Diagenode

Megaruptor

140 publications found.

The genome sequence of the Elbow-stripe Grass-veneer, Agriphilageniculea (Haworth, 1811)
Published: February, 2023

Abstract: 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 chr...
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The genome sequence of the Turnip Sawfly, Athalia rosae(Linnaeus, 1758)
Published: February, 2023

Abstract: 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 pseudomo...
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A high-quality, haplotype-phased genome reconstruction reveals unexpectedhaplotype diversity in a pearl oyster.
Published: December, 2022

Abstract: 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, g...
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The genome sequence of the malaria mosquito, Anopheles funestus,Giles, 1900
Published: November, 2022

Abstract: 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 chromoso...
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Complete Genome Sequence of Lacticaseibacillus rhamnosus DM065,Isolated from the Human Oral Cavity.
Published: November, 2022

Abstract: 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 on...
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Evaluation of the pathogenesis of non-typical strain with α-hemolysin,Vibrio parahaemolyticus 353, isolated from Chinese seafood throughcomparative genome and transcriptome analysis.
Published: November, 2022

Abstract: Vibrio parahaemolyticus outbreaks frequently occur, causing gastrointestinal sickness owing to the consumption of aquatic foods by various virulence factors; however, the mechanism of pathogenesis is still unknown. In this study, a non-typical str...
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Detection and Quantitation of DNA Damage on a Genome-wide ScaleUsing RADAR-seq.
Published: November, 2022

Abstract: The formation and persistence of DNA damage can impact biological processes such as DNA replication and transcription. To maintain genome stability and integrity, organisms rely on robust DNA damage repair pathways. Techniques to detect and locate...
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Predictable and stable epimutations induced during clonal plantpropagation with embryonic transcription factor.
Published: November, 2022

Abstract: Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal ...
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Benchmarking second and third-generation sequencing platforms formicrobial metagenomics.
Published: November, 2022

Abstract: Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generat...
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Mitochondrial RNA editing in Trypanoplasma borreli: new tools, newrevelations
Published: November, 2022

Abstract: The kinetoplastids are unicellular flagellates that derive their name from the ‘kinetoplast’, a region within their single mitochondrion harboring its organellar genome of high DNA content, called kinetoplast (k) DNA. Some protein prod...
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Semi-automated assembly of high-quality diploid human reference genomes.
Published: October, 2022

Abstract: 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 ble...
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Rapid and comprehensive diagnostic method for repeat expansion diseasesusing nanopore sequencing.
Published: October, 2022

Abstract: We developed a diagnostic method for repeat expansion diseases using a long-read sequencer to improve currently available, low throughput diagnostic methods. We employed the real-time target enrichment system of the nanopore GridION sequencer usin...
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Integration of Hi-C with short and long-read genome sequencingreveals the structure of germline rearranged genomes.
Published: October, 2022

Abstract: 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 ...
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Characterization of somatic structural variations in 528 Chineseindividuals with Esophageal squamous cell carcinoma.
Published: October, 2022

Abstract: Esophageal squamous cell carcinoma (ESCC) demonstrates high genome instability. Here, we analyze 528 whole genomes to investigate structural variations' mechanisms and biological functions. SVs show multi-mode distributions in size, indicating dis...
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The Capparis spinosa var. herbacea genome provides the first genomicinstrument for a diversity and evolution study of the Capparaceae family.
Published: October, 2022

Abstract: BACKGROUND: The caper bush Capparis spinosa L., one of the most economically important species of Capparaceae, is a xerophytic shrub that is well adapted to drought and harsh environments. However, genetic studies on this species are limited becau...
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Genomic Characterization and Antimicrobial Susceptibility ofDromedary-Associated from the Horn of Africa.
Published: October, 2022

Abstract: Members of the family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized strains from apparently healthy and diseased camels ( = 84) and cattle ( = 7) in Somalia and Keny...
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The genome sequence of the orange-tip butterfly, Anthocharis cardamines(Linnaeus, 1758)
Published: October, 2022

