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128 results for “chromosome level”
A chromosome-level genome assembly of the highly heterozygous sea urchin Echinometra sp. EZ reveals adaptation in the regulatory regions of stress response genes
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Chromosome-level assembly of two pearl millet (Cenchrus americanus) genomes, functional annotation and transcriptomes
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Chromosome-Level genome assembly and transcriptome analysis of the ural owl, Strix uralensis Pallas, 1771
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A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes
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Data from: Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of Nanopore Sequencing, Bionano and Hi-C technology
<p><i>Onychostoma macrolepis</i> is an emerging commercial cyprinid fish species. It is a model system for studies of sexual dimorphism and genome evolution. Here, we report the chromosome-level assembly of the<i> O.macrolepis</i> genome obtained from the integration of Nanopore long-read sequencing with physical maps produced using Bionano and Hi-C technology. A total of 87.9 Gb of Nanopore sequence provided approximately 100-fold coverage of the genome. The preliminary genome assembly was 883.2 Mb in size with a contig N50 size of 11.2 Mb. The 969 corrected contigs obtained from Bionano optical mapping were assembled into 853 scaffolds and produced an assembly of 886.5 Mb with a scaffold N50 of 16.5 Mb. Finally, using the Hi-C data, 881.3 Mb (99.4% of genome) in 526 scaffolds were anchored and oriented in 25 chromosomes ranging in size from 25.27 to 56.49 Mb. In total, 24,770 protein-coding genes were predicted in the genome, and ~96.85% of the genes were functionally annotated. The annotated assembly contains 93.3% complete genes from the BUSCO reference set. In addition, we identified 409 Mb (46.23% of the genome) of repetitive sequence, and 11,213 non-coding RNAs, in the genome. Evolutionary analysis revealed that <i>O.macrolepis</i> diverged from common carp approximately 24.25 million years ago. The chromosomes of <i>O.macrolepis</i> showed an unambiguous correspondence to the chromosomes of zebrafish. The high-quality genome assembled in this work provides a valuable genomic resource for further biological and evolutionary studies of <i>O. macrolepis</i>.</p>
Data from: Chromosome-level assembly of Southern catfish (Silurus meridionalis) provides insights into visual adaptation to the nocturnal and benthic lifestyles
Southern catfish (<i><span>Silurus meridionalis</span></i>) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries with an important economic value but a drastically declining wild population. In this study, we constructed a chromosome-level draft genome of <i><span>S. meridionalis</span></i> using 69.7 Gb Nanopore long reads and 49.5 Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi-C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9 Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein-coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed that catfish possess a rod-dominated visual system which is responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of UV and violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow color vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod-to-cone ratio leaded to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of conserved noncoding elements (CNEs), which might be associated with the small eyes in catfish. Taken together, our study provided important clues for the adaptation of the catfish visual system to a benthic lifestyle. The draft genome of <i><span>S. meridionalis</span></i> represents a valuable resource for elucidation of molecular mechanism of ecological adaptation, as well as genetic breeding in aquaculture.
