of an MSH4 homolog blocks meiosis in metaphase I andeliminates spore formation in Pleurotus ostreatus.',
			'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
			'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
			'date' => '2020-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
			'doi' => '10.1371/journal.pone.0241749',
			'modified' => '2021-02-19 17:26:09',
			'created' => '2021-02-18 10:21:53',
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			'id' => '80',
			'name' => 'Megaruptor 3 - PacBio',
			'description' => '<p><span>The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.</span></p>',
			'author' => 'Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.',
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			'name' => 'Testimonial Megaruptor 3 - September 11, 2019',
			'description' => '<p>As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.</p>',
			'author' => 'Brewster Kingham, Delaware Biotechnology Institute,  University of Delaware',
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			'name' => 'Testimonial Megaruptor 3',
			'description' => '<p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p>',
			'author' => 'Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen',
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$testimonials = '<blockquote><p><span>The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.</span></p><cite>Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.</cite></blockquote>
'
$featured_testimonials = '<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.</p><cite>Brewster Kingham, Delaware Biotechnology Institute,  University of Delaware</cite></blockquote>
<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p><cite>Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen</cite></blockquote>
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$testimonial = array(
	'id' => '75',
	'name' => 'Testimonial Megaruptor 3',
	'description' => '<p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p>',
	'author' => 'Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen',
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<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
<p><span style="font-weight: 400;">The new 12 sample&nbsp;capacity&nbsp;is optimal for use prior to library preparation on the <a href="https://www.pacb.com/revio/">PacBio Revio</a>, matching the new system's higher throughput and increased&nbsp;efficiency on time.&nbsp;</span></p>
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	'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
	'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
	'date' => '2020-01-01',
	'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
	'doi' => '10.1371/journal.pone.0241749',
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include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
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Notice (8): Undefined variable: header [APP/View/Products/view.ctp, line 755]
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$dataForView = array(
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	'meta_title' => 'The Megaruptor 3',
	'product' => array(
		'Product' => array(
			'id' => '3009',
			'antibody_id' => null,
			'name' => 'Megaruptor<sup>®</sup> 3',
			'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
<p></p>
<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
<ul>
<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
</ul>
</div>
<p></p>
<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
<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>',
			'label1' => 'Demonstrated shearing of DNA from 5 -100 kb',
			'info1' => '<h3>Excellent reproducibility and size distribution achieved with the Megaruptor 3</h3>
<center><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
			'label2' => 'Specifications for the Megaruptor',
			'info2' => '<table style="width: 941px;">
<tbody>
<tr style="height: 55px;">
<th class="text-center" style="width: 296px; height: 55px;"></th>
<th class="text-center" style="width: 255px; height: 55px; background-color: #2b2967; color: white;">Megaruptor 3 regular</th>
<th class="text-center" style="width: 381px; height: 55px; background-color: #af3db2; color: white;">Megaruptor 3 HT with ultrafast protocol</th>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Run duration</td>
<td class="text-center" style="width: 255px; height: 38px;">20 min &ndash; few hours</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 5 min</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Size</td>
<td class="text-center" style="width: 255px; height: 38px;">5 &ndash; 100 kb</td>
<td class="text-center" style="width: 381px; height: 38px;">7 &ndash; 40 kb</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Concentration</td>
<td class="text-center" style="width: 255px; height: 38px;">0 &ndash; 150 ng/&mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 50 ng/&mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Volume</td>
<td class="text-center" style="width: 255px; height: 38px;">40 &ndash; 750 &mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">50 &ndash; 500 &mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Speed settings</td>
<td class="text-center" style="width: 255px; height: 38px;">1 &ndash; 65</td>
<td class="text-center" style="width: 381px; height: 38px;">30 &ndash; 59</td>
</tr>
<tr style="height: 56px;">
<td style="width: 296px; height: 56px;">Throughput</td>
<td class="text-center" style="width: 255px; height: 56px;">96 samples in 1 day</td>
<td class="text-center" style="width: 381px; height: 56px;">96 samples in &lt; 2h</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Shearing disposables</td>
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<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
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<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
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<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
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<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
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<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
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<center><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
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<th class="text-center" style="width: 255px; height: 55px; background-color: #2b2967; color: white;">Megaruptor 3 regular</th>
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<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
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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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			'name' => 'Megaruptor 3 DNAFluid+ Kit',
			'description' => '<h2 style="text-align: left;">The DNAFluid+ Kit for viscous DNA</h2>
<p><span style="font-weight: 400;">The DNAFluid+ Kit for viscous DNA&nbsp; eliminates the challenges of using </span><b>highly viscous extracted DNA samples </b><span style="font-weight: 400;">for any downstream steps and QC. The</span><span style="font-weight: 400;">&nbsp;</span><b><i>DNAFluid+ Kit </i></b><span style="font-weight: 400;">consists of proprietary "<span>Hydropore-Syringe" and "Hydro Tube"&nbsp;</span>shearing accessories that reduce the viscosity of DNA by pre-conditioning&nbsp;high molecular weight DNA prior to shearing on the </span><b><i>Megaruptor 3. </i></b><span style="font-weight: 400;">This combination of the DNAFluid+ Kit and the Megaruptor 3 together achieve effective, automated homogenization of highly viscous DNA samples while keeping the integrity of the DNA and full control of the DNA size prior to any downstream applications.&nbsp;</span></p>
<p><br /> <a href="https://www.diagenode.com/files/products/kits/Application_Note-DNAFluid.pdf"><img src="https://www.diagenode.com/img/banners/banner-appnote-dnafluid.png" /></a></p>',
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			'info1' => '<h3>Validation data: DNAFluid+ Kit for viscous DNA</h3>
<p><span>Validation of the DNA Fluid+ Kit on viscous samples is shown below. HMW DNA was extracted from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit. First, the sample was pre-sheared using the DNA Fluid+ Kit (speed 59) and then diluted to 50 ng/uL and sheared using the Long Hydropore (speed 31) on the Megaruptor 3 system. PacBio HiFi sequencing was performed on the sheared DNA using a 30 hr movie, SMRTbell Express Template Prep Kit 2.0, Binding Kit 2.0, and Sequel II Sequencing Kit 2.0, and Circulomics SRE XS size selection. These results show that Circulomics SRE XS is a good substitute for gel-based size selection and that the DNAFluid+ works well to pre-condition DNA for Long Hydropore shearing without clogging.</span></p>
<h2 class="card-title text-lg">DNA Fluid+ Kit effectively pre-conditions HMW DNA to allow consistent shearing across samples of varying viscosity.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid1.png" /></p>
<p><span>Fig.1. The Femto Pulse traces show fragment size distributions of: 1) native HMW DNA isolated from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit (black curve), 2) after pre-shearing with the Diagenode DNA Fluid+ Kit (blue curve) and 3) after shearing to ~18 kb with the Diagenode Long Hydropore using Megaruptor3 (red curve). Pre-shearing the HMW DNA enables more consistent shearing performance across samples of varying viscosity.</span></p>
<h2 class="card-title text-lg">Excellent read length distribution of sequencing results using DNA treated with DNA Fluid+ Kit.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid2.png" width="600" height="449" /></p>
<p class="text-xs">Fig. 2. After shearing the gDNA that was pre-conditioned with the Diagenode DNA Fluid+ Kit, HiFi read length distribution of GM12878 SMRTbell library shows excellent read length distribution. Sequencing was performed on the PacBio Sequel II system.</p>
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<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</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>
</div>
</div>
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			'meta_title' => 'Next-generation sequencing (NGS) Applications and Methods | Diagenode',
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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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			'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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			'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' => 'The genome sequence of the Elbow-stripe Grass-veneer, Agriphilageniculea (Haworth, 1811)',
			'authors' => 'Boyes  Douglas and Hammond  James',
			'description' => '<p>We present a genome assembly from an individual female Agriphila geniculea (the Elbow-stripe Grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 781.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,132 protein coding genes.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18910.1',
			'doi' => '10.12688/wellcomeopenres.18910.1',
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			'id' => '4664',
			'name' => 'The genome sequence of the Turnip Sawfly, Athalia rosae(Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Broad  Gavin R. and Green  Andrew',
			'description' => '<p>We present a genome assembly from an individual female Athalia rosae (the Turnip Sawfly; Arhropoda; Insecta; Hymenoptera; Athaliidae). The genome sequence is 172 megabases in span. Most of the assembly is scaffolded into eight chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,393 protein coding genes.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18993.1',
			'doi' => '10.12688/wellcomeopenres.18993.1',
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			'name' => 'A high-quality, haplotype-phased genome reconstruction reveals unexpectedhaplotype diversity in a pearl oyster.',
			'authors' => 'Takeuchi  Takeshi et al.',
			'description' => '<p>Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (&gt;38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997\%. Moreover, the haplotypes contain 95.2\% and 95.9\%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3\% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.</p>',
			'date' => '2022-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36351462',
			'doi' => '10.1093/dnares/dsac035',
			'modified' => '2023-02-17 08:49:27',
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			'id' => '4481',
			'name' => 'Complete Genome Sequence of Lacticaseibacillus rhamnosus DM065,Isolated from the Human Oral Cavity.',
			'authors' => 'Park  Do-Young et al.',
			'description' => '<p>The 3.0-Mb complete genome of Lacticaseibacillus rhamnosus strain DM065, which was isolated from the oral cavity of healthy volunteers in South Korea, was sequenced using a combination of PacBio and Illumina technologies. The genome consists of one circular chromosome and two plasmids and lacks antimicrobial resistance genes.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36321910',
			'doi' => '10.1128/mra.00899-22',
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			'id' => '4655',
			'name' => 'The genome sequence of the malaria mosquito, Anopheles funestus,Giles, 1900',
			'authors' => 'Ayala  Diego et al.',
			'description' => '<p>We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18445.1',
			'doi' => '10.12688/wellcomeopenres.18445.1',
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			'name' => 'Semi-automated assembly of high-quality diploid human reference genomes.',
			'authors' => 'Jarvis  Erich D et al.',
			'description' => '<p>The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within &plusmn;1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36261518',
			'doi' => '10.1038/s41586-022-05325-5',
			'modified' => '2022-11-18 12:20:59',
			'created' => '2022-11-15 09:26:20',
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			'id' => '4477',
			'name' => 'Integration of Hi-C with short and long-read genome sequencingreveals the structure of germline rearranged genomes.',
			'authors' => 'Schöpflin  R.et al.',
			'description' => '<p>Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in &gt;300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100&thinsp;kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200&thinsp;kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36309531',
			'doi' => '10.1038/s41467-022-34053-7',
			'modified' => '2022-11-18 12:22:31',
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			'id' => '4485',
			'name' => 'The genome sequence of the orange-tip butterfly, Anthocharis cardamines(Linnaeus, 1758)',
			'authors' => 'Ebdon  S. et al.',
			'description' => '<p>We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74\%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18117.1',
			'doi' => '10.12688/wellcomeopenres.18117.1',
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			'id' => '4486',
			'name' => 'The genome sequence of the satellite, Eupsilia transversa (Hufnagel,1766)',
			'authors' => 'Crowley  L. et al.',
			'description' => '<p>We present a genome assembly from an individual female Eupsilia transversa (the satellite; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 467 megabases in span. The entire assembly (100\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,065 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18105.1',
			'doi' => '10.12688/wellcomeopenres.18105.1',
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			'id' => '4487',
			'name' => 'The genome sequence of the common yellow swallowtail, Papilio machaon(Linnaeus, 1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual female Papilio machaon (the common yellow swallowtail; Arthropoda; Insecta; Lepidoptera; Papilionidae). The genome sequence is 252 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 31 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,323 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18119.1',
			'doi' => '10.12688/wellcomeopenres.18119.1',
			'modified' => '2022-11-18 12:33:33',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4489',
			'name' => 'The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual male Erebia ligea (Arran brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 506 megabases in span. The majority (99.92\%) of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.2 kilobases in length.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18115.1',
			'doi' => '10.12688/wellcomeopenres.18115.1',
			'modified' => '2022-11-18 12:36:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4500',
			'name' => 'Complete Genome Sequence of  Strain DM083 Isolated from HumanTongue Coating.',
			'authors' => 'Park  Do-Young  et al.',
			'description' => '<p>We isolated Lactiplantibacillus plantarum DM083 from the human tongue coating to establish a strain library for oral probiotics. It has a single circular 3,197,299 bp chromosome with a guanine-cytosine (GC) content of 44.6\% without plasmids. Importantly, the genome is devoid of the antimicrobial resistance gene, satisfying the minimum safety requirement for probiotics.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36165646',
			'doi' => '10.1128/mra.00675-22',
			'modified' => '2022-11-21 10:32:09',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4501',
			'name' => 'The genome sequence of the yellow-legged clearwing, Synanthedonvespiformis (Linnaeus, 1761)',
			'authors' => 'Boyes  Douglas and Lees  David',
			'description' => '<p>We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100\% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length. Keywords</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18109.1',
			'doi' => '10.12688/wellcomeopenres.18109.1',
			'modified' => '2022-11-21 10:32:47',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4503',
			'name' => 'The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763)',
			'authors' => 'Boyes  Douglas and Boyes  Clare',
			'description' => '<p>We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18103.1',
			'doi' => '10.12688/wellcomeopenres.18103.1',
			'modified' => '2022-11-21 10:35:00',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4504',
			'name' => 'The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808)',
			'authors' => 'Boyes  Douglas and Gibbs  Melanie',
			'description' => '<p>We present a genome assembly from an individual female Mythimna impura (smoky wainscot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 949 megabases in span. The majority of the assembly (98.39\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,441 protein coding genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18104.1',
			'doi' => '10.12688/wellcomeopenres.18104.1',
			'modified' => '2022-11-21 10:35:36',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4509',
			'name' => 'Comparative analyses of Theobroma cacao and T. grandiflorummitogenomes reveal conserved gene content embedded within complex andplastic structures.',
			'authors' => 'de Abreu  Vinicius A C et al.',
			'description' => '<p>Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and comparative analyses. The two most known species in Theobroma L. (Malvaceae s.l.) genus are T. cacao, and T. grandiflorum. Besides the economic value, both species also show considerable biotechnology potential due to their other derived products, thus, aggregating additional economic value for the agroindustry. Here, we assembled and compared the mtDNA of Theobroma cacao and T. grandiflorum to generate a new genomics resource and unravel evolutionary trends. Graph-based analyses revealed that both mtDNA exhibit multiple alternative arrangements, confirming the dynamism commonly observed in plant mtDNA. The disentangled assembly graph revealed potential predominant circular molecules. The master circle molecules span 543,794&nbsp;bp for T. cacao and 501,598&nbsp;bp for T. grandiflorum, showing 98.9\% of average sequence identity. Both mtDNA contains the same set of 39 plant mitochondrial genes, commonly found in other rosid mitogenomes. The main features are a duplicated copy of atp4, the absence of rpl6, rps2, rps8, and rps11, and the presence of two chimeric open-reading frames. Moreover, we detected few ptDNA integrations mainly represented by tRNAs, and no viral sequences were detected. Phylogenomics analyses indicate Theobroma spp. are nested in Malvaceae family. The main mtDNA differences are related to distinct structural rearrangements and exclusive regions associated with relics of Transposable Elements, supporting the hypothesis of dynamic mitochondrial genome maintenance and divergent evolutionary paths and pressures after species differentiation.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36150535',