Abstract: 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 ...
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The genome sequence of the Arran brown, Erebia ligea (Linnaeus,1758)
Published: October, 2022

Abstract: 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 ...
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Complete Genome Sequence of Strain DM083 Isolated from HumanTongue Coating.
Published: September, 2022

Abstract: 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. Impo...
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The genome sequence of the yellow-legged clearwing, Synanthedonvespiformis (Linnaeus, 1761)
Published: September, 2022

Abstract: 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 chro...
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The genome sequence of the pale mottled willow, Caradrina clavipalpis(Scopoli, 1763)
Published: September, 2022

Abstract: 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 chromoso...
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The genome sequence of the smoky wainscot, Mythimna impura (Hubner,1808)
Published: September, 2022

Abstract: 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 chromo...
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The genome sequence of the wall brown, Lasiommata megera (Linnaeus,1767)
Published: September, 2022

Abstract: 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 ch...
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The genome sequence of the sallow kitten, Furcula furcula (Clerck,1759)
Published: September, 2022

Abstract: 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 p...
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The genome sequence of the peacock moth, Macaria notata (Linnaeus,1758)
Published: September, 2022

Abstract: 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 chrom...
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Comparative analyses of Theobroma cacao and T. grandiflorummitogenomes reveal conserved gene content embedded within complex andplastic structures.
Published: September, 2022

Abstract: 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 gen...
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Plant species-specific basecaller improves actual accuracy of nanoporesequencing
Published: September, 2022

Abstract: 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,...
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Complete Genome Sequences of the Soil Oxalotrophic BacteriumCupriavidus oxalaticus Strain Ox1 and Its DerivedmCherry-Tagged Strain.
Published: August, 2022

Abstract: Here, we report the complete genome sequences of the soil oxalotrophic bacterium Cupriavidus oxalaticus Ox1 and a derived mCherry-tagged strain. The genome size is approximately 6.69 Mb, with a GC content of 66.9\%. The genome sequence of O...
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The improved genome of the nematode Parapristionchus giblindavisiprovides insights into lineage-specific gene family evolution.
Published: August, 2022

Abstract: Nematodes such as Caenorhabditis elegans and Pristionchus pacificus are extremely successful model organisms for comparative biology. Several studies have shown that phenotypic novelty but also conserved processes are controlled by taxon-restricte...
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The chromosome-level genome of Gypsophila paniculata reveals themolecular mechanism of floral development and ethylene insensitivity
Published: August, 2022

Abstract: 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...
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Patients with biallelic GGC repeat expansions in NOTCH2NLCexhibiting a typical neuronal intranuclear inclusion disease phenotype.
Published: August, 2022

Abstract: We report two patients with autosomal dominant neuronal intranuclear inclusion disease (NIID) harboring the biallelic GGC repeat expansion in NOTCH2NLC to uncover the impact of repeat expansion zygosity on the clinical phenotype. The zygosity of t...
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The leaf beetle Chelymorpha alternans propagates a plant pathogen inexchange for pupal protection.
Published: August, 2022

Abstract: 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 ...
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A haplotype resolved chromosomal level avocado genome allows analysis ofnovel avocado genes
Published: August, 2022

Abstract: Avocado (Persea americana) is a member of the magnoliids, an early branching lineage of angiosperms that has high value globally with the fruit being highly nutritious. Here, we report a chromosome-level genome assembly for the commercial avocado ...
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The genome sequence of the hawthorn shieldbug, Acanthosomahaemorrhoidale (Linnaeus, 1758)
Published: July, 2022

Abstract: 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 scaffol...
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Identification of Laportea bulbifera using the Complete ChloroplastGenome as a Super-Barcode
Published: July, 2022

Abstract: Laportea bulbifera, a Miao medicine grown in karst areas, has exerts a unique curative effect on skin itching in the elderly, with an annual sales of > 100 million Yuan. Owing to the shortage of resources and large morphological variations in L...
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The genome sequence of the dun-bar pinion, Cosmia trapezina(Linnaeus, 1758)
Published: July, 2022

