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199 results for “genome reference”
Variant metadata for 1K genomes reference panel
<p>1K genomes reference panel - variant metadata</p>
Simulated samples and reference genomes of 25 pathogens
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Figure 5 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 5. Phylogenetic relationships of control regions inferred by the maximum likelihood (ML) method. Statistical support is shown on the branches: bootstrap values (above) and posterior probability (below). BI, Bayesian inference; CR, control region.
Figure 1 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 1. Evolution of mitochondrial genomes in Antarctic notothenioids modified from Zhuang & Cheng (2010). Abbreviations: 12S, 12S ribosomal RNA; CR, control region; Cyt b, cytochrome b; E, tRNAGlu; F, tRNAPhe; ND, nicotinamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; T, tRNAThr.
Figure 4. A in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 4. A, linear representation of three types of gene content from the partial cytochrome b (Cyt b) to 12S rRNA in the mitochondrial (mt) genome of the mackerel icefish. Black and dark grey arrows respectively represent the first and the second duplicates. The first duplicate of the type-1 genome contains full-length nicotinamide adenine dinucleotide (reduced form) dehydrogenase subunit 6 (ND6) and tRNAGlu. Type-2 contains a half-sized ND6 only. Type-3 does not contain ND6 or tRNAGlu. B, PCR amplifications for detecting ND6 and tRNAGlu in the three types of mt genome of the mackerel icefish. PCR fragments between Cyt b and control region (CR) 2 (Cyt b-CR2) and between CR2 and CR3 (CR2-CR3) contain the first and second copies of ND6, respectively. The PCR fragment between ND5 and Cyt b (ND5-Cyt b) did not contain ND6 or tRNAGlu. M, size marker. Lanes 1, 2, 7, and 10 are type-1 individuals. Lanes 3, 4, 8 and 11 are type-2 individuals. Lanes 5, 6, 9, and 12 are type-3 individuals. Abbreviations: E, tRNAGlu; F, tRNAPhe; P, tRNAPro; T, tRNAThr.
Figure 3 in The complete mitochondrial genome of the mackerel icefish, Champsocephalus gunnari (Actinopterygii: Channichthyidae), with reference to the evolution of mitochondrial genomes in Antarctic notothenioids
Figure 3. Map of the mackerel icefish mitochondrial (mt) genome as a circular diagram. The map represents the mt genome of a type-1 individual in which ND6 and tRNAGlu were transposed to a position between tRNAThr and tRNAPro flanked by intergenic spacers (UN3 and UN4), and the ND6- to -CR segment was duplicated once. Fourteen protein-coding genes, two rRNA genes, and noncoding regions are labelled with abbreviations. Twenty-four tRNA genes are shown by a one-letter amino acid code. Different codons used by each of tRNALeu and tRNASer are shown in parentheses. Genes transcribed from the heavy strand and light strand are respectively presented outside and inside the circle. Heavy- and light-strand replication origins are represented by OH and OL, respectively. Abbreviations: 12S, 12S ribosomal RNA; 16S, 16S ribosomal RNA; A, tRNAAla; ATP, ATP synthase; C, tRNACys; CO, cytochrome oxidase; Cyt b, cytochrome b; D, tRNAAsp; E, tRNAGlu; F, tRNAPhe; G, tRNAGly; H, tRNAHis; I, tRNAIle; K, tRNALys; L, tRNALeu; M, tRNAMet; N, tRNAAsn; ND, nicotiamide adenine dinucleotide (reduced form) dehydrogenase; P, tRNAPro; Q, tRNAGln; R, tRNAArg; S, tRNASer; T, tRNAThr; V, tRNAVal; W, tRNATrp; Y, tRNATyr.
Data from: Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits
<p>The data directory here includes all of the data and scripts necessary to recreate the results and plots for the manuscript titled "Chromosome-scale reference genome and RAD-based genetic map of yellow starthistle (Centaurea solstitialis) reveal putative structural variation and QTLs associated with invader traits". These data include a genetic map, QTL analysis, paleolog analysis, gene synteny analysis, and assembly validation for yellow starthistle (Centaurea solstitialis).</p>
A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
<p><span>Despite increasing sequencing efforts, numerous fish families still lack a reference genome, which complicates genetic research. One such understudied family is the sand lances (Ammodytidae, literally: 'sand burrower'), a globally distributed clade of over 30 fish species that tend to avoid tidal currents by burrowing into the sand. Here, we present the first annotated chromosome-level genome assembly of the great sand eel (<em>Hyperoplus</em> <em>lanceolatus</em>). The genome assembly was generated using Oxford Nanopore Technologies long sequencing reads and Illumina short reads for polishing. The final assembly has a total length of 808.5 Mbp, of which 97.1% were anchored into 24 chromosome-scale scaffolds using proximity-ligation scaffolding. The assembly is highly contiguous with a scaffold and contig N50 of 33.7 Mbp and 31.3 Mbp, respectively, and has a BUSCO completeness score of 96.9%. The presented genome assembly is a valuable resource for future studies of sand lances, as they are of great ecological and commercial importance and may also contribute to studies aiming to resolve the suprafamiliar taxonomy of bony fishes.</span></p>
Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
<p><span>The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes that likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the <em>Hox</em> gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.</span></p>
High-resolution KIR allele annotations for HPRC 47 assemblies and other reference genomes using SKIRT
<p><strong>Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to annotate, identify, and discover hundreds of novel alleles, more than a dozen structural variations among KIR genes, and all haplotypes carrying novel alleles, confirming KIR genetic diversity. The use of HPRC data needs to comply with the rules announced by HPRC.</strong></p>
Single-cell somatic copy number variants in brain using different amplification methods and reference genomes
<p>Variable and constant sized bins for GRCh38 and T2T-Chm13 were generated using the buildGenome scripts provided with Ginkgo (<a href="https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts">https://github.com/robertaboukhalil/ginkgo/tree/master/genomes/scripts</a>).</p>
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A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants
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Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
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Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
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Data from: Genome resources of <em>Xanthomonas vasicola</em> strains from various hosts: Reference-guided chromosome and plasmid assemblies for enhanced pathogen genomics
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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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Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome
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A chromosome-scale reference genome assembly of the great sand eel, Hyperoplus lanceolatus
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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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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.