			'doi' => '10.1016/j.gene.2022.146904',
			'modified' => '2022-11-21 10:36:50',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4505',
			'name' => 'The genome sequence of the wall brown, Lasiommata megera (Linnaeus,1767)',
			'authors' => 'Lohse  Konrad and Wright  Charlotte',
			'description' => '<p>We present a genome assembly from an individual female Lasiommata megera (the wall brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 488 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 30 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18106.1',
			'doi' => '10.12688/wellcomeopenres.18106.1',
			'modified' => '2023-02-17 08:54:13',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4507',
			'name' => 'The genome sequence of the sallow kitten, Furcula furcula (Clerck,1759)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100\%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18112.1',
			'doi' => '10.12688/wellcomeopenres.18112.1',
			'modified' => '2023-02-17 08:55:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4508',
			'name' => 'The genome sequence of the peacock moth, Macaria notata (Linnaeus,1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18108.1',
			'doi' => '10.12688/wellcomeopenres.18108.1',
			'modified' => '2023-02-17 08:56:15',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4513',
			'name' => 'Plant species-specific basecaller improves actual accuracy of nanoporesequencing',
			'authors' => 'Ferguson  Scott et al.',
			'description' => '<p>Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specific basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specific basecaller models. We also evaluate accuracy gains from ONT&rsquo;s improved flowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1919465%2Fv1',
			'doi' => '10.21203/rs.3.rs-1919465/v1',
			'modified' => '2023-02-17 08:57:19',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => 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) 21 => array(
			'id' => '4450',
			'name' => 'The leaf beetle Chelymorpha alternans propagates a plant pathogen inexchange for pupal protection.',
			'authors' => 'Berasategui  Aileen et al.',
			'description' => '<p>Many insects rely on microbial protection in the early stages of their development. However, in contrast to symbiont-mediated defense of eggs and young instars, the role of microbes in safeguarding pupae remains relatively unexplored, despite the susceptibility of the immobile stage to antagonistic challenges. Here, we outline the importance of symbiosis in ensuring pupal protection by describing a mutualistic partnership between the ascomycete Fusarium oxysporum and Chelymorpha alternans, a leaf beetle. The symbiont rapidly proliferates at the onset of pupation, extensively and conspicuously coating C.&nbsp;alternans during metamorphosis. The fungus confers defense against predation as symbiont elimination results in reduced pupal survivorship. In exchange, eclosing beetles vector F.&nbsp;oxysporum to their host plants, resulting in a systemic infection. By causing wilt disease, the fungus retained its phytopathogenic capacity in light of its symbiosis with C.&nbsp;alternans. Despite possessing a relatively reduced genome, F.&nbsp;oxysporum encodes metabolic pathways that reflect its dual lifestyle as a plant pathogen and a defensive insect symbiont. These include virulence factors underlying plant colonization, along with mycotoxins that may contribute to the defensive biochemistry of the insect host. Collectively, our findings shed light on a mutualism predicated on pupal protection of an herbivorous beetle in exchange for symbiont dissemination and propagation.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35987210',
			'doi' => '10.1016/j.cub.2022.07.065',
			'modified' => '2022-10-21 09:29:09',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4431',
			'name' => 'The genome sequence of the hawthorn shieldbug, Acanthosomahaemorrhoidale (Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Mulley  John',
			'description' => '<p>We present a genome assembly from an individual male Acanthosoma haemorrhoidale (hawthorn shieldbug; Arthropoda; Insecta; Hemiptera; Acanthosomatidae). The genome sequence is 866 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 7 chromosomal pseudomolecules with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 18.9 kilobases in length.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17926.1',
			'doi' => '10.12688/wellcomeopenres.17926.1',
			'modified' => '2022-09-28 09:09:34',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4433',
			'name' => 'The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87\%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://wellcomeopenresearch.org/articles/7-189',
			'doi' => '10.12688/wellcomeopenres.17925.1',
			'modified' => '2022-09-28 09:13:35',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4518',
			'name' => 'Equilibrated evolution of the mixed auto-/allopolyploidhaplotype-resolved genome of the invasive hexaploid Prussian carp.',
			'authors' => 'Kuhl  Heiner et al.',
			'description' => '<p>Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35835759',
			'doi' => '10.1038/s41467-022-31515-w',
			'modified' => '2023-02-17 08:58:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4372',
			'name' => 'Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing',
			'authors' => 'Yang  X. et al.',
			'description' => '<p>The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (haplotype 1 (H1): 3.1 Gb, haplotype 2 (H2): 2.9 Gb). The continuity (H1: contig N50 = 28.2 Mb, H2: contig N50 = 25.9 Mb) and completeness (BUSCO: H1 = 94.9\%, H2 = 93.5\%) are substantially better than those of other Chinese genomes, for example, HX1, NH1.0, and YH2.0. By comparing HJ genome with GRCh38, we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2, respectively. In addition, we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2, respectively. Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.fmre.2022.02.005',
			'doi' => '10.1016/j.fmre.2022.02.005',
			'modified' => '2022-08-04 16:11:38',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4523',
			'name' => 'Complete Genome Sequence of Herpes Simplex Virus 2 StrainG.',
			'authors' => 'Chang  Weizhong et al.',
			'description' => '<p>Herpes simplex virus type (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the '&alpha;' sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the '&alpha;' sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35336943',
			'doi' => '10.3390/v14030536',
			'modified' => '2023-02-17 09:03:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4464',
			'name' => 'The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900',
			'authors' => 'Macadam  Craig et al. ',
			'description' => '<p>We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79\%) is scaffolded into 12 chromosomal pseudomolecules, with the X sex chromosome assembled. The X chromosome was found at half coverage, but no Y chromosome was found. The mitochondrial genome was assembled, and is 16.0 kb in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17684.1',
			'doi' => '10.12688/wellcomeopenres.17684.1',
			'modified' => '2022-10-21 09:51:18',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4465',
			'name' => 'The genome sequence of the furry-claspered furrow bee, Lasioglossumlativentre (Schenck, 1853)',
			'authors' => 'Falk  Steven and Monks  Joseph',
			'description' => '<p>We present a genome assembly from an individual male Lasioglossum lativentre (the furry-claspered furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 479 megabases in span. The majority of the assembly (75.22\%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome was also assembled, and is 15.3 kilobases in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17706.1',
			'doi' => '10.12688/wellcomeopenres.17706.1',
			'modified' => '2022-10-21 09:51:46',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => 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) 30 => array(
			'id' => '4369',
			'name' => 'The genome sequence of a parasitoid wasp,  Forster, 1771.',
			'authors' => 'Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual female (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64\%) is scaffolded into 12 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 10,622 protein coding genes.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419493',
			'doi' => '10.12688/wellcomeopenres.17683.1',
			'modified' => '2022-08-04 16:21:40',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4506',
			'name' => 'The genome sequence of the brimstone moth, Opisthograptis luteolata(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas and Phillips  Dominic',
			'description' => '<p>We present a genome assembly from an individual male (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226159',
			'doi' => '10.12688/wellcomeopenres.18101.1',
			'modified' => '2023-02-17 08:59:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4529',
			'name' => 'The genome sequence of Gymnosoma rotundatum (Linnaeus, 1758), aparasitoid ladybird fly',
			'authors' => 'Smith  Matthew',
			'description' => '<p>We present a genome assembly from an individual male (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 779 megabases in span. The majority of the assembly (97.07\%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419492',
			'doi' => '10.12688/wellcomeopenres.17782.1',
			'modified' => '2023-02-17 09:00:46',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4256',
			'name' => 'Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca).',
			'authors' => 'Huang Yi et al.',
			'description' => '<p>Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2\%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.</p>',
			'date' => '2021-11-01',
			'pmid' => 'https://doi.org/10.1093%2Fjhered%2Fesab071',
			'doi' => '10.1093/jhered/esab071',
			'modified' => '2022-05-20 09:47:15',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => 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) 35 => array(
			'id' => '4308',
			'name' => 'De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus).',
			'authors' => 'Pickett, Brandon D and Glass, Jessica R and Ridge, PerryG and Kauwe, John S K',
			'description' => '<p>The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95\% complete, and the genome is comprised of 16.9\% repetitive elements. The assembly was annotated with 33.1&thinsp;K protein-coding genes, 71.4\% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://doi.org/10.1093%2Fg3journal%2Fjkab229',
			'doi' => '10.1093/g3journal/jkab229',
			'modified' => '2022-06-20 09:08:51',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => 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) 37 => 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) 38 => array(
			'id' => '4123',
			'name' => 'Familial thrombocytopenia due to a complex structural variant resulting ina WAC-ANKRD26 fusion transcript.',
			'authors' => 'Wahlster, Lara and Verboon, Jeffrey M and Ludwig, Leif S and Black, Susan Cand Luo, Wendy and Garg, Kopal and Voit, Richard A and Collins, Ryan L andGarimella, Kiran and Costello, Maura and Chao, Katherine R and Goodrich,Julia K and DiTroia, Stephanie ',
			'description' => '<p>Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleotide variants that prevent silencing of ANKRD26 expression during hematopoietic differentiation. Short-read whole-exome and genome sequencing approaches were unable to identify a causal variant in this family. Using long-read whole-genome sequencing, a large complex structural variant involving a paired-duplication inversion was identified. Through functional studies, we show that this structural variant results in a pathogenic gain-of-function WAC-ANKRD26 fusion transcript. Our findings illustrate how complex structural variants that may be missed by conventional genome sequencing approaches can cause human disease.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33857290',
			'doi' => '10.1084/jem.20210444',
			'modified' => '2021-12-07 09:58:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4134',
			'name' => 'PCIP-seq: simultaneous sequencing of integrated viral genomes and theirinsertion sites with long reads.',
			'authors' => 'Artesi, M. et al.',
			'description' => '<p>The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33823910',
			'doi' => '10.1186/s13059-021-02307-0',
			'modified' => '2021-12-10 17:12:45',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => 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) 41 => array(
			'id' => '4122',
			'name' => 'Comparison of long read sequencing technologies in interrogating bacteriaand fly genomes.',
			'authors' => 'Tvedte, Eric S and Gasser, Mark and Sparklin, Benjamin C and Michalski,Jane and Hjelmen, Carl E and Johnston, J Spencer and Zhao, Xuechu andBromley, Robin and Tallon, Luke J and Sadzewicz, Lisa and Rasko, David Aand Hotopp, Julie C Dunning',
			'description' => '<p>The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33768248',
			'doi' => '10.1093/g3journal/jkab083',
			'modified' => '2021-12-07 09:57:33',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => 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) 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' => '4037',
			'name' => 'Complete Genome Sequence of  sp. Strain Nx66, Isolated from WatersContaminated with Petrochemicals in El Saf-Saf Valley, Algeria.',
			'authors' => 'Chéraiti, Nardjess and Plewniak, Frédéric and Tighidet, Salima andSayeh, Amalia and Gil, Lisa and Malherbe, Ludivine and Memmi, Yosr andZilliox, Laurence and Vandecasteele, Céline and Boyer, Pierre andLopez-Roques, Céline and Jaulhac, Benoît and Bensou',
			'description' => '<p>sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 &times; 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42&thinsp;Mb and one plasmid of 34.22&thinsp;kb.</p>',
			'date' => '2020-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29457705',
			'doi' => '10.1128/MRA.01130-20',
			'modified' => '2021-02-18 17:13:56',
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		(int) 47 => array(
			'id' => '4043',
			'name' => 'Contrasting signatures of genomic divergence during sympatric speciation.',
			'authors' => 'Kautt, Andreas F and Kratochwil, Claudius F and Nater, Alexander andMachado-Schiaffino, Gonzalo and Olave, Melisa and Henning, Frederico andTorres-Dowdall, Julián and Härer, Andreas and Hulsey, C Darrin andFranchini, Paolo and Pippel, Martin and Myers,',
			'description' => '<p>The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33116308',
			'doi' => '10.1038/s41586-020-2845-0',
			'modified' => '2021-02-19 13:51:04',
			'created' => '2021-02-18 10:21:53',
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		(int) 48 => array(
			'id' => '4066',
			'name' => 'Genome structure and content of the rice root-knot nematode ().',
			'authors' => 'Phan, Ngan Thi and Orjuela, Julie and Danchin, Etienne G J and Klopp,Christophe and Perfus-Barbeoch, Laetitia and Kozlowski, Djampa K andKoutsovoulos, Georgios D and Lopez-Roques, Céline and Bouchez, Olivier andZahm, Margot and Besnard, Guillaume and B',
			'description' => '<p>Discovered in the 1960s, is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294&nbsp;kb, totaling 41.5&nbsp;Mb). The completeness scores of our assembly are among the highest currently published for genomes. We predicted 10,284 protein-coding genes spanning 75.5\% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61\% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of .&nbsp; and its closest relatives.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33144944',
			'doi' => '10.1002/ece3.6680',
			'modified' => '2021-02-19 17:46:50',
			'created' => '2021-02-18 10:21:53',
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		(int) 49 => array(
			'id' => '4074',
			'name' => 'Repeat expansions confer WRN dependence in microsatellite-unstablecancers.',
			'authors' => 'van Wietmarschen, Niek and Sridharan, Sriram and Nathan, William J andTubbs, Anthony and Chan, Edmond M and Callen, Elsa and Wu, Wei and Belinky,Frida and Tripathi, Veenu and Wong, Nancy and Foster, Kyla and Noorbakhsh,Javad and Garimella, Kiran and Cr',
			'description' => '<p>The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32999459',
			'doi' => '10.1038/s41586-020-2769-8',
			'modified' => '2021-02-19 18:07:45',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
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		),
		(int) 50 => array(
			'id' => '4081',
			'name' => 'Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient withe14a3 BCR-ABL1 transcript using Nanopore sequencing.',
			'authors' => 'Zhao, Hu and Chen, Yuan and Shen, Chanjuan and Li, Lingshu and Li, Qingzhaoand Tan, Kui and Huang, Huang and Hu, Guoyu',
			'description' => '<p>BACKGROUND: The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations. Here, we present a CML patient with e14a3 BCR-ABL1 transcript and t(9;22;12) variant Philadelphia (Ph) chromosome. METHODS: Cytogenetic analysis and fluorescence in situ hybridization (FISH) was performed to identify the chromosomal aberrations and gene fusions. Rare fusion transcript was verified by a reverse transcription-polymerase chain reaction (RT-PCR). Breakpoints were characterized and validated using Oxford Nanopore Technologies (ONT) (Oxford, UK) and Sanger sequencing, respectively. RESULTS: The karyotype showed the translocation t(9;22;12)(q34;q11.2;q24) [20] and FISH indicated 40\% positive BCR-ABL1 fusion signals. The RT-PCR suggested e14a3 type fusion transcript. The ONT sequencing analysis identified specific positions of translocation breakpoints: chr22:23633040-chr9:133729579, chr12:121567595-chr22:24701405, which were confirmed using Sanger sequencing. The patient achieved molecular remission 3 months after imatinib therapy. CONCLUSIONS: The present study indicates Nanopore sequencing as a valid strategy, which can characterize breakpoints precisely in special clinical cases with atypical structural variations. CML patients with e14a3 transcripts may have good clinical course in the tyrosine kinase inhibitor era, as reviewed here.</p>',
			'date' => '2020-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32949441',
			'doi' => '10.1002/jgm.3276',
			'modified' => '2021-03-15 16:56:36',
			'created' => '2021-02-18 10:21:53',
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		(int) 51 => array(
			'id' => '4059',
			'name' => 'Interruption of an MSH4 homolog blocks meiosis in metaphase I andeliminates spore formation in Pleurotus ostreatus.',
			'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
			'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
			'date' => '2020-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
			'doi' => '10.1371/journal.pone.0241749',
			'modified' => '2021-02-19 17:26:09',
			'created' => '2021-02-18 10:21:53',
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			'description' => '<p><span>The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.</span></p>',
			'author' => 'Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.',
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			'description' => '<p>As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.</p>',
			'author' => 'Brewster Kingham, Delaware Biotechnology Institute,  University of Delaware',
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			'description' => '<p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p>',
			'author' => 'Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen',
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$testimonials = '<blockquote><p><span>The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.</span></p><cite>Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.</cite></blockquote>
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$featured_testimonials = '<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.</p><cite>Brewster Kingham, Delaware Biotechnology Institute,  University of Delaware</cite></blockquote>
<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p><cite>Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen</cite></blockquote>