Abstract: 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 chromos...
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Oxford Nanopore R10.4 long-read sequencing enables the generation ofnear-finished bacterial genomes from pure cultures and metagenomes withoutshort-read or reference polishing.
Published: July, 2022

Abstract: Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to inclu...
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Complete Genome Sequences of Multidrug-Resistant Campylobactercoli Strains YH501, YH503, and YH504, from Retail Chicken.
Published: July, 2022

Abstract: Campylobacter coli is an important foodborne pathogen that can cause inflammation of the intestine and diarrhea in humans. The complete genomes, including megaplasmids, of C. coli strains YH501, YH503, and YH504 from retail chicken were sequenced ...
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High-Quality Genome Assembly of Nannochloris desiccata 2437 andIts Associated Bacterial Community.
Published: July, 2022

Abstract: High-quality genome sequences were generated for the nonaxenic marine microalga Nannochloris desiccata UTEX 2437 and eight of its associated environmental bacterial species. UTEX 2437 is diploid, and its 20.738-Mbp nuclear genome sequence is assem...
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Equilibrated evolution of the mixed auto-/allopolyploidhaplotype-resolved genome of the invasive hexaploid Prussian carp.
Published: July, 2022

Abstract: 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 sequenc...
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Long-read Oxford nanopore sequencing reveals a de novo case of complexchromosomal rearrangement involving chromosomes 2, 7, and 13.
Published: June, 2022

Abstract: BACKGROUND: Complex chromosomal rearrangements (CCRs) are associated with high reproductive risk, infertility, abnormalities in offspring, and recurrent miscarriage in women. It is essential to accurately characterize apparently balanced chromosom...
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Accumulation of endosymbiont genomes in an insect autosome followed byendosymbiont replacement.
Published: May, 2022

Abstract: Eukaryotic genomes can acquire bacterial DNA via lateral gene transfer (LGT). A prominent source of LGT is Wolbachia, a widespread endosymbiont of arthropods and nematodes that is transmitted maternally through female germline cells. The DNA trans...
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DNA Hypermethylation and a Specific Methylation Spectrum on theX Chromosome in Turner Syndrome as Determined by NanoporeSequencing
Published: May, 2022

Abstract: The molecular genetic mechanism of Turner syndrome (TS) still leaves much to be discovered. Methods: TS (45X0) patients and age-matched controls (46XX and 46XY) were selected. The nanopore sequencing combined with trio-whole exome sequencing (trio...
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Familial long-read sequencing increases yield of de novo mutations.
Published: April, 2022

Abstract: Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide patt...
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Transposon activity, local duplications and propagation of structuralvariants across haplotypes drive the evolution of the Drosophila S2cell line.
Published: April, 2022

Abstract: BACKGROUND: Immortalized cell lines are widely used model systems whose genomes are often highly rearranged and polyploid. However, their genome structure is seldom deciphered and is thus not accounted for during analyses. We therefore used linked...
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The genome sequence of Anoplius nigerrimus (Scopoli, 1763), a spiderwasp
Published: April, 2022

Abstract: We present a genome assembly from an individual Anoplius nigerrimus (Arthropoda; Insecta; Hymenoptera; Pompilidae) of unknown sex. The genome sequence is 624 megabases in span. In total, 45.75\% of the assembly is scaffolded into 15 chromosomal ps...
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Haplotype-resolved Chinese male genome assembly based on high-fidelitysequencing
Published: March, 2022

Abstract: 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...
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Phylogenomics and Comparative Genomics Highlight SpecificGenetic Features in Species.
Published: March, 2022

Abstract: The species in Polyporales are ecologically and economically relevant wood decayers used in traditional medicine, but their genomic traits are still poorly documented. In the present study, we carried out a phylogenomic and comparative genomic ana...
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Complete Genome Sequence of Herpes Simplex Virus 2 StrainG.
Published: March, 2022

Abstract: 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 regi...
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Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes
Published: February, 2022

Abstract: Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0,...
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Chromosomal rearrangements with stable repertoires of genes andtransposable elements in an invasive forest-pathogenic fungus
Published: February, 2022