Data from: Chromosome-level genome assembly of Paralithodes platypus provides insights into evolution and adaptation of king crabs
<p>The blue king crab, <i>Paralithodes platypus</i>, which belongs to the Lithodidae family, is a commercially and ecologically important species. However, a high-quality reference genome for the king crab has not yet been reported. Here, we assembled the first chromosome-level blue king crab genome, which contains 104 chromosomes and an N50 length of 51.15 Mb. Furthermore, we determined that the large genome size can be attributed to the insertion of long interspersed nuclear elements and long tandem repeats. Genome assembly assessment showed that 96.54% of the assembled transcripts could be aligned to the assembled genome. Phylogenetic analysis showed the blue king crab to have a close relationship with the Eubrachyura crabs, from which it diverged 272.5 million years ago. Population history analyses indicated that the effective population of the blue king crab declined sharply and then gradually increased from the Cretaceous and Neogene periods, respectively. Furthermore, gene families related to developmental pathways, steroid and thyroid hormone synthesis, and inflammatory regulation, were expanded in the genome, suggesting that these genes contributed substantially to the environmental adaptation and unique body plan evolution of the blue king crab. The high-quality reference genome reported here provides a solid molecular basis for further study of the blue king crab's development and environmental adaptation.</p>
Chromosome‐level genome assembly of Lethenteron reissneri provides insights into lamprey evolution
<p>The reissner lamprey<i> Lethenteron reissneri</i> belonging to Cyclostomata, serves as a bridge between invertebrates and jawed vertebrates, and is considered the most direct ancestor of vertebrates. However, the genetic mechanisms underlying the adaptive evolution of lampreys remain unclear. Here, we supplied the genome data and annotation data of <em>Lethenteron reissneri</em>. Total 5 files were uploaded, including the assembled genome of <i>Lethenteron reissneri</i>, the gene annotation file in gff format, the gene function annotation file, the LIP gene sequences of 50 species used in the article, and the readme file. This study not only provides the first chromosome-level reference genome in Cyclostomata, but also indicates the unique biology and adaptive evolution of lampreys.</p>
Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
<p class="p">The leaf resemblance of <i><span>Kallima</span></i> (Nymphalidae) butterflies<i> </i>is an important ecological adaptive mechanism that increases survival. However, the genetic mechanism underlying ecological adaptation remains unclear owing to a dearth of genomic information. Herein, we revealed the karyotype (n = 31) of the dead-leaf butterfly <i><span>Kallima inach</span></i><i><span>us</span></i>, assembled its high-quality chromosome-level reference genome (568.92 Mb; contig N50: 19.20 Mb), and identified its Z and candidate W chromosomes. To our knowledge, this is the first study to report on these aspects of this species. In the assembled genome, 15,309 protein-coding genes and 49.86% repeat elements were annotated. Phylogenetic analysis showed that <i><span>K. inachus</span></i> diverged from <i><span>Melitaea cinxia </span></i>(no leaf resemblance), both of which are in Nymphalinae, around 40 million years ago. Demographic analysis indicated that the effective population size of <i><span>K. inach</span></i><i><span>us</span></i> decreased during the last interglacial period in the Pleistocene. The wings of adults with the pigmentary gene <i><span>ebony</span></i> knocked out using CRISPR/Cas9 showed phenotypes in which the orange dorsal region and entire ventral surface darkened, suggesting its vital role in the ecological adaption of dead-leaf butterflies. Our results provide important genome resources for investigating the genetic mechanism underlying protective resemblance in dead-leaf butterflies and insights into the molecular basis of protective coloration.</p>
Chromosome-level genome assembly of Triticum turgidum var 'Kronos'
<p> </p> <h2><strong>This data is made available under the Toronto Agreement. </strong></h2> <p><strong>All of the data listed here is available under the prepublication data sharing principle of the </strong><a href="https://www.nature.com/articles/461168a"><strong>Toronto agreement</strong></a><strong> (1). By using this data, you agree to:</strong></p> <ul> <li><strong>respect the rights of the data producers and contributors to analyze and publish the first global analyses and certain other reserved analyses of this data set in a peer-reviewed publication.</strong></li> <li><strong>not redistribute, release, or otherwise provide access to the data to anyone outside of the group, until the data has been published & submitted to the public data repositories.</strong></li> <li><strong>contact the authors to discuss any plans to publish data or analyses that utilize this data to avoid the overlap of any planned analyses.</strong></li> <li><strong>fully cite the prepublication data along with any applicable versioning details.</strong></li> <li><strong>understand that this data as accessed is precompetitive and is not patentable in its present state.</strong></li> </ul> <p><strong>This agreement does not expire by time but only upon publication of the first global analysis by the data producers and contributors.