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	'description' => '<p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p>',
	'author' => 'Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen',
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<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
<p><span style="font-weight: 400;">The new 12 sample&nbsp;capacity&nbsp;is optimal for use prior to library preparation on the <a href="https://www.pacb.com/revio/">PacBio Revio</a>, matching the new system's higher throughput and increased&nbsp;efficiency on time.&nbsp;</span></p>
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	'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
	'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
	'date' => '2020-01-01',
	'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
	'doi' => '10.1371/journal.pone.0241749',
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View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
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<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
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<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
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<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
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<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
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<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
<ul>
<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
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<p></p>
<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
<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><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
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<td class="text-center" style="width: 636px; height: 38px;" colspan="2">Multiple orifice hydrodynamic pore</td>
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<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
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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' => '<h2 style="text-align: left;">The DNAFluid+ Kit for viscous DNA</h2>
<p><span style="font-weight: 400;">The DNAFluid+ Kit for viscous DNA&nbsp; eliminates the challenges of using </span><b>highly viscous extracted DNA samples </b><span style="font-weight: 400;">for any downstream steps and QC. The</span><span style="font-weight: 400;">&nbsp;</span><b><i>DNAFluid+ Kit </i></b><span style="font-weight: 400;">consists of proprietary "<span>Hydropore-Syringe" and "Hydro Tube"&nbsp;</span>shearing accessories that reduce the viscosity of DNA by pre-conditioning&nbsp;high molecular weight DNA prior to shearing on the </span><b><i>Megaruptor 3. </i></b><span style="font-weight: 400;">This combination of the DNAFluid+ Kit and the Megaruptor 3 together achieve effective, automated homogenization of highly viscous DNA samples while keeping the integrity of the DNA and full control of the DNA size prior to any downstream applications.&nbsp;</span></p>
<p><br /> <a href="https://www.diagenode.com/files/products/kits/Application_Note-DNAFluid.pdf"><img src="https://www.diagenode.com/img/banners/banner-appnote-dnafluid.png" /></a></p>',
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			'info1' => '<h3>Validation data: DNAFluid+ Kit for viscous DNA</h3>
<p><span>Validation of the DNA Fluid+ Kit on viscous samples is shown below. HMW DNA was extracted from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit. First, the sample was pre-sheared using the DNA Fluid+ Kit (speed 59) and then diluted to 50 ng/uL and sheared using the Long Hydropore (speed 31) on the Megaruptor 3 system. PacBio HiFi sequencing was performed on the sheared DNA using a 30 hr movie, SMRTbell Express Template Prep Kit 2.0, Binding Kit 2.0, and Sequel II Sequencing Kit 2.0, and Circulomics SRE XS size selection. These results show that Circulomics SRE XS is a good substitute for gel-based size selection and that the DNAFluid+ works well to pre-condition DNA for Long Hydropore shearing without clogging.</span></p>
<h2 class="card-title text-lg">DNA Fluid+ Kit effectively pre-conditions HMW DNA to allow consistent shearing across samples of varying viscosity.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid1.png" /></p>
<p><span>Fig.1. The Femto Pulse traces show fragment size distributions of: 1) native HMW DNA isolated from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit (black curve), 2) after pre-shearing with the Diagenode DNA Fluid+ Kit (blue curve) and 3) after shearing to ~18 kb with the Diagenode Long Hydropore using Megaruptor3 (red curve). Pre-shearing the HMW DNA enables more consistent shearing performance across samples of varying viscosity.</span></p>
<h2 class="card-title text-lg">Excellent read length distribution of sequencing results using DNA treated with DNA Fluid+ Kit.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid2.png" width="600" height="449" /></p>
<p class="text-xs">Fig. 2. After shearing the gDNA that was pre-conditioned with the Diagenode DNA Fluid+ Kit, HiFi read length distribution of GM12878 SMRTbell library shows excellent read length distribution. Sequencing was performed on the PacBio Sequel II system.</p>
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<p>Sterile Hydropores, Syringes, and Hydro Tubes 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>
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<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
<p><span style="font-weight: 400;">The new 12 sample&nbsp;capacity&nbsp;is optimal for use prior to library preparation on the <a href="https://www.pacb.com/revio/">PacBio Revio</a>, matching the new system's higher throughput and increased&nbsp;efficiency on time.&nbsp;</span></p>
<p>See video on how to use your 12 sample cassette:</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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<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>
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<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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			'name' => 'Megaruptor<sup>&reg;</sup> 3 Quick guide',
			'description' => '<p>The Megaruptor<sup>&reg;</sup> 3 is intended for laboratory use. It is not suitable for clinical use. Use of the Megaruptor 3 in any manner other than as directed herein could cause harm to persons and may void the warranty. Diagenode will not be responsible for injury or damage resulting from improper use of the Megaruptor 3.</p>',
			'image_id' => '185',
			'type' => 'Quick guide',
			'url' => 'files/products/shearing_technology/megaruptor/megaruptor-quick-guide.pdf',
			'slug' => 'megaruptor-3-quick-guide',
			'meta_keywords' => 'Megaruptor 3 Quick guide',
			'meta_description' => 'Megaruptor 3 Quick guide',
			'modified' => '2019-03-21 16:04:50',
			'created' => '2019-03-21 16:04:50',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => 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',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '1169',
			'name' => 'Sage Science size selection with Diagenode Megaruptor',
			'description' => '<p>Best practices: Sage Science size selection with Diagenode Megaruptor shearing for long-read sequencing library preparation</p>',
			'image_id' => null,
			'type' => 'Application Note',
			'url' => 'files/application_notes/AN-SageScience-DiagenodeMegaruptor.pdf',
			'slug' => 'sagescience-diagenodemegaruptor-appnote',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2023-08-25 14:17:07',
			'created' => '2023-08-25 14:17:07',
			'ProductsDocument' => array(
				[maximum depth reached]
			)
		)
	),
	'Feature' => array(
		(int) 0 => array(
			'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]
			)
		),
		(int) 1 => 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) 2 => array(
			'id' => '31',
			'name' => '1 to 8 samples in parallel 	',
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2019-02-20 17:53:02',
			'created' => '2019-02-20 17:53:02',
			'ProductsFeature' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '35',
			'name' => 'Tuneable to between 5 - 100 kb',
			'slug' => '',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2019-02-20 17:57:48',
			'created' => '2019-02-20 17:57:48',
			'ProductsFeature' => array(
				[maximum depth reached]
			)
		)
	),
	'Image' => array(
		(int) 0 => array(
			'id' => '1787',
			'name' => 'product/shearing_technologies/B06010003_megaruptor3.jpg',
			'alt' => 'Megaruptor 3',
			'modified' => '2019-03-05 16:00:39',
			'created' => '2018-12-20 16:39:37',
			'ProductsImage' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '1791',
			'name' => 'product/shearing_technologies/B06010003-megaruptor3-1.jpg',
			'alt' => 'Removable cassette',
			'modified' => '2019-03-05 16:00:19',
			'created' => '2019-03-05 15:54:34',
			'ProductsImage' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '1792',
			'name' => 'product/shearing_technologies/B06010003-megaruptor3-2.jpg',
			'alt' => 'Screen',
			'modified' => '2019-03-05 16:00:10',
			'created' => '2019-03-05 15:56:34',
			'ProductsImage' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '1793',
			'name' => 'product/shearing_technologies/B06010003-megaruptor3-3.jpg',
			'alt' => 'Megaruptor 3 with removable cassette',
			'modified' => '2019-03-05 15:59:57',
			'created' => '2019-03-05 15:57:26',
			'ProductsImage' => array(
				[maximum depth reached]
			)
		)
	),
	'Promotion' => array(),
	'Protocol' => array(),
	'Publication' => array(
		(int) 0 => array(
			'id' => '4663',
			'name' => 'The genome sequence of the Elbow-stripe Grass-veneer, Agriphilageniculea (Haworth, 1811)',
			'authors' => 'Boyes  Douglas and Hammond  James',
			'description' => '<p>We present a genome assembly from an individual female Agriphila geniculea (the Elbow-stripe Grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 781.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,132 protein coding genes.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18910.1',
			'doi' => '10.12688/wellcomeopenres.18910.1',
			'modified' => '2023-03-07 08:31:00',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '4664',
			'name' => 'The genome sequence of the Turnip Sawfly, Athalia rosae(Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Broad  Gavin R. and Green  Andrew',
			'description' => '<p>We present a genome assembly from an individual female Athalia rosae (the Turnip Sawfly; Arhropoda; Insecta; Hymenoptera; Athaliidae). The genome sequence is 172 megabases in span. Most of the assembly is scaffolded into eight chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,393 protein coding genes.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18993.1',
			'doi' => '10.12688/wellcomeopenres.18993.1',
			'modified' => '2023-03-07 08:31:39',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '4539',
			'name' => 'A high-quality, haplotype-phased genome reconstruction reveals unexpectedhaplotype diversity in a pearl oyster.',
			'authors' => 'Takeuchi  Takeshi et al.',
			'description' => '<p>Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (&gt;38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997\%. Moreover, the haplotypes contain 95.2\% and 95.9\%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3\% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.</p>',
			'date' => '2022-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36351462',
			'doi' => '10.1093/dnares/dsac035',
			'modified' => '2023-02-17 08:49:27',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '4481',
			'name' => 'Complete Genome Sequence of Lacticaseibacillus rhamnosus DM065,Isolated from the Human Oral Cavity.',
			'authors' => 'Park  Do-Young et al.',
			'description' => '<p>The 3.0-Mb complete genome of Lacticaseibacillus rhamnosus strain DM065, which was isolated from the oral cavity of healthy volunteers in South Korea, was sequenced using a combination of PacBio and Illumina technologies. The genome consists of one circular chromosome and two plasmids and lacks antimicrobial resistance genes.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36321910',
			'doi' => '10.1128/mra.00899-22',
			'modified' => '2022-11-18 12:27:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4655',
			'name' => 'The genome sequence of the malaria mosquito, Anopheles funestus,Giles, 1900',
			'authors' => 'Ayala  Diego et al.',
			'description' => '<p>We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18445.1',
			'doi' => '10.12688/wellcomeopenres.18445.1',
			'modified' => '2023-03-07 08:54:22',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4475',
			'name' => 'Semi-automated assembly of high-quality diploid human reference genomes.',
			'authors' => 'Jarvis  Erich D et al.',
			'description' => '<p>The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within &plusmn;1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36261518',
			'doi' => '10.1038/s41586-022-05325-5',
			'modified' => '2022-11-18 12:20:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4477',
			'name' => 'Integration of Hi-C with short and long-read genome sequencingreveals the structure of germline rearranged genomes.',
			'authors' => 'Schöpflin  R.et al.',
			'description' => '<p>Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in &gt;300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100&thinsp;kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200&thinsp;kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36309531',
			'doi' => '10.1038/s41467-022-34053-7',
			'modified' => '2022-11-18 12:22:31',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4485',
			'name' => 'The genome sequence of the orange-tip butterfly, Anthocharis cardamines(Linnaeus, 1758)',
			'authors' => 'Ebdon  S. et al.',
			'description' => '<p>We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74\%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18117.1',
			'doi' => '10.12688/wellcomeopenres.18117.1',
			'modified' => '2022-11-18 12:32:05',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4486',
			'name' => 'The genome sequence of the satellite, Eupsilia transversa (Hufnagel,1766)',
			'authors' => 'Crowley  L. et al.',
			'description' => '<p>We present a genome assembly from an individual female Eupsilia transversa (the satellite; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 467 megabases in span. The entire assembly (100\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,065 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18105.1',
			'doi' => '10.12688/wellcomeopenres.18105.1',
			'modified' => '2022-11-18 12:32:51',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4487',
			'name' => 'The genome sequence of the common yellow swallowtail, Papilio machaon(Linnaeus, 1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual female Papilio machaon (the common yellow swallowtail; Arthropoda; Insecta; Lepidoptera; Papilionidae). The genome sequence is 252 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 31 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,323 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18119.1',
			'doi' => '10.12688/wellcomeopenres.18119.1',
			'modified' => '2022-11-18 12:33:33',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4489',
			'name' => 'The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual male Erebia ligea (Arran brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 506 megabases in span. The majority (99.92\%) of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.2 kilobases in length.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18115.1',
			'doi' => '10.12688/wellcomeopenres.18115.1',
			'modified' => '2022-11-18 12:36:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4500',
			'name' => 'Complete Genome Sequence of  Strain DM083 Isolated from HumanTongue Coating.',
			'authors' => 'Park  Do-Young  et al.',
			'description' => '<p>We isolated Lactiplantibacillus plantarum DM083 from the human tongue coating to establish a strain library for oral probiotics. It has a single circular 3,197,299 bp chromosome with a guanine-cytosine (GC) content of 44.6\% without plasmids. Importantly, the genome is devoid of the antimicrobial resistance gene, satisfying the minimum safety requirement for probiotics.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36165646',
			'doi' => '10.1128/mra.00675-22',
			'modified' => '2022-11-21 10:32:09',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4501',
			'name' => 'The genome sequence of the yellow-legged clearwing, Synanthedonvespiformis (Linnaeus, 1761)',
			'authors' => 'Boyes  Douglas and Lees  David',
			'description' => '<p>We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100\% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length. Keywords</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18109.1',
			'doi' => '10.12688/wellcomeopenres.18109.1',
			'modified' => '2022-11-21 10:32:47',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4503',
			'name' => 'The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763)',
			'authors' => 'Boyes  Douglas and Boyes  Clare',
			'description' => '<p>We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18103.1',
			'doi' => '10.12688/wellcomeopenres.18103.1',
			'modified' => '2022-11-21 10:35:00',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4504',
			'name' => 'The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808)',
			'authors' => 'Boyes  Douglas and Gibbs  Melanie',
			'description' => '<p>We present a genome assembly from an individual female Mythimna impura (smoky wainscot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 949 megabases in span. The majority of the assembly (98.39\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,441 protein coding genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18104.1',
			'doi' => '10.12688/wellcomeopenres.18104.1',
			'modified' => '2022-11-21 10:35:36',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4509',
			'name' => 'Comparative analyses of Theobroma cacao and T. grandiflorummitogenomes reveal conserved gene content embedded within complex andplastic structures.',
			'authors' => 'de Abreu  Vinicius A C et al.',
			'description' => '<p>Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and comparative analyses. The two most known species in Theobroma L. (Malvaceae s.l.) genus are T. cacao, and T. grandiflorum. Besides the economic value, both species also show considerable biotechnology potential due to their other derived products, thus, aggregating additional economic value for the agroindustry. Here, we assembled and compared the mtDNA of Theobroma cacao and T. grandiflorum to generate a new genomics resource and unravel evolutionary trends. Graph-based analyses revealed that both mtDNA exhibit multiple alternative arrangements, confirming the dynamism commonly observed in plant mtDNA. The disentangled assembly graph revealed potential predominant circular molecules. The master circle molecules span 543,794&nbsp;bp for T. cacao and 501,598&nbsp;bp for T. grandiflorum, showing 98.9\% of average sequence identity. Both mtDNA contains the same set of 39 plant mitochondrial genes, commonly found in other rosid mitogenomes. The main features are a duplicated copy of atp4, the absence of rpl6, rps2, rps8, and rps11, and the presence of two chimeric open-reading frames. Moreover, we detected few ptDNA integrations mainly represented by tRNAs, and no viral sequences were detected. Phylogenomics analyses indicate Theobroma spp. are nested in Malvaceae family. The main mtDNA differences are related to distinct structural rearrangements and exclusive regions associated with relics of Transposable Elements, supporting the hypothesis of dynamic mitochondrial genome maintenance and divergent evolutionary paths and pressures after species differentiation.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36150535',
			'doi' => '10.1016/j.gene.2022.146904',
			'modified' => '2022-11-21 10:36:50',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4505',
			'name' => 'The genome sequence of the wall brown, Lasiommata megera (Linnaeus,1767)',
			'authors' => 'Lohse  Konrad and Wright  Charlotte',
			'description' => '<p>We present a genome assembly from an individual female Lasiommata megera (the wall brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 488 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 30 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18106.1',