Abstract: Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity has been often reported in Fungi, which may explain their apparent ability to quickly adap...
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Genomic characterisation of three GES-producing Enterobacteralesisolated in the Czech Republic.
Published: February, 2022

Abstract: OBJECTIVES: The aim of the study is to characterise the genomic features of three GES-producing Enterobacterales isolates from Czech hospitals. METHODS: In 2020, during a routine screening of the hospital's surfaces in Prague General Hospital, two...
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The genome sequence of a stonefly, Nemurella pictetii Klapalek, 1900
Published: February, 2022

Abstract: 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 pseudomol...
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The genome sequence of the furry-claspered furrow bee, Lasioglossumlativentre (Schenck, 1853)
Published: February, 2022

Abstract: 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 sc...
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The genome sequence of a parasitoid wasp, Forster, 1771.
Published: January, 2022

Abstract: 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 ...
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The genome sequence of the brimstone moth, Opisthograptis luteolata(Linnaeus, 1758)
Published: January, 2022

Abstract: 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 pseudo...
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Improved chromosome-level genome assembly of the Glanville fritillarybutterfly () integrating Pacific Biosciences long reads and ahigh-density linkage map
Published: January, 2022

Abstract: 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 ...
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The genome sequence of Gymnosoma rotundatum (Linnaeus, 1758), aparasitoid ladybird fly
Published: January, 2022

Abstract: 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 se...
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Reference genome assembly of the big berry Manzanita (Arctostaphylosglauca).
Published: November, 2021

Abstract: 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 ...
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PRINCESS: comprehensive detection of haplotype resolved SNVs, SVs,and methylation.
Published: September, 2021

Abstract: Long-read sequencing has been shown to have advantages in structural variation (SV) detection and methylation calling. Many studies focus either on SV, methylation, or phasing of SNV; however, only the combination of variants provides a comprehens...
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Establishing community reference samples, data and call sets forbenchmarking cancer mutation detection using whole-genome sequencing.
Published: September, 2021

Abstract: 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 set...
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LeafGo: Leaf to Genome, a quick workflow to produce high-quality denovo plant genomes using long-read sequencing technology.
Published: September, 2021

Abstract: Currently, different sequencing platforms are used to generate plant genomes and no workflow has been properly developed to optimize time, cost, and assembly quality. We present LeafGo, a complete de novo plant genome workflow, that starts from ti...
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De novo genome assembly of the marine teleost, bluefin trevally (Caranxmelampygus).
Published: September, 2021

Abstract: 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 c...
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Targeted long-read sequencing identifies missing disease-causingvariation.
Published: August, 2021

Abstract: 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-eval...
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Evidence of an epidemic spread of KPC-producing in Czech hospitals
Published: August, 2021

Abstract: 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 2018–2019, a total of 108 KPC-producing Enterobacterales were recovered fr...
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The USDA-ARS Ag100Pest Initiative: High-Quality GenomeAssemblies for Agricultural Pest Arthropod Research
Published: July, 2021

Abstract: Simple Summary High-quality genome assemblies are essential tools for modern biological research. In the past, creating genome assemblies was prohibitively expensive and time-consuming for most non-model insect species due to, in part, the technic...
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Familial thrombocytopenia due to a complex structural variant resulting ina WAC-ANKRD26 fusion transcript.
Published: June, 2021

Abstract: 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...
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The American lobster genome reveals insights on longevity, neural, andimmune adaptations.
Published: June, 2021

Abstract: The American lobster, , is integral to marine ecosystems and supports an important commercial fishery. This iconic species also serves as a valuable model for deciphering neural networks controlling rhythmic motor patterns and olfaction. Here, we ...
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Analysis of the Coptis chinensis genome reveals the diversification ofprotoberberine-type alkaloids.
Published: June, 2021

Abstract: Chinese goldthread (Coptis chinensis Franch.), a member of the Ranunculales, represents an important early-diverging eudicot lineage with diverse medicinal applications. Here, we present a high-quality chromosome-scale genome assembly and annotati...
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Infectivity assessment of porcine endogenous retrovirus usinghigh-throughput sequencing technologies.
Published: June, 2021