</strong><br><strong>(1) Toronto International Data Release Workshop Authors. Prepublication data sharing. </strong><em><strong>Nature</strong></em><strong> 461, 168–170 (2009). </strong><a href="https://doi.org/10.1038/461168a"><strong>https://doi.org/10.1038/461168a</strong></a></p> <p> </p> <ul> <li><em>If you have questions about <strong>the use</strong> of this dataset, please contact Ksenia Krasileva: kseniak [at] berkeley.edu</em></li> </ul> <p> </p> <p><strong>Updates in Zenodo v7</strong></p> <p>This update includes annotations of non-coding RNAs. Please refer to our <a href="https://github.com/s-kyungyong/Kronos">github</a> to understand how this datasets were produced. Please check additional datasets here: <a href="https://zenodo.org/records/15801566">Chromosome-level genome assembly of Triticum turgidum var 'Kronos' additional datasets.</a></p> <p> </p> <p><strong>Acknowledgement</strong></p> <p>This work has been funded by the United States Department of Agriculture - National Institute for Food and Agriculture Award (2021-67013-35726). <br><br><br></p>
Chromosome-level Reference Genome of the Critically Endangered Tree Kmeria septentrionalis
<p><i>Kmeria septentrionalis, </i>a critically endangered tree endemic to Guangxi in China and listed on the International Union for Conservation of Nature's Red List, suffers from a lack of genetic information and a paucity of high-quality genome data. In our study, we construct and annotate a complete <i>K. septentrionalis</i> genome at the chromosome level, assess its quality, and contextualize it with the genomic data of other relative plants. The genome is measured at 2.57 Gb with a contig N50 of 11.93 Mb. Using Hi-C guided genome assembly, we assembled 496 out of the initial 705 raw contigs into 19 pseudochromosomes that have a scaffold N50 of 135.08 Mb. The assembled 2.54 Gb anchored genome has achieved 98.9% completeness, and contains 35,927 genes, of which 94.15% could be functional annotated. </p>
A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)
<p><span>The Orange wheat blossom midge <i>Sitodiplosis mosellana </i>Géhin (Diptera: Cecidomyiidae), an important insect pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. In this study, we assembled the first chromosomal level genome for <i>S. mosellana</i> using PacBio long-read, Illumina short-read sequences and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored four pseudochromosomes, accounting for 99.67% of the assembled genome. The assembly showed high integrity and quality, with 91.7% of short reads mapped to the genome and a coverage rate of 99.8%. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single-Copy Orthologs. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that <i>S. mosellana</i> and its close relative the swede midge <i>Contarinia nasturtii</i> diverged about 32.7 million years ago. <i>S. mosellana</i> genome showed high chromosomal synteny with the genome of <i>Drosophila melanogaster</i> and <i>Anopheles gambiae</i>. The key gene families involved in chemosensation and detoxification of plant secondary chemistry were analysed<i>.</i> The high-quality <i>S. mosellana</i> genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges as well as insect-plant interactions and co-evolution, and their relatives more generally.</span></p>
A chromosome-level genome assembly of Gekko japonicus
<p>We assembled and annotated a chromosome-level genome of <em>Gekko japonicus.</em></p>
Genome annotation associated with the publication "Chromosome-level genome assembly of the Cape cliff lizard (Hemicordylus capensis)"
<p>Genome annotation associated with the publication "Chromosome-level genome assembly of the Cape cliff lizard (<em>Hemicordylus capensis</em>)"</p> <p>rHemCap1.1.gff3 - Genome annotation in GFF3 format<br> rHemCap1.1.proteins.fa - Multi-fasta file of protein coding genes<br> rHemCap1.1.cds-transcripts.fa - Multi-fasta file of transcripts (CDS)</p> <p> </p>
Repeat annotation of a chromosomal-level assembly of the Callosobruchus maculatus genome
<p>A curated repeat library <c.mac_HiC_plus_beetle_library.lib> was constructed by manually curating the most abundant interspersed repeats identified using RepeatModeler (Smit et al., 2010). The curated library was combined with a beetle-specific library, constructed using RepeatMasker’s queryRepeatDatabase.pl script (-species coleoptera). The genome repeat annotation was generated with RepeatMasker (Smit and Hubley, 2010).</p>
Chromosome-level Genome Assembly of Euphorbia peplus
<p>Code used in genome assembly and annotation: https://github.com/ariellerjohnson/Euphorbia-peplus-genome-project Raw data is available in NCBI PRJNA837952 Euphorbia peplus Genome sequencing and assembly. Also check out our interactive genome browser: https://euphorbgenomes.biohpc.cornell.edu/ And our interactive expression browser: https://bar.utoronto.ca/efp_euphorbia/cgi-bin/efpWeb.cgi</p>
Chromosome-level clam genome helps elucidate the molecular basis of adaptation to a buried lifestyle
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Data from: Chromosome-level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines
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Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
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A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae)
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.