			'doi' => '10.12688/wellcomeopenres.18106.1',
			'modified' => '2023-02-17 08:54:13',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4507',
			'name' => 'The genome sequence of the sallow kitten, Furcula furcula (Clerck,1759)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100\%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18112.1',
			'doi' => '10.12688/wellcomeopenres.18112.1',
			'modified' => '2023-02-17 08:55:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4508',
			'name' => 'The genome sequence of the peacock moth, Macaria notata (Linnaeus,1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18108.1',
			'doi' => '10.12688/wellcomeopenres.18108.1',
			'modified' => '2023-02-17 08:56:15',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4513',
			'name' => 'Plant species-specific basecaller improves actual accuracy of nanoporesequencing',
			'authors' => 'Ferguson  Scott et al.',
			'description' => '<p>Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specific basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specific basecaller models. We also evaluate accuracy gains from ONT&rsquo;s improved flowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1919465%2Fv1',
			'doi' => '10.21203/rs.3.rs-1919465/v1',
			'modified' => '2023-02-17 08:57:19',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => 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) 21 => array(
			'id' => '4450',
			'name' => 'The leaf beetle Chelymorpha alternans propagates a plant pathogen inexchange for pupal protection.',
			'authors' => 'Berasategui  Aileen et al.',
			'description' => '<p>Many insects rely on microbial protection in the early stages of their development. However, in contrast to symbiont-mediated defense of eggs and young instars, the role of microbes in safeguarding pupae remains relatively unexplored, despite the susceptibility of the immobile stage to antagonistic challenges. Here, we outline the importance of symbiosis in ensuring pupal protection by describing a mutualistic partnership between the ascomycete Fusarium oxysporum and Chelymorpha alternans, a leaf beetle. The symbiont rapidly proliferates at the onset of pupation, extensively and conspicuously coating C.&nbsp;alternans during metamorphosis. The fungus confers defense against predation as symbiont elimination results in reduced pupal survivorship. In exchange, eclosing beetles vector F.&nbsp;oxysporum to their host plants, resulting in a systemic infection. By causing wilt disease, the fungus retained its phytopathogenic capacity in light of its symbiosis with C.&nbsp;alternans. Despite possessing a relatively reduced genome, F.&nbsp;oxysporum encodes metabolic pathways that reflect its dual lifestyle as a plant pathogen and a defensive insect symbiont. These include virulence factors underlying plant colonization, along with mycotoxins that may contribute to the defensive biochemistry of the insect host. Collectively, our findings shed light on a mutualism predicated on pupal protection of an herbivorous beetle in exchange for symbiont dissemination and propagation.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35987210',
			'doi' => '10.1016/j.cub.2022.07.065',
			'modified' => '2022-10-21 09:29:09',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4431',
			'name' => 'The genome sequence of the hawthorn shieldbug, Acanthosomahaemorrhoidale (Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Mulley  John',
			'description' => '<p>We present a genome assembly from an individual male Acanthosoma haemorrhoidale (hawthorn shieldbug; Arthropoda; Insecta; Hemiptera; Acanthosomatidae). The genome sequence is 866 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 7 chromosomal pseudomolecules with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 18.9 kilobases in length.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17926.1',
			'doi' => '10.12688/wellcomeopenres.17926.1',
			'modified' => '2022-09-28 09:09:34',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4433',
			'name' => 'The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87\%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://wellcomeopenresearch.org/articles/7-189',
			'doi' => '10.12688/wellcomeopenres.17925.1',
			'modified' => '2022-09-28 09:13:35',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4518',
			'name' => 'Equilibrated evolution of the mixed auto-/allopolyploidhaplotype-resolved genome of the invasive hexaploid Prussian carp.',
			'authors' => 'Kuhl  Heiner et al.',
			'description' => '<p>Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35835759',
			'doi' => '10.1038/s41467-022-31515-w',
			'modified' => '2023-02-17 08:58:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4372',
			'name' => 'Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing',
			'authors' => 'Yang  X. et al.',
			'description' => '<p>The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (haplotype 1 (H1): 3.1 Gb, haplotype 2 (H2): 2.9 Gb). The continuity (H1: contig N50 = 28.2 Mb, H2: contig N50 = 25.9 Mb) and completeness (BUSCO: H1 = 94.9\%, H2 = 93.5\%) are substantially better than those of other Chinese genomes, for example, HX1, NH1.0, and YH2.0. By comparing HJ genome with GRCh38, we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2, respectively. In addition, we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2, respectively. Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.fmre.2022.02.005',
			'doi' => '10.1016/j.fmre.2022.02.005',
			'modified' => '2022-08-04 16:11:38',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4523',
			'name' => 'Complete Genome Sequence of Herpes Simplex Virus 2 StrainG.',
			'authors' => 'Chang  Weizhong et al.',
			'description' => '<p>Herpes simplex virus type (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the '&alpha;' sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the '&alpha;' sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35336943',
			'doi' => '10.3390/v14030536',
			'modified' => '2023-02-17 09:03:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4464',
			'name' => 'The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900',
			'authors' => 'Macadam  Craig et al. ',
			'description' => '<p>We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79\%) is scaffolded into 12 chromosomal pseudomolecules, with the X sex chromosome assembled. The X chromosome was found at half coverage, but no Y chromosome was found. The mitochondrial genome was assembled, and is 16.0 kb in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17684.1',
			'doi' => '10.12688/wellcomeopenres.17684.1',
			'modified' => '2022-10-21 09:51:18',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4465',
			'name' => 'The genome sequence of the furry-claspered furrow bee, Lasioglossumlativentre (Schenck, 1853)',
			'authors' => 'Falk  Steven and Monks  Joseph',
			'description' => '<p>We present a genome assembly from an individual male Lasioglossum lativentre (the furry-claspered furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 479 megabases in span. The majority of the assembly (75.22\%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome was also assembled, and is 15.3 kilobases in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17706.1',
			'doi' => '10.12688/wellcomeopenres.17706.1',
			'modified' => '2022-10-21 09:51:46',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => 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) 30 => array(
			'id' => '4369',
			'name' => 'The genome sequence of a parasitoid wasp,  Forster, 1771.',
			'authors' => 'Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual female (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64\%) is scaffolded into 12 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 10,622 protein coding genes.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419493',
			'doi' => '10.12688/wellcomeopenres.17683.1',
			'modified' => '2022-08-04 16:21:40',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4506',
			'name' => 'The genome sequence of the brimstone moth, Opisthograptis luteolata(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas and Phillips  Dominic',
			'description' => '<p>We present a genome assembly from an individual male (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226159',
			'doi' => '10.12688/wellcomeopenres.18101.1',
			'modified' => '2023-02-17 08:59:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4529',
			'name' => 'The genome sequence of Gymnosoma rotundatum (Linnaeus, 1758), aparasitoid ladybird fly',
			'authors' => 'Smith  Matthew',
			'description' => '<p>We present a genome assembly from an individual male (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 779 megabases in span. The majority of the assembly (97.07\%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419492',
			'doi' => '10.12688/wellcomeopenres.17782.1',
			'modified' => '2023-02-17 09:00:46',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4256',
			'name' => 'Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca).',
			'authors' => 'Huang Yi et al.',
			'description' => '<p>Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2\%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.</p>',
			'date' => '2021-11-01',
			'pmid' => 'https://doi.org/10.1093%2Fjhered%2Fesab071',
			'doi' => '10.1093/jhered/esab071',
			'modified' => '2022-05-20 09:47:15',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => 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) 35 => array(
			'id' => '4308',
			'name' => 'De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus).',
			'authors' => 'Pickett, Brandon D and Glass, Jessica R and Ridge, PerryG and Kauwe, John S K',
			'description' => '<p>The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95\% complete, and the genome is comprised of 16.9\% repetitive elements. The assembly was annotated with 33.1&thinsp;K protein-coding genes, 71.4\% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://doi.org/10.1093%2Fg3journal%2Fjkab229',
			'doi' => '10.1093/g3journal/jkab229',
			'modified' => '2022-06-20 09:08:51',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => 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) 37 => 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) 38 => array(
			'id' => '4123',
			'name' => 'Familial thrombocytopenia due to a complex structural variant resulting ina WAC-ANKRD26 fusion transcript.',
			'authors' => 'Wahlster, Lara and Verboon, Jeffrey M and Ludwig, Leif S and Black, Susan Cand Luo, Wendy and Garg, Kopal and Voit, Richard A and Collins, Ryan L andGarimella, Kiran and Costello, Maura and Chao, Katherine R and Goodrich,Julia K and DiTroia, Stephanie ',
			'description' => '<p>Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleotide variants that prevent silencing of ANKRD26 expression during hematopoietic differentiation. Short-read whole-exome and genome sequencing approaches were unable to identify a causal variant in this family. Using long-read whole-genome sequencing, a large complex structural variant involving a paired-duplication inversion was identified. Through functional studies, we show that this structural variant results in a pathogenic gain-of-function WAC-ANKRD26 fusion transcript. Our findings illustrate how complex structural variants that may be missed by conventional genome sequencing approaches can cause human disease.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33857290',
			'doi' => '10.1084/jem.20210444',
			'modified' => '2021-12-07 09:58:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4134',
			'name' => 'PCIP-seq: simultaneous sequencing of integrated viral genomes and theirinsertion sites with long reads.',
			'authors' => 'Artesi, M. et al.',
			'description' => '<p>The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33823910',
			'doi' => '10.1186/s13059-021-02307-0',
			'modified' => '2021-12-10 17:12:45',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => 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) 41 => array(
			'id' => '4122',
			'name' => 'Comparison of long read sequencing technologies in interrogating bacteriaand fly genomes.',
			'authors' => 'Tvedte, Eric S and Gasser, Mark and Sparklin, Benjamin C and Michalski,Jane and Hjelmen, Carl E and Johnston, J Spencer and Zhao, Xuechu andBromley, Robin and Tallon, Luke J and Sadzewicz, Lisa and Rasko, David Aand Hotopp, Julie C Dunning',
			'description' => '<p>The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33768248',
			'doi' => '10.1093/g3journal/jkab083',
			'modified' => '2021-12-07 09:57:33',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => 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) 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' => '4037',
			'name' => 'Complete Genome Sequence of  sp. Strain Nx66, Isolated from WatersContaminated with Petrochemicals in El Saf-Saf Valley, Algeria.',
			'authors' => 'Chéraiti, Nardjess and Plewniak, Frédéric and Tighidet, Salima andSayeh, Amalia and Gil, Lisa and Malherbe, Ludivine and Memmi, Yosr andZilliox, Laurence and Vandecasteele, Céline and Boyer, Pierre andLopez-Roques, Céline and Jaulhac, Benoît and Bensou',
			'description' => '<p>sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 &times; 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42&thinsp;Mb and one plasmid of 34.22&thinsp;kb.</p>',
			'date' => '2020-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29457705',
			'doi' => '10.1128/MRA.01130-20',
			'modified' => '2021-02-18 17:13:56',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4043',
			'name' => 'Contrasting signatures of genomic divergence during sympatric speciation.',
			'authors' => 'Kautt, Andreas F and Kratochwil, Claudius F and Nater, Alexander andMachado-Schiaffino, Gonzalo and Olave, Melisa and Henning, Frederico andTorres-Dowdall, Julián and Härer, Andreas and Hulsey, C Darrin andFranchini, Paolo and Pippel, Martin and Myers,',
			'description' => '<p>The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33116308',
			'doi' => '10.1038/s41586-020-2845-0',
			'modified' => '2021-02-19 13:51:04',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4066',
			'name' => 'Genome structure and content of the rice root-knot nematode ().',
			'authors' => 'Phan, Ngan Thi and Orjuela, Julie and Danchin, Etienne G J and Klopp,Christophe and Perfus-Barbeoch, Laetitia and Kozlowski, Djampa K andKoutsovoulos, Georgios D and Lopez-Roques, Céline and Bouchez, Olivier andZahm, Margot and Besnard, Guillaume and B',
			'description' => '<p>Discovered in the 1960s, is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294&nbsp;kb, totaling 41.5&nbsp;Mb). The completeness scores of our assembly are among the highest currently published for genomes. We predicted 10,284 protein-coding genes spanning 75.5\% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61\% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of .&nbsp; and its closest relatives.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33144944',
			'doi' => '10.1002/ece3.6680',
			'modified' => '2021-02-19 17:46:50',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '4074',
			'name' => 'Repeat expansions confer WRN dependence in microsatellite-unstablecancers.',
			'authors' => 'van Wietmarschen, Niek and Sridharan, Sriram and Nathan, William J andTubbs, Anthony and Chan, Edmond M and Callen, Elsa and Wu, Wei and Belinky,Frida and Tripathi, Veenu and Wong, Nancy and Foster, Kyla and Noorbakhsh,Javad and Garimella, Kiran and Cr',
			'description' => '<p>The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32999459',
			'doi' => '10.1038/s41586-020-2769-8',
			'modified' => '2021-02-19 18:07:45',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '4081',
			'name' => 'Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient withe14a3 BCR-ABL1 transcript using Nanopore sequencing.',
			'authors' => 'Zhao, Hu and Chen, Yuan and Shen, Chanjuan and Li, Lingshu and Li, Qingzhaoand Tan, Kui and Huang, Huang and Hu, Guoyu',
			'description' => '<p>BACKGROUND: The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations. Here, we present a CML patient with e14a3 BCR-ABL1 transcript and t(9;22;12) variant Philadelphia (Ph) chromosome. METHODS: Cytogenetic analysis and fluorescence in situ hybridization (FISH) was performed to identify the chromosomal aberrations and gene fusions. Rare fusion transcript was verified by a reverse transcription-polymerase chain reaction (RT-PCR). Breakpoints were characterized and validated using Oxford Nanopore Technologies (ONT) (Oxford, UK) and Sanger sequencing, respectively. RESULTS: The karyotype showed the translocation t(9;22;12)(q34;q11.2;q24) [20] and FISH indicated 40\% positive BCR-ABL1 fusion signals. The RT-PCR suggested e14a3 type fusion transcript. The ONT sequencing analysis identified specific positions of translocation breakpoints: chr22:23633040-chr9:133729579, chr12:121567595-chr22:24701405, which were confirmed using Sanger sequencing. The patient achieved molecular remission 3 months after imatinib therapy. CONCLUSIONS: The present study indicates Nanopore sequencing as a valid strategy, which can characterize breakpoints precisely in special clinical cases with atypical structural variations. CML patients with e14a3 transcripts may have good clinical course in the tyrosine kinase inhibitor era, as reviewed here.</p>',
			'date' => '2020-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32949441',
			'doi' => '10.1002/jgm.3276',
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			'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
			'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
			'date' => '2020-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
			'doi' => '10.1371/journal.pone.0241749',
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			'author' => 'Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.',
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<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
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<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p><cite>Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen</cite></blockquote>
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<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
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<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
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	'created' => '2019-03-05 15:57:26',
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		'image_id' => '1793'
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$labelize = object(Closure) {
	
}
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$label = '<img src="/img/banners/banner-customizer-back.png" alt=""/>'
$document = array(
	'id' => '1169',
	'name' => 'Sage Science size selection with Diagenode Megaruptor',
	'description' => '<p>Best practices: Sage Science size selection with Diagenode Megaruptor shearing for long-read sequencing library preparation</p>',
	'image_id' => null,
	'type' => 'Application Note',
	'url' => 'files/application_notes/AN-SageScience-DiagenodeMegaruptor.pdf',
	'slug' => 'sagescience-diagenodemegaruptor-appnote',
	'meta_keywords' => '',
	'meta_description' => '',
	'modified' => '2023-08-25 14:17:07',
	'created' => '2023-08-25 14:17:07',
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		'product_id' => '3009',
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$publication = array(
	'id' => '4059',
	'name' => 'Interruption of an MSH4 homolog blocks meiosis in metaphase I andeliminates spore formation in Pleurotus ostreatus.',
	'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
	'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
	'date' => '2020-01-01',
	'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
	'doi' => '10.1371/journal.pone.0241749',
	'modified' => '2021-02-19 17:26:09',
	'created' => '2021-02-18 10:21:53',
	'ProductsPublication' => array(
		'id' => '4980',
		'product_id' => '3009',
		'publication_id' => '4059'
	)
)
$externalLink = ' <a href="https://www.ncbi.nlm.nih.gov/pubmed/33147286" target="_blank"><i class="fa fa-external-link"></i></a>'
include - APP/View/Products/view.ctp, line 755
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
ProductsController::slug() - APP/Controller/ProductsController.php, line 1052
ReflectionMethod::invokeArgs() - [internal], line ??