Abstract: Xenogenic cell-based therapeutic products are expected to alleviate the chronic shortage of human donor organs. For example, porcine islet cell products are currently under development for the treatment of human diabetes. As porcine cells possess ...
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Chromosomal inversion polymorphisms in two sympatric ascidian lineages.
Published: April, 2021

Abstract: Chromosomal rearrangements can reduce fitness of heterozygotes and can thereby prevent gene flow. Therefore, such rearrangements can play a role in local adaptation and speciation. In particular, inversions are considered to be a major potential c...
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PCIP-seq: simultaneous sequencing of integrated viral genomes and theirinsertion sites with long reads.
Published: April, 2021

Abstract: 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...
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Complete vertebrate mitogenomes reveal widespread repeats and geneduplications.
Published: April, 2021

Abstract: 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 Genome...
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Comparison of long read sequencing technologies in interrogating bacteriaand fly genomes.
Published: March, 2021

Abstract: 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 p...
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Chromosomal rearrangements but no change of genes and transposable elementsrepertoires in an invasive forest-pathogenic fungus
Published: March, 2021

Abstract: Chromosomal rearrangements have been largely described among eukaryotes, and may have important consequences on evolution of species. High genome plasticity have been often reported in Fungi, that may explain their apparent ability to quickly adap...
Read more »

A single nucleotide polymorphism variant located in the cis-regulatoryregion of the ABCG2 gene is associated with mallard egg colour.
Published: March, 2021

Abstract: 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 ...
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Genomic Characterization of VIM and MCR Co-Producers: The First TwoClinical Cases, in Italy.
Published: January, 2021

Abstract: BACKGROUND: the co-production of carbapenemases and -genes represents a worrisome event in the treatment of infections. The aim of the study was to characterize the genomic features of two clinical complex (ECC) isolates, co-producing VIM and MCR ...
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Chromosome-scale genome assembly provides insights into the evolution andflavor synthesis of passion fruit (Passiflora edulis Sims).
Published: January, 2021

Abstract: 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 Mb chromosome-scale genome assembly of passion fruit, with 98.91\% (~13...
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Rapid and ongoing evolution of repetitive sequence structures in humancentromeres.
Published: December, 2020

Abstract: 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 l...
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Efficient hybrid de novo assembly of human genomes with WENGAN.
Published: December, 2020

Abstract: 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 ...
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Complete Genome Sequence of sp. Strain Nx66, Isolated from WatersContaminated with Petrochemicals in El Saf-Saf Valley, Algeria.
Published: November, 2020

Abstract: sp. strain Nx66 was isolated from waters contaminated by petrochemical effluents collected in Algeria. Its genome was sequenced using Illumina MiSeq (2 × 150-bp read pairs) and Oxford Nanopore (long reads) technologies and was assembled usin...
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Contrasting signatures of genomic divergence during sympatric speciation.
Published: October, 2020

Abstract: 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 count...
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Genome structure and content of the rice root-knot nematode ().
Published: October, 2020

Abstract: 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 unavaila...
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Repeat expansions confer WRN dependence in microsatellite-unstablecancers.
Published: October, 2020

Abstract: 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 break...
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Breakpoint mapping of a t(9;22;12) chronic myeloid leukaemia patient withe14a3 BCR-ABL1 transcript using Nanopore sequencing.
Published: September, 2020

Abstract: 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 ...
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Complete Genome Sequence of the Type Strain Pectobacterium punjabenseSS95, Isolated from a Potato Plant with Blackleg Symptoms.
Published: August, 2020

Abstract: Pectobacterium punjabense is a newly described species causing blackleg disease in potato plants. Therefore, by the combination of long (Oxford Nanopore Technologies, MinION) and short (Illumina MiSeq) reads, we sequenced the complete genome of P....
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Sizing, stabilising, and cloning repeat-expansions for gene targeting constructs.
Published: July, 2020

Abstract: Aberrant microsatellite repeat-expansions at specific loci within the human genome cause several distinct, heritable, and predominantly neurological, disorders. Creating models for these diseases poses a challenge, due to the instability of such r...
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Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach.
Published: July, 2020

Abstract: A meta-analysis of genome-wide association studies (GWAS) identified eight loci that are associated with heart rate variability (HRV), but candidate genes in these loci remain uncharacterized. We developed an image- and CRISPR/Cas9-based pipeline ...
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Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69Escherichia coli Strain in Italy
Published: July, 2020

Abstract: Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VI...
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Genomic Insight of VIM-harboring IncA Plasmid from a ClinicalST69 Escherichia coli Strain in Italy
Published: July, 2020

Abstract: Background: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VI...
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Tandem gene duplications drive divergent evolution of caffeine and crocin biosynthetic pathways in plants.
Published: June, 2020

Abstract: BACKGROUND: Plants have evolved a panoply of specialized metabolites that increase their environmental fitness. Two examples are caffeine, a purine psychotropic alkaloid, and crocins, a group of glycosylated apocarotenoid pigments. Both classes of...
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Diversity of Pectobacteriaceae Species in Potato Growing Regions in Northern Morocco.
Published: June, 2020

Abstract: Dickeya and Pectobacterium pathogens are causative agents of several diseases that affect many crops worldwide. This work investigated the species diversity of these pathogens in Morocco, where Dickeya pathogens have only been isolated from potato...
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Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato.
Published: June, 2020

Abstract: Structural variants (SVs) underlie important crop improvement and domestication traits. However, resolving the extent, diversity, and quantitative impact of SVs has been challenging. We used long-read nanopore sequencing to capture 238,490 SVs in ...
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Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.
Published: February, 2020

Abstract: Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostas...
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LongQC: A Quality Control Tool for Third GenerationSequencing Long Read Data
Published: February, 2020

Abstract: We propose LongQC as an easy and automated quality control tool for genomic datasets generated by third generation sequencing (TGS) technologies such as Oxford Nanopore technologies (ONT) and SMRT sequencing from Pacific Bioscience (PacBio). Key s...
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Genome Sequence of sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.
Published: January, 2020

Abstract: An extremely halophilic archaeon, sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromos...
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The round goby genome provides insights into mechanisms that may facilitate biological invasions.
Published: January, 2020

Abstract: BACKGROUND: The invasive benthic round goby (Neogobius melanostomus) is the most successful temperate invasive fish and has spread in aquatic ecosystems on both sides of the Atlantic. Invasive species constitute powerful in situ experimental syste...
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The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome.
Published: January, 2020

Abstract: BACKGROUND: Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnos...
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A highly contiguous genome assembly of the bat hawkmoth Hyles vespertilio (Lepidoptera: Sphingidae).
Published: January, 2020

Abstract: BACKGROUND: Adapted to different ecological niches, moth species belonging to the Hyles genus exhibit a spectacular diversity of larval color patterns. These species diverged ∼7.5 million years ago, making this rather young genus an interestin...
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Nanopore Sequencing and Its Clinical Applications.
Published: January, 2020

Abstract: Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA...
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Interruption of an MSH4 homolog blocks meiosis in metaphase I andeliminates spore formation in Pleurotus ostreatus.
Published: January, 2020

Abstract: 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 (SPOP...
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Detection of Abrin-Like and Prepropulchellin-Like Toxin Genes and Transcripts Using Whole Genome Sequencing and Full-Length Transcript Sequencing of .
Published: November, 2019

Abstract: The sequenced genome and the leaf transcriptome of a near relative of and was analyzed to characterize the genetic basis of toxin gene expression. From the high-quality genome assembly, a total of 26 potential coding regions were identified that c...
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NanoSatellite: accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION.
Published: November, 2019

Abstract: Technological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human g...
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Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull.
Published: October, 2019