Controller::invokeAction() - CORE/Cake/Controller/Controller.php, line 491
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 193
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 118

Notice (8): Undefined variable: campaign_id [APP/View/Products/view.ctp, line 755]
Code Context
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$dataForView = array(
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	'meta_keywords' => '',
	'meta_description' => '',
	'meta_title' => 'The Megaruptor 3',
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			'id' => '3009',
			'antibody_id' => null,
			'name' => 'Megaruptor<sup>®</sup> 3',
			'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
<p></p>
<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
<ul>
<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
</ul>
</div>
<p></p>
<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
<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>',
			'label1' => 'Demonstrated shearing of DNA from 5 -100 kb',
			'info1' => '<h3>Excellent reproducibility and size distribution achieved with the Megaruptor 3</h3>
<center><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
			'label2' => 'Specifications for the Megaruptor',
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<tbody>
<tr style="height: 55px;">
<th class="text-center" style="width: 296px; height: 55px;"></th>
<th class="text-center" style="width: 255px; height: 55px; background-color: #2b2967; color: white;">Megaruptor 3 regular</th>
<th class="text-center" style="width: 381px; height: 55px; background-color: #af3db2; color: white;">Megaruptor 3 HT with ultrafast protocol</th>
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<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Run duration</td>
<td class="text-center" style="width: 255px; height: 38px;">20 min &ndash; few hours</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 5 min</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Size</td>
<td class="text-center" style="width: 255px; height: 38px;">5 &ndash; 100 kb</td>
<td class="text-center" style="width: 381px; height: 38px;">7 &ndash; 40 kb</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Concentration</td>
<td class="text-center" style="width: 255px; height: 38px;">0 &ndash; 150 ng/&mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 50 ng/&mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Volume</td>
<td class="text-center" style="width: 255px; height: 38px;">40 &ndash; 750 &mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">50 &ndash; 500 &mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Speed settings</td>
<td class="text-center" style="width: 255px; height: 38px;">1 &ndash; 65</td>
<td class="text-center" style="width: 381px; height: 38px;">30 &ndash; 59</td>
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<tr style="height: 56px;">
<td style="width: 296px; height: 56px;">Throughput</td>
<td class="text-center" style="width: 255px; height: 56px;">96 samples in 1 day</td>
<td class="text-center" style="width: 381px; height: 56px;">96 samples in &lt; 2h</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Shearing disposables</td>
<td class="text-center" style="width: 636px; height: 38px;" colspan="2">Multiple orifice hydrodynamic pore</td>
</tr>
<tr style="height: 32px;">
<td style="width: 296px; height: 32px;">Hardware</td>
<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
</tr>
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			(int) 39 => array(
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			(int) 41 => array(
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			(int) 42 => array(
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			(int) 43 => array(
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			(int) 44 => array(
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			(int) 45 => array(
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			(int) 46 => array(
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$language = 'en'
$meta_keywords = ''
$meta_description = ''
$meta_title = 'The Megaruptor 3'
$product = array(
	'Product' => array(
		'id' => '3009',
		'antibody_id' => null,
		'name' => 'Megaruptor<sup>®</sup> 3',
		'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p>The Megaruptor&reg; 3 was designed to provide the best experience&nbsp;with the fragmentation of DNA from <strong>5 kb - 100 kb</strong>. Shearing performance is independent of the source, concentration, temperature, or salt content of a DNA sample. Our user-friendly system allows for <strong>8 samples to be processed simultaneously&nbsp;</strong>without additional user input. A <a href="https://www.diagenode.com/p/megaruptor-cassette-12">12 sample cassette</a>&nbsp;<span style="font-weight: 400;">is also available for purchase separately for increased throughput.&nbsp;</span>Just set the desired parameters and the automated system takes care of the rest. <span style="font-weight: 400;">The shearing with the Megaruptor leads to optimal long-read sequencing using <strong>PacBio&reg;'s</strong>, and <strong>Oxford Nanopore&trade;</strong> technologies' systems.</span></p>
<p></p>
<div style="padding: 30px; background-color: #dad6e3;">
<p style="font-size: 1.2em; color: #2b2967;"><strong>Discover the NEW Megaruptor 3 HT</strong></p>
<p>The <strong>Megaruptor 3 HT</strong> offers an <strong>ultrafast protocol</strong> for increased sample processing speed to accommodate high-throughput sequencing projects. When using the ultrafast protocol, the <strong>Megaruptor 3 HT allows shearing of 96 samples in 2h into fragments of 7 to 40 kb</strong>.</p>
<p><strong>The NEW Megaruptor 3 HT will give you:</strong></p>
<ul>
<li><strong>High throughput:</strong> Processes 96 samples in 2 h.</li>
<li><strong>Flexibility:</strong> Allows the fragment size range (within 7 to 40 kb) to be chosen for hands-free operation.</li>
<li><strong>Unmatched quality:</strong> Provides the tight DNA fragment distribution necessary for high quality long-read sequencing.</li>
<li><strong>Reliable:</strong> enables processing of highly viscous samples.</li>
<li><strong>Ergonomic:</strong> Includes a user-friendly interface and has a small footprint.</li>
</ul>
</div>
<p></p>
<center><a href="https://go.diagenode.com/dnafluid" class="tiny details button">Validation of the DNA Fluid+ Kit on viscous samples with the Circulomics Nanobind CBB Big DNA Kit.</a></center><center></center><center><iframe width="700" height="394" src="https://www.youtube.com/embed/VaWEK1vjbOY?rel=0" frameborder="0" allow="accelerometer; encrypted-media; gyroscope; picture-in-picture" allowfullscreen="allowfullscreen"></iframe></center>
<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>',
		'label1' => 'Demonstrated shearing of DNA from 5 -100 kb',
		'info1' => '<h3>Excellent reproducibility and size distribution achieved with the Megaruptor 3</h3>
<center><img src="https://www.diagenode.com/img/product/shearing_technologies/mega3-results.png" /></center>
<p><strong>A</strong>: Fragment Analyzer profiles of human genomic DNA samples (25 ng/&mu;l; 200 &mu;l/sample) sheared to 6, 10 and 30 kb. <strong>B</strong>: DNA samples sheared at different speed settings of the Megaruptor were analyzed by Pulsed Field Gel Electrophoresis (PFGE) in 1% agarose gel. (NS: Not Sheared)</p>',
		'label2' => 'Specifications for the Megaruptor',
		'info2' => '<table style="width: 941px;">
<tbody>
<tr style="height: 55px;">
<th class="text-center" style="width: 296px; height: 55px;"></th>
<th class="text-center" style="width: 255px; height: 55px; background-color: #2b2967; color: white;">Megaruptor 3 regular</th>
<th class="text-center" style="width: 381px; height: 55px; background-color: #af3db2; color: white;">Megaruptor 3 HT with ultrafast protocol</th>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Run duration</td>
<td class="text-center" style="width: 255px; height: 38px;">20 min &ndash; few hours</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 5 min</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Size</td>
<td class="text-center" style="width: 255px; height: 38px;">5 &ndash; 100 kb</td>
<td class="text-center" style="width: 381px; height: 38px;">7 &ndash; 40 kb</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Concentration</td>
<td class="text-center" style="width: 255px; height: 38px;">0 &ndash; 150 ng/&mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">1 &ndash; 50 ng/&mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Volume</td>
<td class="text-center" style="width: 255px; height: 38px;">40 &ndash; 750 &mu;l</td>
<td class="text-center" style="width: 381px; height: 38px;">50 &ndash; 500 &mu;l</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Speed settings</td>
<td class="text-center" style="width: 255px; height: 38px;">1 &ndash; 65</td>
<td class="text-center" style="width: 381px; height: 38px;">30 &ndash; 59</td>
</tr>
<tr style="height: 56px;">
<td style="width: 296px; height: 56px;">Throughput</td>
<td class="text-center" style="width: 255px; height: 56px;">96 samples in 1 day</td>
<td class="text-center" style="width: 381px; height: 56px;">96 samples in &lt; 2h</td>
</tr>
<tr style="height: 38px;">
<td style="width: 296px; height: 38px;">Shearing disposables</td>
<td class="text-center" style="width: 636px; height: 38px;" colspan="2">Multiple orifice hydrodynamic pore</td>
</tr>
<tr style="height: 32px;">
<td style="width: 296px; height: 32px;">Hardware</td>
<td class="text-center" style="width: 636px; height: 32px;" colspan="2">State-of-the-art electronics<br />Large memory for new features<br />Extensive fine-tuning options<br />Robust titanium pins</td>
</tr>
</tbody>
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<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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			'name' => 'Megaruptor 3 DNAFluid+ Kit',
			'description' => '<h2 style="text-align: left;">The DNAFluid+ Kit for viscous DNA</h2>
<p><span style="font-weight: 400;">The DNAFluid+ Kit for viscous DNA&nbsp; eliminates the challenges of using </span><b>highly viscous extracted DNA samples </b><span style="font-weight: 400;">for any downstream steps and QC. The</span><span style="font-weight: 400;">&nbsp;</span><b><i>DNAFluid+ Kit </i></b><span style="font-weight: 400;">consists of proprietary "<span>Hydropore-Syringe" and "Hydro Tube"&nbsp;</span>shearing accessories that reduce the viscosity of DNA by pre-conditioning&nbsp;high molecular weight DNA prior to shearing on the </span><b><i>Megaruptor 3. </i></b><span style="font-weight: 400;">This combination of the DNAFluid+ Kit and the Megaruptor 3 together achieve effective, automated homogenization of highly viscous DNA samples while keeping the integrity of the DNA and full control of the DNA size prior to any downstream applications.&nbsp;</span></p>
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			'info1' => '<h3>Validation data: DNAFluid+ Kit for viscous DNA</h3>
<p><span>Validation of the DNA Fluid+ Kit on viscous samples is shown below. HMW DNA was extracted from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit. First, the sample was pre-sheared using the DNA Fluid+ Kit (speed 59) and then diluted to 50 ng/uL and sheared using the Long Hydropore (speed 31) on the Megaruptor 3 system. PacBio HiFi sequencing was performed on the sheared DNA using a 30 hr movie, SMRTbell Express Template Prep Kit 2.0, Binding Kit 2.0, and Sequel II Sequencing Kit 2.0, and Circulomics SRE XS size selection. These results show that Circulomics SRE XS is a good substitute for gel-based size selection and that the DNAFluid+ works well to pre-condition DNA for Long Hydropore shearing without clogging.</span></p>
<h2 class="card-title text-lg">DNA Fluid+ Kit effectively pre-conditions HMW DNA to allow consistent shearing across samples of varying viscosity.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid1.png" /></p>
<p><span>Fig.1. The Femto Pulse traces show fragment size distributions of: 1) native HMW DNA isolated from GM12878 cells using the Circulomics Nanobind CBB Big DNA Kit (black curve), 2) after pre-shearing with the Diagenode DNA Fluid+ Kit (blue curve) and 3) after shearing to ~18 kb with the Diagenode Long Hydropore using Megaruptor3 (red curve). Pre-shearing the HMW DNA enables more consistent shearing performance across samples of varying viscosity.</span></p>
<h2 class="card-title text-lg">Excellent read length distribution of sequencing results using DNA treated with DNA Fluid+ Kit.</h2>
<p><img src="https://www.diagenode.com/img/product/shearing_technologies/DNAFluid2.png" width="600" height="449" /></p>
<p class="text-xs">Fig. 2. After shearing the gDNA that was pre-conditioned with the Diagenode DNA Fluid+ Kit, HiFi read length distribution of GM12878 SMRTbell library shows excellent read length distribution. Sequencing was performed on the PacBio Sequel II system.</p>
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<p>Sterile Hydropores, Syringes, and Hydro Tubes 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>
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			'format' => '16 samples',
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			'meta_title' => 'Megaruptor DNAFluid+ kit',
			'meta_keywords' => 'homogenization, viscous, HMW, DNA',
			'meta_description' => 'Megaruptor DNAFluid+  kit',
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			'description' => '<p><a href="https://go.diagenode.com/l/928883/2023-04-06/3jhlc"><img src="https://www.diagenode.com/img/banners/pacbio-mega-promo-2023.png" /></a></p>
<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
<p><span style="font-weight: 400;">The new 12 sample&nbsp;capacity&nbsp;is optimal for use prior to library preparation on the <a href="https://www.pacb.com/revio/">PacBio Revio</a>, matching the new system's higher throughput and increased&nbsp;efficiency on time.&nbsp;</span></p>
<p>See video on how to use your 12 sample cassette:</p>
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			'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>
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</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>
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<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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			'created' => '2019-03-05 15:57:26',
			'ProductsImage' => array(
				[maximum depth reached]
			)
		)
	),
	'Promotion' => array(),
	'Protocol' => array(),
	'Publication' => array(
		(int) 0 => array(
			'id' => '4663',
			'name' => 'The genome sequence of the Elbow-stripe Grass-veneer, Agriphilageniculea (Haworth, 1811)',
			'authors' => 'Boyes  Douglas and Hammond  James',
			'description' => '<p>We present a genome assembly from an individual female Agriphila geniculea (the Elbow-stripe Grass-veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 781.6 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,132 protein coding genes.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18910.1',
			'doi' => '10.12688/wellcomeopenres.18910.1',
			'modified' => '2023-03-07 08:31:00',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '4664',
			'name' => 'The genome sequence of the Turnip Sawfly, Athalia rosae(Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Broad  Gavin R. and Green  Andrew',
			'description' => '<p>We present a genome assembly from an individual female Athalia rosae (the Turnip Sawfly; Arhropoda; Insecta; Hymenoptera; Athaliidae). The genome sequence is 172 megabases in span. Most of the assembly is scaffolded into eight chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,393 protein coding genes.</p>',
			'date' => '2023-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18993.1',
			'doi' => '10.12688/wellcomeopenres.18993.1',
			'modified' => '2023-03-07 08:31:39',
			'created' => '2023-02-28 12:19:11',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '4539',
			'name' => 'A high-quality, haplotype-phased genome reconstruction reveals unexpectedhaplotype diversity in a pearl oyster.',
			'authors' => 'Takeuchi  Takeshi et al.',