Abstract: Genome editing followed by reproductive cloning was previously used to produce two hornless dairy bulls. We crossed one genome-edited dairy bull, homozygous for the dominant P Celtic POLLED allele, with horned cows (pp) and obtained six heterozygo...
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Complete Genome Sequence of an Enterohemorrhagic Escherichia coli O111:H8 Strain Recovered from a Large Outbreak in Japan Associated with Consumption of Raw Beef.
Published: October, 2019

Abstract: We present the complete genome sequence of an enterohemorrhagic O111:H8 strain. This strain was isolated from a hemolytic-uremic syndrome patient and was responsible for a large outbreak associated with the consumption of raw beef in 2011.
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Long-read sequencing and haplotype linkage analysis enabled preimplantation genetic testing for patients carrying pathogenic inversions.
Published: August, 2019

Abstract: BACKGROUND: Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capa...
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Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome.
Published: August, 2019

Abstract: The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of single-molecule real-time (SMRT) sequ...
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Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine.
Published: July, 2019

Abstract: BACKGROUND: Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Rus...
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Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system.
Published: June, 2019

Abstract: BACKGROUND: Complete and contiguous genome assemblies greatly improve the quality of subsequent systems-wide functional profiling studies and the ability to gain novel biological insights. While a de novo genome assembly of an isolated bacterial s...
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A chromosome-scale genome assembly of cucumber (Cucumis sativus L.).
Published: June, 2019

Abstract: BACKGROUND: Accurate and complete reference genome assemblies are fundamental for biological research. Cucumber is an important vegetable crop and model system for sex determination and vascular biology. Low-coverage Sanger sequences and high-cove...
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Genome Sequence and Methylation Patterns of sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.
Published: May, 2019

Abstract: sp. strain BOL3-1 was isolated from Salar de Uyuni, Bolivia, and sequenced using single-molecule real-time sequencing. Its 3.7-Mbp genome was analyzed for gene content and methylation patterns and incorporated into the Haloarchaeal Genomes Databas...
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The Reference Genome Sequence of Scutellaria baicalensis Provides Insights into the Evolution of Wogonin Biosynthesis.
Published: April, 2019

Abstract: Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, "Huang Qin," are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome se...
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Biocompatible N-acetyl cysteine reduces graphene oxide and persists at the surface as a green radical scavenger.
Published: March, 2019

Abstract: We demonstrate that N-acetyl cysteine (NAC) reduces graphene oxide (GO) at room temperature. This represents a new green method to produce reduced GO (rGO). NAC adheres to the rGO surface as demonstrated by several spectroscopy techniques and avoi...
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The alternative reality of plant mitochondrial DNA
Published: March, 2019

Abstract: Plant mitochondrial genomes are usually assembled and displayed as circular maps based on the widely-held assumption that circular genome molecules are the primary form of mitochondrial DNA, despite evidence to the contrary. Many plant mitochondri...
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Characterizing the Major Structural Variant Alleles of the Human Genome.
Published: January, 2019

Abstract: In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1...
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Complete Genome Sequence and Methylome Analysis of Micrococcus luteus SA211, a Halophilic, Lithium-Tolerant Actinobacterium from Argentina.
Published: January, 2019

Abstract: Micrococcus luteus has been found in a wide range of habitats. We report the complete genome sequence and methylome analysis of strain SA211 isolated from a hypersaline, lithium-rich, high-altitude salt flat in Argentina with single-molecule real-...
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Reference genome for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine
Published: December, 2018

Abstract: Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). This study reports on an integrated genome analysis workflow for BCG, resulting in the completely assembled genome sequence...
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SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica).
Published: November, 2018

Abstract: Background: The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioural and genetic studies. To facilitate further population genetics and genomic studies, here we present a reference...
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Improved reference genome of Aedes aegypti informs arbovirus vector control.
Published: November, 2018

Abstract: Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to...
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Whole-genome landscape of Medicago truncatula symbiotic genes.
Published: November, 2018

Abstract: Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemb...
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Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.
Published: November, 2018

Abstract: Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increas...
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The Genomic Basis of Color Pattern Polymorphism in the Harlequin Ladybird.
Published: October, 2018

Abstract: Many animal species comprise discrete phenotypic forms. A common example in natural populations of insects is the occurrence of different color patterns, which has motivated a rich body of ecological and genetic research [1-6]. The occurrence of d...
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Long-read sequence capture of the hemoglobin gene clusters across gadid species.
Published: October, 2018

Abstract: Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not de...
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Genomic Structural Variations Within Five Continental Populations of .
Published: October, 2018

Abstract: Chromosomal structural variations (SV) including insertions, deletions, inversions, and translocations occur within the genome and can have a significant effect on organismal phenotype. Some of these effects are caused by structural variations con...
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Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis.
Published: September, 2018

Abstract: Background: For a proportion of individuals judged clinically to have a recessive Mendelian disease, only one heterozygous pathogenic variant can be found from clinical whole exome sequencing (WES), posing a challenge to genetic diagnosis and gene...
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Long-read sequencing across the C9orf72 'GGGGCC' repeat expansion: implications for clinical use and genetic discovery efforts in human disease.
Published: August, 2018

Abstract: BACKGROUND: Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (GC) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementi...
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The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines.
Published: August, 2018

Abstract: DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been descr...
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Long-read sequence capture of the haemoglobin gene clusters across codfish species.
Published: August, 2018

Abstract: Combining high-throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short-read technology. These approaches are not de...
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A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits.
Published: June, 2018

Abstract: Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our obje...
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Draft genome of the Peruvian scallop Argopecten purpuratus.
Published: April, 2018

Abstract: Background: The Peruvian scallop, Argopecten purpuratus, is mainly cultured in southern Chile and Peru was introduced into China in the last century. Unlike other Argopecten scallops, the Peruvian scallop normally has a long life span of up to 7 t...
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Overview of Next-Generation Sequencing Technologies.
Published: April, 2018

Abstract: High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of correspondin...
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Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains.
Published: January, 2018

Abstract: BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, ...
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Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus.
Published: October, 2017

Abstract: The nematode Pristionchus pacificus is an established model for integrative evolutionary biology and comparative studies with Caenorhabditis elegans. While an existing genome draft facilitated the identification of several genes controlling variou...
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De novo PacBio long-read and phased avian genome assemblies correct and add to reference genes generated with intermediate and short reads
Published: October, 2017

Abstract: Reference-quality genomes are expected to provide a resource for studying gene structure, function, and evolution. However, often genes of interest are not completely or accurately assembled, leading to unknown errors in analyses or additional clo...
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Comparative Analysis of Ralstonia solanacearum Methylomes
Published: April, 2017

Abstract: Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identifie...
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Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum
Published: September, 2016

Abstract: The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood-infecting fungus and a serious threat to grape production worldwide. The capability of colonizing woody tissue combined with the secreti...
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Complete genome of Staphylococcus aureus Tager 104 provides evidence of its relation to modern systemic hospital-acquired strains
Published: March, 2016

Abstract: Background Staphylococcus aureus (S. aureus) infections range in severity due to expression of certain virulence factors encoded on mobile genetic elements (MGE). As such, characterization of these MGE, as well as single nucleotide pol...
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Diversification of bacterial genome content through distinct mechanisms over different timescales.
Published: November, 2014

Abstract: Bacterial populations often consist of multiple co-circulating lineages. Determining how such population structures arise requires understanding what drives bacterial diversification. Using 616 systematically sampled genomes, we show that Streptoc...
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Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance
Published: November, 2014

Abstract: A scarlet fever outbreak began in mainland China and Hong Kong in 2011 (refs. 1–6). Macrolide- and tetracycline-resistant Streptococcus pyogenes emm12 isolates represent the majority of clinical cases. Recently, we identified two m...
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Microevolution of Burkholderia pseudomallei during an acute infection.
Published: September, 2014

Abstract: We used whole-genome sequencing to evaluate 69 independent colonies of Burkholderia pseudomallei isolated from seven body sites of a patient with acute disseminated melioidosis. Fourteen closely related genotypes were found, providing evidence for...
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