			'description' => '<p>Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified in animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, genome assembly of the pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This assembly includes 14 pairs of long scaffolds (&gt;38 Mb) corresponding to chromosomes (2n = 28). The accuracy of the assembly, as measured by an analysis of k-mers, is estimated to be 99.99997\%. Moreover, the haplotypes contain 95.2\% and 95.9\%, respectively, complete and single-copy BUSCO genes, demonstrating the high quality of the assembly. Transposons comprise 53.3\% of the assembly and are a major contributor to structural variations. Despite overall collinearity between haplotypes, one of the chromosomal scaffolds contains megabase-scale non-syntenic regions, which necessarily have never been detected and resolved in conventional haplotype-merged assemblies. These regions encode expanded gene families of NACHT, DZIP3/hRUL138-like HEPN, and immunoglobulin domains, multiplying the immunity gene repertoire, which we hypothesize is important for the innate immune capability of pearl oysters. The pearl oyster genome provides insight into remarkable haplotype diversity in animals.</p>',
			'date' => '2022-12-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36351462',
			'doi' => '10.1093/dnares/dsac035',
			'modified' => '2023-02-17 08:49:27',
			'created' => '2022-11-24 08:49:52',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 3 => array(
			'id' => '4481',
			'name' => 'Complete Genome Sequence of Lacticaseibacillus rhamnosus DM065,Isolated from the Human Oral Cavity.',
			'authors' => 'Park  Do-Young et al.',
			'description' => '<p>The 3.0-Mb complete genome of Lacticaseibacillus rhamnosus strain DM065, which was isolated from the oral cavity of healthy volunteers in South Korea, was sequenced using a combination of PacBio and Illumina technologies. The genome consists of one circular chromosome and two plasmids and lacks antimicrobial resistance genes.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36321910',
			'doi' => '10.1128/mra.00899-22',
			'modified' => '2022-11-18 12:27:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 4 => array(
			'id' => '4655',
			'name' => 'The genome sequence of the malaria mosquito, Anopheles funestus,Giles, 1900',
			'authors' => 'Ayala  Diego et al.',
			'description' => '<p>We present a genome assembly from an individual female Anopheles funestus (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae). The genome sequence is 251 megabases in span. The majority of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-11-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18445.1',
			'doi' => '10.12688/wellcomeopenres.18445.1',
			'modified' => '2023-03-07 08:54:22',
			'created' => '2023-02-21 09:59:46',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 5 => array(
			'id' => '4475',
			'name' => 'Semi-automated assembly of high-quality diploid human reference genomes.',
			'authors' => 'Jarvis  Erich D et al.',
			'description' => '<p>The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within &plusmn;1\% of the length of CHM13. Nearly 48\% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36261518',
			'doi' => '10.1038/s41586-022-05325-5',
			'modified' => '2022-11-18 12:20:59',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 6 => array(
			'id' => '4477',
			'name' => 'Integration of Hi-C with short and long-read genome sequencingreveals the structure of germline rearranged genomes.',
			'authors' => 'Schöpflin  R.et al.',
			'description' => '<p>Structural variants are a common cause of disease and contribute to a large extent to inter-individual variability, but their detection and interpretation remain a challenge. Here, we investigate 11 individuals with complex genomic rearrangements including germline chromothripsis by combining short- and long-read genome sequencing (GS) with Hi-C. Large-scale genomic rearrangements are identified in Hi-C interaction maps, allowing for an independent assessment of breakpoint calls derived from the GS methods, resulting in &gt;300 genomic junctions. Based on a comprehensive breakpoint detection and Hi-C, we achieve a reconstruction of whole rearranged chromosomes. Integrating information on the three-dimensional organization of chromatin, we observe that breakpoints occur more frequently than expected in lamina-associated domains (LADs) and that a majority reshuffle topologically associating domains (TADs). By applying phased RNA-seq, we observe an enrichment of genes showing allelic imbalanced expression (AIG) within 100&thinsp;kb around the breakpoints. Interestingly, the AIGs hit by a breakpoint (19/22) display both up- and downregulation, thereby suggesting different mechanisms at play, such as gene disruption and rearrangements of regulatory information. However, the majority of interpretable genes located 200&thinsp;kb around a breakpoint do not show significant expression changes. Thus, there is an overall robustness in the genome towards large-scale chromosome rearrangements.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36309531',
			'doi' => '10.1038/s41467-022-34053-7',
			'modified' => '2022-11-18 12:22:31',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 7 => array(
			'id' => '4485',
			'name' => 'The genome sequence of the orange-tip butterfly, Anthocharis cardamines(Linnaeus, 1758)',
			'authors' => 'Ebdon  S. et al.',
			'description' => '<p>We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74\%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18117.1',
			'doi' => '10.12688/wellcomeopenres.18117.1',
			'modified' => '2022-11-18 12:32:05',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 8 => array(
			'id' => '4486',
			'name' => 'The genome sequence of the satellite, Eupsilia transversa (Hufnagel,1766)',
			'authors' => 'Crowley  L. et al.',
			'description' => '<p>We present a genome assembly from an individual female Eupsilia transversa (the satellite; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 467 megabases in span. The entire assembly (100\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 18,065 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18105.1',
			'doi' => '10.12688/wellcomeopenres.18105.1',
			'modified' => '2022-11-18 12:32:51',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 9 => array(
			'id' => '4487',
			'name' => 'The genome sequence of the common yellow swallowtail, Papilio machaon(Linnaeus, 1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual female Papilio machaon (the common yellow swallowtail; Arthropoda; Insecta; Lepidoptera; Papilionidae). The genome sequence is 252 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 31 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,323 protein coding genes.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18119.1',
			'doi' => '10.12688/wellcomeopenres.18119.1',
			'modified' => '2022-11-18 12:33:33',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 10 => array(
			'id' => '4489',
			'name' => 'The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758)',
			'authors' => 'Lohse  K. et al.',
			'description' => '<p>We present a genome assembly from an individual male Erebia ligea (Arran brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 506 megabases in span. The majority (99.92\%) of the assembly is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.2 kilobases in length.</p>',
			'date' => '2022-10-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18115.1',
			'doi' => '10.12688/wellcomeopenres.18115.1',
			'modified' => '2022-11-18 12:36:34',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 11 => array(
			'id' => '4500',
			'name' => 'Complete Genome Sequence of  Strain DM083 Isolated from HumanTongue Coating.',
			'authors' => 'Park  Do-Young  et al.',
			'description' => '<p>We isolated Lactiplantibacillus plantarum DM083 from the human tongue coating to establish a strain library for oral probiotics. It has a single circular 3,197,299 bp chromosome with a guanine-cytosine (GC) content of 44.6\% without plasmids. Importantly, the genome is devoid of the antimicrobial resistance gene, satisfying the minimum safety requirement for probiotics.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36165646',
			'doi' => '10.1128/mra.00675-22',
			'modified' => '2022-11-21 10:32:09',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 12 => array(
			'id' => '4501',
			'name' => 'The genome sequence of the yellow-legged clearwing, Synanthedonvespiformis (Linnaeus, 1761)',
			'authors' => 'Boyes  Douglas and Lees  David',
			'description' => '<p>We present a genome assembly from an individual male Synanthedon vespiformis (the yellow-legged clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 287 megabases in span. Of the assembly, 100\% is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.3 kilobases in length. Keywords</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18109.1',
			'doi' => '10.12688/wellcomeopenres.18109.1',
			'modified' => '2022-11-21 10:32:47',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 13 => array(
			'id' => '4503',
			'name' => 'The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763)',
			'authors' => 'Boyes  Douglas and Boyes  Clare',
			'description' => '<p>We present a genome assembly from an individual male Caradrina clavipalpis (pale mottled willow; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 474 megabases in span. The entire assembly (100\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18103.1',
			'doi' => '10.12688/wellcomeopenres.18103.1',
			'modified' => '2022-11-21 10:35:00',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 14 => array(
			'id' => '4504',
			'name' => 'The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808)',
			'authors' => 'Boyes  Douglas and Gibbs  Melanie',
			'description' => '<p>We present a genome assembly from an individual female Mythimna impura (smoky wainscot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 949 megabases in span. The majority of the assembly (98.39\%) is scaffolded into 32 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 15,441 protein coding genes.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18104.1',
			'doi' => '10.12688/wellcomeopenres.18104.1',
			'modified' => '2022-11-21 10:35:36',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 15 => array(
			'id' => '4509',
			'name' => 'Comparative analyses of Theobroma cacao and T. grandiflorummitogenomes reveal conserved gene content embedded within complex andplastic structures.',
			'authors' => 'de Abreu  Vinicius A C et al.',
			'description' => '<p>Unlike the chloroplast genomes (ptDNA), the plant mitochondrial genomes (mtDNA) are much more plastic in structure and size but maintain a conserved and essential gene set related to oxidative phosphorylation. Moreover, the plant mitochondrial genes and mtDNA are good markers for phylogenetic, evolutive, and comparative analyses. The two most known species in Theobroma L. (Malvaceae s.l.) genus are T. cacao, and T. grandiflorum. Besides the economic value, both species also show considerable biotechnology potential due to their other derived products, thus, aggregating additional economic value for the agroindustry. Here, we assembled and compared the mtDNA of Theobroma cacao and T. grandiflorum to generate a new genomics resource and unravel evolutionary trends. Graph-based analyses revealed that both mtDNA exhibit multiple alternative arrangements, confirming the dynamism commonly observed in plant mtDNA. The disentangled assembly graph revealed potential predominant circular molecules. The master circle molecules span 543,794&nbsp;bp for T. cacao and 501,598&nbsp;bp for T. grandiflorum, showing 98.9\% of average sequence identity. Both mtDNA contains the same set of 39 plant mitochondrial genes, commonly found in other rosid mitogenomes. The main features are a duplicated copy of atp4, the absence of rpl6, rps2, rps8, and rps11, and the presence of two chimeric open-reading frames. Moreover, we detected few ptDNA integrations mainly represented by tRNAs, and no viral sequences were detected. Phylogenomics analyses indicate Theobroma spp. are nested in Malvaceae family. The main mtDNA differences are related to distinct structural rearrangements and exclusive regions associated with relics of Transposable Elements, supporting the hypothesis of dynamic mitochondrial genome maintenance and divergent evolutionary paths and pressures after species differentiation.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36150535',
			'doi' => '10.1016/j.gene.2022.146904',
			'modified' => '2022-11-21 10:36:50',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 16 => array(
			'id' => '4505',
			'name' => 'The genome sequence of the wall brown, Lasiommata megera (Linnaeus,1767)',
			'authors' => 'Lohse  Konrad and Wright  Charlotte',
			'description' => '<p>We present a genome assembly from an individual female Lasiommata megera (the wall brown; Arthropoda; Insecta; Lepidoptera; Nymphalidae). The genome sequence is 488 megabases in span. The majority of the assembly (99.97\%) is scaffolded into 30 chromosomal pseudomolecules with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18106.1',
			'doi' => '10.12688/wellcomeopenres.18106.1',
			'modified' => '2023-02-17 08:54:13',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 17 => array(
			'id' => '4507',
			'name' => 'The genome sequence of the sallow kitten, Furcula furcula (Clerck,1759)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Furcula furcula (the sallow kitten; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 736 megabases in span. The entire assembly (100\%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 17.2 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18112.1',
			'doi' => '10.12688/wellcomeopenres.18112.1',
			'modified' => '2023-02-17 08:55:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 18 => array(
			'id' => '4508',
			'name' => 'The genome sequence of the peacock moth, Macaria notata (Linnaeus,1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Macaria notata (the peacock moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 394 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 29 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.18108.1',
			'doi' => '10.12688/wellcomeopenres.18108.1',
			'modified' => '2023-02-17 08:56:15',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 19 => array(
			'id' => '4513',
			'name' => 'Plant species-specific basecaller improves actual accuracy of nanoporesequencing',
			'authors' => 'Ferguson  Scott et al.',
			'description' => '<p>Long-read sequencing platforms offered by Oxford Nanopore Technologies (ONT) allow native DNA containing epigenetic modifications to be directly sequenced, but can be limited by lower per-base accuracies. A key step post-sequencing is basecalling, the process of converting raw electrical signals produced by the sequencing device into nucleotide sequences. This is challenging as current basecallers are primarily based on mixtures of model species for training. Here we utilise both ONT PromethION and higher accuracy PacBio Sequel II HiFi sequencing on two plants, Phebalium stellatum and Xanthorrhoea johnsonii, to train species-specific basecaller models with the aim of improving per-base accuracy. We investigate sequencing accuracies achieved by ONT basecallers and assess accuracy gains by training single-species and species-specific basecaller models. We also evaluate accuracy gains from ONT&rsquo;s improved flowcells (R10.4, FLO-PRO112) and sequencing kits (SQK-LSK112). For the truth dataset for both model training and accuracy assessment, we developed highly accurate, contiguous diploid reference genomes with PacBio Sequel II HiFi reads.</p>',
			'date' => '2022-09-01',
			'pmid' => 'https://doi.org/10.21203%2Frs.3.rs-1919465%2Fv1',
			'doi' => '10.21203/rs.3.rs-1919465/v1',
			'modified' => '2023-02-17 08:57:19',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 20 => 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) 21 => array(
			'id' => '4450',
			'name' => 'The leaf beetle Chelymorpha alternans propagates a plant pathogen inexchange for pupal protection.',
			'authors' => 'Berasategui  Aileen et al.',
			'description' => '<p>Many insects rely on microbial protection in the early stages of their development. However, in contrast to symbiont-mediated defense of eggs and young instars, the role of microbes in safeguarding pupae remains relatively unexplored, despite the susceptibility of the immobile stage to antagonistic challenges. Here, we outline the importance of symbiosis in ensuring pupal protection by describing a mutualistic partnership between the ascomycete Fusarium oxysporum and Chelymorpha alternans, a leaf beetle. The symbiont rapidly proliferates at the onset of pupation, extensively and conspicuously coating C.&nbsp;alternans during metamorphosis. The fungus confers defense against predation as symbiont elimination results in reduced pupal survivorship. In exchange, eclosing beetles vector F.&nbsp;oxysporum to their host plants, resulting in a systemic infection. By causing wilt disease, the fungus retained its phytopathogenic capacity in light of its symbiosis with C.&nbsp;alternans. Despite possessing a relatively reduced genome, F.&nbsp;oxysporum encodes metabolic pathways that reflect its dual lifestyle as a plant pathogen and a defensive insect symbiont. These include virulence factors underlying plant colonization, along with mycotoxins that may contribute to the defensive biochemistry of the insect host. Collectively, our findings shed light on a mutualism predicated on pupal protection of an herbivorous beetle in exchange for symbiont dissemination and propagation.</p>',
			'date' => '2022-08-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35987210',
			'doi' => '10.1016/j.cub.2022.07.065',
			'modified' => '2022-10-21 09:29:09',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 22 => array(
			'id' => '4431',
			'name' => 'The genome sequence of the hawthorn shieldbug, Acanthosomahaemorrhoidale (Linnaeus, 1758)',
			'authors' => 'Crowley  Liam M. and Mulley  John',
			'description' => '<p>We present a genome assembly from an individual male Acanthosoma haemorrhoidale (hawthorn shieldbug; Arthropoda; Insecta; Hemiptera; Acanthosomatidae). The genome sequence is 866 megabases in span. The majority of the assembly (99.98\%) is scaffolded into 7 chromosomal pseudomolecules with the X and Y sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 18.9 kilobases in length.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17926.1',
			'doi' => '10.12688/wellcomeopenres.17926.1',
			'modified' => '2022-09-28 09:09:34',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 23 => array(
			'id' => '4433',
			'name' => 'The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas et al.',
			'description' => '<p>We present a genome assembly from an individual male Cosmia trapezina (dun-bar pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 825 megabases in span. The majority of the assembly (99.87\%) is scaffolded into 32 chromosomal pseudomolecules with the Z chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://wellcomeopenresearch.org/articles/7-189',
			'doi' => '10.12688/wellcomeopenres.17925.1',
			'modified' => '2022-09-28 09:13:35',
			'created' => '2022-09-08 16:32:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 24 => array(
			'id' => '4518',
			'name' => 'Equilibrated evolution of the mixed auto-/allopolyploidhaplotype-resolved genome of the invasive hexaploid Prussian carp.',
			'authors' => 'Kuhl  Heiner et al.',
			'description' => '<p>Understanding genome evolution of polyploids requires dissection of their often highly similar subgenomes and haplotypes. Polyploid animal genome assemblies so far restricted homologous chromosomes to a 'collapsed' representation. Here, we sequenced the genome of the asexual Prussian carp, which is a close relative of the goldfish, and present a haplotype-resolved chromosome-scale assembly of a hexaploid animal. Genome-wide comparisons of the 150 chromosomes with those of two ancestral diploid cyprinids and the allotetraploid goldfish and common carp revealed the genomic structure, phylogeny and genome duplication history of its genome. It consists of 25 syntenic, homeologous chromosome groups and evolved by a recent autoploid addition to an allotetraploid ancestor. We show that de-polyploidization of the alloploid subgenomes on the individual gene level occurred in an equilibrated fashion. Analysis of the highly conserved actinopterygian gene set uncovered a subgenome dominance in duplicate gene loss of one ancestral chromosome set.</p>',
			'date' => '2022-07-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35835759',
			'doi' => '10.1038/s41467-022-31515-w',
			'modified' => '2023-02-17 08:58:06',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 25 => array(
			'id' => '4372',
			'name' => 'Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing',
			'authors' => 'Yang  X. et al.',
			'description' => '<p>The advantages of both the length and accuracy of high-fidelity (HiFi) reads enable chromosome-scale haplotype-resolved genome assembly. In this study, we sequenced a cell line named HJ, established from a Chinese Han male individual by using HiFi and Hi-C. We assembled two high-quality haplotypes of the HJ genome (haplotype 1 (H1): 3.1 Gb, haplotype 2 (H2): 2.9 Gb). The continuity (H1: contig N50 = 28.2 Mb, H2: contig N50 = 25.9 Mb) and completeness (BUSCO: H1 = 94.9\%, H2 = 93.5\%) are substantially better than those of other Chinese genomes, for example, HX1, NH1.0, and YH2.0. By comparing HJ genome with GRCh38, we reported the mutation landscape of HJ and found that 176 and 213 N-gaps were filled in H1 and H2, respectively. In addition, we detected 12.9 Mb and 13.4 Mb novel sequences containing 246 and 135 protein-coding genes in H1 and H2, respectively. Our results demonstrate the advantages of HiFi reads in haplotype-resolved genome assembly and provide two high-quality haplotypes of a potential Chinese genome as a reference for the Chinese Han population.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://doi.org/10.1016%2Fj.fmre.2022.02.005',
			'doi' => '10.1016/j.fmre.2022.02.005',
			'modified' => '2022-08-04 16:11:38',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 26 => array(
			'id' => '4523',
			'name' => 'Complete Genome Sequence of Herpes Simplex Virus 2 StrainG.',
			'authors' => 'Chang  Weizhong et al.',
			'description' => '<p>Herpes simplex virus type (HSV-2) is a common causative agent of genital tract infections. Moreover, HSV-2 and HIV infection can mutually increase the risk of acquiring another virus infection. Due to the high GC content and highly repetitive regions in HSV-2 genomes, only the genomes of four strains have been completely sequenced (HG52, 333, SD90e, and MS). Strain G is commonly used for HSV-2 research, but only a partial genome sequence has been assembled with Illumina sequencing reads. In the current study, we de novo assembled and annotated the complete genome of strain G using PacBio long sequencing reads, which can span the repetitive regions, analyzed the '&alpha;' sequence, which plays key roles in HSV-2 genome circulation, replication, cleavage, and packaging of progeny viral DNA, identified the packaging signals homologous to HSV-1 within the '&alpha;' sequence, and determined both termini of the linear genome and cleavage site for the process of concatemeric HSV-2 DNA produced via rolling-circle replication. In addition, using Oxford Nanopore Technology sequencing reads, we visualized four HSV-2 genome isomers at the nucleotide level for the first time. Furthermore, the coding sequences of HSV-2 strain G have been compared with those of HG52, 333, and MS. Moreover, phylogenetic analysis of strain G and other diverse HSV-2 strains has been conducted to determine their evolutionary relationship. The results will aid clinical research and treatment development of HSV-2.</p>',
			'date' => '2022-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35336943',
			'doi' => '10.3390/v14030536',
			'modified' => '2023-02-17 09:03:22',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 27 => array(
			'id' => '4464',
			'name' => 'The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900',
			'authors' => 'Macadam  Craig et al. ',
			'description' => '<p>We present a genome assembly from an individual male Nemurella pictetii (Arthropoda; Insecta; Plecoptera; Nemouridae). The genome sequence is 257 megabases in span. The majority of the assembly (99.79\%) is scaffolded into 12 chromosomal pseudomolecules, with the X sex chromosome assembled. The X chromosome was found at half coverage, but no Y chromosome was found. The mitochondrial genome was assembled, and is 16.0 kb in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17684.1',
			'doi' => '10.12688/wellcomeopenres.17684.1',
			'modified' => '2022-10-21 09:51:18',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 28 => array(
			'id' => '4465',
			'name' => 'The genome sequence of the furry-claspered furrow bee, Lasioglossumlativentre (Schenck, 1853)',
			'authors' => 'Falk  Steven and Monks  Joseph',
			'description' => '<p>We present a genome assembly from an individual male Lasioglossum lativentre (the furry-claspered furrow bee; Arthropoda; Insecta; Hymenoptera; Halictidae). The genome sequence is 479 megabases in span. The majority of the assembly (75.22\%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome was also assembled, and is 15.3 kilobases in length.</p>',
			'date' => '2022-02-01',
			'pmid' => 'https://doi.org/10.12688%2Fwellcomeopenres.17706.1',
			'doi' => '10.12688/wellcomeopenres.17706.1',
			'modified' => '2022-10-21 09:51:46',
			'created' => '2022-09-28 09:53:13',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 29 => 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) 30 => array(
			'id' => '4369',
			'name' => 'The genome sequence of a parasitoid wasp,  Forster, 1771.',
			'authors' => 'Broad  Gavin',
			'description' => '<p>We present a genome assembly from an individual female (Arthropoda; Insecta; Hymenoptera; Ichneumonidae). The genome sequence is 315 megabases in span. The majority of the assembly (82.64\%) is scaffolded into 12 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl has identified 10,622 protein coding genes.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419493',
			'doi' => '10.12688/wellcomeopenres.17683.1',
			'modified' => '2022-08-04 16:21:40',
			'created' => '2022-08-04 14:55:36',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 31 => array(
			'id' => '4506',
			'name' => 'The genome sequence of the brimstone moth, Opisthograptis luteolata(Linnaeus, 1758)',
			'authors' => 'Boyes  Douglas and Phillips  Dominic',
			'description' => '<p>We present a genome assembly from an individual male (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99\%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/36226159',
			'doi' => '10.12688/wellcomeopenres.18101.1',
			'modified' => '2023-02-17 08:59:01',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 32 => array(
			'id' => '4529',
			'name' => 'The genome sequence of Gymnosoma rotundatum (Linnaeus, 1758), aparasitoid ladybird fly',
			'authors' => 'Smith  Matthew',
			'description' => '<p>We present a genome assembly from an individual male (Arthropoda; Insecta; Diptera; Tachinidae). The genome sequence is 779 megabases in span. The majority of the assembly (97.07\%) is scaffolded into six chromosomal pseudomolecules, with the X sex chromosome assembled.</p>',
			'date' => '2022-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/35419492',
			'doi' => '10.12688/wellcomeopenres.17782.1',
			'modified' => '2023-02-17 09:00:46',
			'created' => '2022-11-15 09:26:20',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 33 => array(
			'id' => '4256',
			'name' => 'Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca).',
			'authors' => 'Huang Yi et al.',
			'description' => '<p>Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2\%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.</p>',
			'date' => '2021-11-01',
			'pmid' => 'https://doi.org/10.1093%2Fjhered%2Fesab071',
			'doi' => '10.1093/jhered/esab071',
			'modified' => '2022-05-20 09:47:15',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 34 => 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) 35 => array(
			'id' => '4308',
			'name' => 'De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus).',
			'authors' => 'Pickett, Brandon D and Glass, Jessica R and Ridge, PerryG and Kauwe, John S K',
			'description' => '<p>The bluefin trevally, Caranx melampygus, also known as the bluefin kingfish or bluefin jack, is known for its remarkable, bright-blue fins. This marine teleost is a widely prized sportfish, but few resources have been devoted to the genomics and conservation of this species because it is not targeted by large-scale commercial fisheries. Population declines from recreational and artisanal overfishing have been observed in Hawai'i, USA, resulting in both an interest in aquaculture and concerns about the long-term conservation of this species. Most research to-date has been performed in Hawai'i, raising questions about the status of bluefin trevally populations across its Indo-Pacific range. Genomic resources allow for expanded research on stock status, genetic diversity, and population demography. We present a high quality, 711 Mb nuclear genome assembly of a Hawaiian bluefin trevally from noisy long-reads with a contig NG50 of 1.2 Mb and longest contig length of 8.9 Mb. As measured by single-copy orthologs, the assembly was 95\% complete, and the genome is comprised of 16.9\% repetitive elements. The assembly was annotated with 33.1&thinsp;K protein-coding genes, 71.4\% of which were assigned putative functions, using RNA-seq data from eight tissues from the same individual. This is the first whole-genome assembly published for the carangoid genus Caranx. Using this assembled genome, a multiple sequentially Markovian coalescent model was implemented to assess population demography. Estimates of effective population size suggest population expansion has occurred since the Late Pleistocene. This genome will be a valuable resource for comparative phylogenomic studies of carangoid fishes and will help elucidate demographic history and delineate stock structure for bluefin trevally populations throughout the Indo-Pacific.</p>',
			'date' => '2021-09-01',
			'pmid' => 'https://doi.org/10.1093%2Fg3journal%2Fjkab229',
			'doi' => '10.1093/g3journal/jkab229',
			'modified' => '2022-06-20 09:08:51',
			'created' => '2022-05-19 10:41:50',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 36 => 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) 37 => 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) 38 => array(
			'id' => '4123',
			'name' => 'Familial thrombocytopenia due to a complex structural variant resulting ina WAC-ANKRD26 fusion transcript.',
			'authors' => 'Wahlster, Lara and Verboon, Jeffrey M and Ludwig, Leif S and Black, Susan Cand Luo, Wendy and Garg, Kopal and Voit, Richard A and Collins, Ryan L andGarimella, Kiran and Costello, Maura and Chao, Katherine R and Goodrich,Julia K and DiTroia, Stephanie ',
			'description' => '<p>Advances in genome sequencing have resulted in the identification of the causes for numerous rare diseases. However, many cases remain unsolved with standard molecular analyses. We describe a family presenting with a phenotype resembling inherited thrombocytopenia 2 (THC2). THC2 is generally caused by single nucleotide variants that prevent silencing of ANKRD26 expression during hematopoietic differentiation. Short-read whole-exome and genome sequencing approaches were unable to identify a causal variant in this family. Using long-read whole-genome sequencing, a large complex structural variant involving a paired-duplication inversion was identified. Through functional studies, we show that this structural variant results in a pathogenic gain-of-function WAC-ANKRD26 fusion transcript. Our findings illustrate how complex structural variants that may be missed by conventional genome sequencing approaches can cause human disease.</p>',
			'date' => '2021-06-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33857290',
			'doi' => '10.1084/jem.20210444',
			'modified' => '2021-12-07 09:58:17',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 39 => array(
			'id' => '4134',
			'name' => 'PCIP-seq: simultaneous sequencing of integrated viral genomes and theirinsertion sites with long reads.',
			'authors' => 'Artesi, M. et al.',
			'description' => '<p>The integration of a viral genome into the host genome has a major impact on the trajectory of the infected cell. Integration location and variation within the associated viral genome can influence both clonal expansion and persistence of infected cells. Methods based on short-read sequencing can identify viral insertion sites, but the sequence of the viral genomes within remains unobserved. We develop PCIP-seq, a method that leverages long reads to identify insertion sites and sequence their associated viral genome. We apply the technique to exogenous retroviruses HTLV-1, BLV, and HIV-1, endogenous retroviruses, and human papillomavirus.</p>',
			'date' => '2021-04-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33823910',
			'doi' => '10.1186/s13059-021-02307-0',
			'modified' => '2021-12-10 17:12:45',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 40 => 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) 41 => array(
			'id' => '4122',
			'name' => 'Comparison of long read sequencing technologies in interrogating bacteriaand fly genomes.',
			'authors' => 'Tvedte, Eric S and Gasser, Mark and Sparklin, Benjamin C and Michalski,Jane and Hjelmen, Carl E and Johnston, J Spencer and Zhao, Xuechu andBromley, Robin and Tallon, Luke J and Sadzewicz, Lisa and Rasko, David Aand Hotopp, Julie C Dunning',
			'description' => '<p>The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.</p>',
			'date' => '2021-03-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33768248',
			'doi' => '10.1093/g3journal/jkab083',
			'modified' => '2021-12-07 09:57:33',
			'created' => '2021-12-06 15:53:19',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 42 => 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) 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' => '4037',
			'name' => 'Complete Genome Sequence of  sp. Strain Nx66, Isolated from WatersContaminated with Petrochemicals in El Saf-Saf Valley, Algeria.',
			'authors' => 'Chéraiti, Nardjess and Plewniak, Frédéric and Tighidet, Salima andSayeh, Amalia and Gil, Lisa and Malherbe, Ludivine and Memmi, Yosr andZilliox, Laurence and Vandecasteele, Céline and Boyer, Pierre andLopez-Roques, Céline and Jaulhac, Benoît and Bensou',
			'description' => '<p>sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 &times; 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled using Unicycler. It is composed of one chromosome of 3.42&thinsp;Mb and one plasmid of 34.22&thinsp;kb.</p>',
			'date' => '2020-11-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/29457705',
			'doi' => '10.1128/MRA.01130-20',
			'modified' => '2021-02-18 17:13:56',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 47 => array(
			'id' => '4043',
			'name' => 'Contrasting signatures of genomic divergence during sympatric speciation.',
			'authors' => 'Kautt, Andreas F and Kratochwil, Claudius F and Nater, Alexander andMachado-Schiaffino, Gonzalo and Olave, Melisa and Henning, Frederico andTorres-Dowdall, Julián and Härer, Andreas and Hulsey, C Darrin andFranchini, Paolo and Pippel, Martin and Myers,',
			'description' => '<p>The transition from 'well-marked varieties' of a single species into 'well-defined species'-especially in the absence of geographic barriers to gene flow (sympatric speciation)-has puzzled evolutionary biologists ever since Darwin. Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs, but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories. Here, within a young species complex of neotropical cichlid fishes (Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33116308',
			'doi' => '10.1038/s41586-020-2845-0',
			'modified' => '2021-02-19 13:51:04',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 48 => array(
			'id' => '4066',
			'name' => 'Genome structure and content of the rice root-knot nematode ().',
			'authors' => 'Phan, Ngan Thi and Orjuela, Julie and Danchin, Etienne G J and Klopp,Christophe and Perfus-Barbeoch, Laetitia and Kozlowski, Djampa K andKoutsovoulos, Georgios D and Lopez-Roques, Céline and Bouchez, Olivier andZahm, Margot and Besnard, Guillaume and B',
			'description' => '<p>Discovered in the 1960s, is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, using a combination of Oxford Nanopore Technologies and Illumina sequencing data, we generated a highly contiguous reference genome (283 scaffolds with an N50 length of 294&nbsp;kb, totaling 41.5&nbsp;Mb). The completeness scores of our assembly are among the highest currently published for genomes. We predicted 10,284 protein-coding genes spanning 75.5\% of the genome. Among them, 67 are identified as possibly originating from horizontal gene transfers (mostly from bacteria), which supposedly contribute to nematode infection, nutrient processing, and plant defense manipulation. Besides, we detected 575 canonical transposable elements (TEs) belonging to seven orders and spanning 2.61\% of the genome. These TEs might promote genomic plasticity putatively related to the evolution of parasitism. This high-quality genome assembly constitutes a major improvement regarding previously available versions and represents a valuable molecular resource for future phylogenomic studies of species. In particular, this will foster comparative genomic studies to trace back the evolutionary history of .&nbsp; and its closest relatives.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33144944',
			'doi' => '10.1002/ece3.6680',
			'modified' => '2021-02-19 17:46:50',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 49 => array(
			'id' => '4074',
			'name' => 'Repeat expansions confer WRN dependence in microsatellite-unstablecancers.',
			'authors' => 'van Wietmarschen, Niek and Sridharan, Sriram and Nathan, William J andTubbs, Anthony and Chan, Edmond M and Callen, Elsa and Wu, Wei and Belinky,Frida and Tripathi, Veenu and Wong, Nancy and Foster, Kyla and Noorbakhsh,Javad and Garimella, Kiran and Cr',
			'description' => '<p>The RecQ DNA helicase WRN is a synthetic lethal target for cancer cells with microsatellite instability (MSI), a form of genetic hypermutability that arises from impaired mismatch repair. Depletion of WRN induces widespread DNA double-strand breaks in MSI cells, leading to cell cycle arrest and/or apoptosis. However, the mechanism by which WRN protects MSI-associated cancers from double-strand breaks remains unclear. Here we show that TA-dinucleotide repeats are highly unstable in MSI cells and undergo large-scale expansions, distinct from previously described insertion or deletion mutations of a few nucleotides. Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activate the ATR checkpoint kinase, and require unwinding by the WRN helicase. In the absence of WRN, the expanded TA-dinucleotide repeats are susceptible to cleavage by the MUS81 nuclease, leading to massive chromosome shattering. These findings identify a distinct biomarker that underlies the synthetic lethal dependence on WRN, and support the development of therapeutic agents that target WRN for MSI-associated cancers.</p>',
			'date' => '2020-10-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32999459',
			'doi' => '10.1038/s41586-020-2769-8',
			'modified' => '2021-02-19 18:07:45',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 50 => array(
			'id' => '4081',
			'name' => 'Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient withe14a3 BCR-ABL1 transcript using Nanopore sequencing.',
			'authors' => 'Zhao, Hu and Chen, Yuan and Shen, Chanjuan and Li, Lingshu and Li, Qingzhaoand Tan, Kui and Huang, Huang and Hu, Guoyu',
			'description' => '<p>BACKGROUND: The genetic changes in chronic myeloid leukaemia (CML) have been well established, although challenges persist in cases with rare fusion transcripts or complex variant translocations. Here, we present a CML patient with e14a3 BCR-ABL1 transcript and t(9;22;12) variant Philadelphia (Ph) chromosome. METHODS: Cytogenetic analysis and fluorescence in situ hybridization (FISH) was performed to identify the chromosomal aberrations and gene fusions. Rare fusion transcript was verified by a reverse transcription-polymerase chain reaction (RT-PCR). Breakpoints were characterized and validated using Oxford Nanopore Technologies (ONT) (Oxford, UK) and Sanger sequencing, respectively. RESULTS: The karyotype showed the translocation t(9;22;12)(q34;q11.2;q24) [20] and FISH indicated 40\% positive BCR-ABL1 fusion signals. The RT-PCR suggested e14a3 type fusion transcript. The ONT sequencing analysis identified specific positions of translocation breakpoints: chr22:23633040-chr9:133729579, chr12:121567595-chr22:24701405, which were confirmed using Sanger sequencing. The patient achieved molecular remission 3 months after imatinib therapy. CONCLUSIONS: The present study indicates Nanopore sequencing as a valid strategy, which can characterize breakpoints precisely in special clinical cases with atypical structural variations. CML patients with e14a3 transcripts may have good clinical course in the tyrosine kinase inhibitor era, as reviewed here.</p>',
			'date' => '2020-09-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/32949441',
			'doi' => '10.1002/jgm.3276',
			'modified' => '2021-03-15 16:56:36',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		),
		(int) 51 => array(
			'id' => '4059',
			'name' => 'Interruption of an MSH4 homolog blocks meiosis in metaphase I andeliminates spore formation in Pleurotus ostreatus.',
			'authors' => 'Lavrijssen, Brian and Baars, Johan P and Lugones, Luis G and Scholtmeijer,Karin and Sedaghat Telgerd, Narges and Sonnenberg, Anton S M and van Peer,Arend F',
			'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
			'date' => '2020-01-01',
			'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
			'doi' => '10.1371/journal.pone.0241749',
			'modified' => '2021-02-19 17:26:09',
			'created' => '2021-02-18 10:21:53',
			'ProductsPublication' => array(
				[maximum depth reached]
			)
		)
	),
	'Testimonial' => array(
		(int) 0 => array(
			'id' => '80',
			'name' => 'Megaruptor 3 - PacBio',
			'description' => '<p><span>The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.</span></p>',
			'author' => 'Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.',
			'featured' => false,
			'slug' => 'testimonial-mega3-pacbio',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2020-11-19 14:49:23',
			'created' => '2020-11-19 14:49:23',
			'ProductsTestimonial' => array(
				[maximum depth reached]
			)
		),
		(int) 1 => array(
			'id' => '76',
			'name' => 'Testimonial Megaruptor 3 - September 11, 2019',
			'description' => '<p>As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.</p>',
			'author' => 'Brewster Kingham, Delaware Biotechnology Institute,  University of Delaware',
			'featured' => true,
			'slug' => 'megaruptor3-testimonial-2',
			'meta_keywords' => '',
			'meta_description' => '',
			'modified' => '2019-09-11 15:44:18',
			'created' => '2019-09-11 15:44:18',
			'ProductsTestimonial' => array(
				[maximum depth reached]
			)
		),
		(int) 2 => array(
			'id' => '75',
			'name' => 'Testimonial Megaruptor 3',
			'description' => '<p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
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			'author' => 'Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen',
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$testimonials = '<blockquote><p><span>The Megaruptor 3 enables us to shear to HMW DNA to consistent and narrow size ranges. This is critical for construction of PacBio libraries and most importantly for samples with limiting amounts of DNA. The fact that it is easy to use is a significant plus in a busy lab.</span></p><cite>Alvaro Hernandez, Ph.D., Director of the High-Throughput Sequencing and Genotyping Unit of the Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign.</cite></blockquote>
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$featured_testimonials = '<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>As a PacBio Certified Service Provider it is critical that sample processing in my laboratory is precise and reproducible. For genome sequencing projects, the fragmentation of genomic DNA to precise and reproducible sizes is essential in order to optimize conditions for library preparation, sequencing, and downstream assembly. For this my laboratory relies on the Megaruptor system. The Megaruptor is the optimal system for long DNA fragment generation and tight fragment length distribution.</p><cite>Brewster Kingham, Delaware Biotechnology Institute,  University of Delaware</cite></blockquote>
<blockquote><span class="label-green" style="margin-bottom:16px;margin-left:-22px">TESTIMONIAL</span><p>The NGS Competence Center T&uuml;bingen (NCCT), together with four other national centers, has been established by the DFG (German Research Foundation) to support research projects with diverse needs of high-throughput sequencing technologies.</p>
<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
<p>Finally, handling of the Megaruptor 3 is quick, with a simple interface. Diagenode is fast in delivering consumables and these are ready-to-go. Sample preparation requires one pipetting step. You need to enter 2 parameters of your sample: volume and concentration in addition to the speed related to your desired size. It is a safe process without sample cross-contamination. It is easy to control whether the sample is going through the hydropore. The system is fast; for the concentration and speed conditions we have tested, runs were completed between half an hour and 2 hours.</p><cite>Elena Buena Atienza and Dr. Nicolas Casadei, Institute of Medical Genetics and Applied Genomics, University Clinics Tübingen</cite></blockquote>
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<p>Long-read sequencing is very helpful to answer scientific questions in various topics such as microbiology or clinical research. We have noticed that the data yield of Nanopore sequencing can be notably increased by shearing the high molecular weight genomic DNA with an average size distribution of ~30kb and obtaining a read length N50 of 30kb. In this context, the Megaruptor 3 was critical to achieve long, homogenous and reproducible DNA preparation.</p>
<p>Megaruptor 3 is able to shear different molecular weight ranges up to 100kb; provided the input genomic DNA is of high-molecular weight. We have tested the Megaruptor 3 with genomic DNA from human blood, fibroblasts and difficult samples such as bacterial genomic DNA with high viscosity. With the Megaruptor 3 we have easily sheared up to 8 samples in parallel, saving preparation time. We have tested concentrations as low as 5 ng/&micro;L and up to 70 ng/&micro;L, saving sample material for optimization and meeting downstream requirements for library preparation. &nbsp;</p>
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<p><a href="https://www.diagenode.com/en/p/megaruptor-3">The Megaruptor 3</a> comes with a default cassette that processes 8 samples at once. We now offer a <strong>12 sample cassette</strong> for 50% higher throughput that <strong>easily fits</strong>&nbsp;into your existing Megaruptor 3.&nbsp;<span style="font-weight: 400;">Our user-friendly system allows </span><b>&nbsp;samples to be processed simultaneously </b><span style="font-weight: 400;">without additional user input.</span></p>
<p><span style="font-weight: 400;">The new 12 sample&nbsp;capacity&nbsp;is optimal for use prior to library preparation on the <a href="https://www.pacb.com/revio/">PacBio Revio</a>, matching the new system's higher throughput and increased&nbsp;efficiency on time.&nbsp;</span></p>
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	'description' => '<p>Pleurotus ostreatus, one of the most widely cultivated edible mushrooms, produces high numbers of spores causing severe respiratory health problems for people, clogging of filters and spoilage of produce. A non-sporulating commercial variety (SPOPPO) has been successfully introduced into the market in 2006. This variety was generated by introgression breeding of a natural mutation into a commercial variety. Our cytological studies revealed that meiosis in the natural and derived sporeless strains was blocked in metaphase I, apparently resulting in a loss of spore formation. The gene(s) underlying this phenotype were mapped to an 80 kb region strongly linked to sporelessness and identified by transformation of wild type genes of this region into a sporeless strain. Sporulation was restored by re-introduction of the DNA sequence encoding the P. ostreatus meiotic recombination gene MSH4 homolog (poMSH4). Subsequent molecular analysis showed that poMSH4 in the sporeless P. ostreatus was interrupted by a DNA fragment containing a region encoding a CxC5/CxC6 cysteine cluster associated with Copia-type retrotransposons. The block of meiosis in metaphase I by a poMSH4 null mutant suggests that this protein plays an essential role in both Class I and II crossovers in mushrooms, similar to animals (mice), but unlike in plants. MSH4 was previously shown to be a target for breeding of sporeless varieties in P. pulmonarius, and the null mutant of the MSH4 homolog of S. commune (scMSH4) confers an extremely low level of spore formation. We propose that MSH4 homologs are likely to be a breeding target for sporeless strains both within Pleurotus sp. and in other Agaricales.</p>',
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	'pmid' => 'https://www.ncbi.nlm.nih.gov/pubmed/33147286',
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