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200 results for “Genomic Resources”
Alliance of Genome Resources Sequence Variants
<p>Variant Call Format (VCF) formatted spreadsheets of sequence variants associated with phenotypic alleles from the Alliance of Genome Resources. Variants are in Human Genome Variation Society (HGVS) nomenclature syntax.</p> <p>Files include variants in VCF format for the following organisms:</p> <ul> <li>Caenorhabditis elegans (nematode; NCBI:txid 6239)</li> <li>Danio rerio (zebrafish;NCBI:txid 7955)</li> <li>Drosophila melanogaster (fruit fly; NCBI:txid 7227)</li> <li>Mus musculus (mouse; NCBI:txid10090)</li> <li>Rattus norvegicus (rat; NCBI:txid 10116)</li> </ul>
Near-Chromosomal-Level Genome of the Red Palm Weevil (Rhynchophorus ferrugineus), a Potential Resource for Genome-Based Pest Control.
<p>Red palm weevil genome annotation data set</p>
Genomic resources of the Podospora anserina species complex
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Genomic identification of direct seeding and evolutionary lineages by combining heterogeneous genomic resources
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High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers
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Whole genome sequences of 23 species from the Drosophila montium species group (Diptera: Drosophilidae): a resource for testing evolutionary hypotheses
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Genomic and phenotypic evolution of Escherichia coli in a novel citrate-only resource environment
Evolutionary innovations allow populations to colonize new ecological niches. We previously reported that aerobic growth on citrate (Cit+) evolved in an Escherichia coli population during adaptation to a minimal glucose medium containing citrate (DM25). Cit+ variants can also grow in citrate-only medium (DM0), a novel environment for E. coli. To study adaptation to this niche, we founded two sets of Cit+ populations and evolved them for 2500 generations in DM0 or DM25. The evolved lineages acquired numerous parallel mutations, many mediated by transposable elements. Several also evolved amplifications of regions containing the maeA gene. Unexpectedly, some evolved populations and clones show apparent declines in fitness. We also found evidence of substantial cell death in Cit+ clones. Our results thus demonstrate rapid trait refinement and adaptation to the new citrate niche, while also suggesting a recalcitrant mismatch between E. coli physiology and growth on citrate.
Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths
<p>Here we provide scripts and parameters for genome assembly and annotation, as well as the manually annotated circadian genes of <i>period</i> (PER), <i>timeless</i> (TIM), <i>Clock</i> (CLK), <i>cycle</i> (CYC) and cryptochrome (CRY), five detoxification gene families of cytochrome P450 monooxygenase (P450s), glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs), UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC) transporters, IR, OR, OBP, GR genes from the genome of <span class="fontstyle01"><span>the peach fruit moth (PFM), </span></span><span class="fontstyle01"><span><i>Carposina sasakii</i></span></span><span class="fontstyle01"><span> Matsumura (Lepidoptera: Carposinidae, superfamily Copromorphoidea) and genomes of its related species.</span></span></p>
Data from: A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans
Comprising over 15 000 living species, decapods (crabs, shrimp and lobsters) are the most instantly recognizable crustaceans, representing a considerable global food source. Although decapod systematics have received much study, limitations of morphological and Sanger sequence data have yet to produce a consensus for higher-level relationships. Here, we introduce a new anchored hybrid enrichment kit for decapod phylogenetics designed from genomic and transcriptomic sequences that we used to capture new high-throughput sequence data from 94 species, including 58 of 179 extant decapod families, and 11 of 12 major lineages. The enrichment kit yields 410 loci (greater than 86 000 bp) conserved across all lineages of Decapoda, more clade-specific molecular data than any prior study. Phylogenomic analyses recover a robust decapod tree of life strongly supporting the monophyly of all infraorders, and monophyly of each of the reptant, 'lobster' and 'crab' groups, with some results supporting pleocyemate monophyly. We show that crown decapods diverged in the Late Ordovician and most crown lineages diverged in the Triassic–Jurassic, highlighting a cryptic Palaeozoic history, and post-extinction diversification. New insights into decapod relationships provide a phylogenomic window into morphology and behaviour, and a basis to rapidly and cheaply expand sampling in this economically and ecologically significant invertebrate clade.
Data from: "Discovery and characterization of 80 SNPs and 1,624 SSRs in the transcriptome of Atlantic mackerel (Scomber scombrus, L)" in Genomic Resources Notes Accepted 1 June 2015 to 31 July 2015
This paper reports on SNP discovery in the Atlantic mackerel transcriptome, using next generation sequencing technologies and applying developed methodology already proven successful for the European anchovy. A total of 9,966 high quality transcriptome contigs were assembled, from which 951 putative SNPs were discovered. In all, 479 putative SNPs and 1,624 simple sequence repeats (SSRs) suitable for genotyping were identified. A subset of 96 was selected for genotyping; from these, 80 SNPs were considered polymorphic and reliably scored after genotyping of 105 individuals from three locations in the Eastern Atlantic Ocean. These markers will be valuable for future studies on population genetic structure assessment and for product tracing.
Genomic resources for the little pocket mouse (Perognathus longimembris longimembris)
<p>The little pocket mouse, <em class="italic">Perognathus longimembris</em>, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of <em class="italic">Perognathus longimembris longimembris</em> generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, <em class="italic">P. l. pacificus</em>, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.</p>
Supporting data for: The de novo genome of the Black-necked Snakefly (Venustoraphidia nigricollis Albarda, 1891): A resource to study the evolution of living fossils
<p>Snakeflies (Raphidioptera) are the smallest order of holometabolous insects that have kept their distinct and name-giving appearance since the Mesozoic, probably since the Jurassic, and possibly even since their emergence in the Carboniferous, more than 300 million years ago. Despite their interesting nature and numerous publications on their morphology, taxonomy, systematics, and biogeography, snakeflies have never received much attention from the general public, and only a few studies were devoted to their molecular biology. Due to this lack of molecular data, it is therefore unknown, if the conserved morphological nature of these living fossils translates to conserved genomic structures. Here, we present the first genome of the species and of the entire order of Raphidioptera. The final genome assembly has a total length of 669 Mbp and reached a high continuity with an N50 of 5.07 Mbp. Further quality controls also indicate a high completeness and no meaningful contamination. The newly generated data was used in a large-scaled phylogenetic analysis of snakeflies using shared orthologous sequences. Quartet score and gene-concordance analyses revealed high amounts of conflicting signals within this group that might speak for substantial incomplete lineage sorting and introgression after their presumed re-radiation after the asteroid impact 66 million years ago. Overall, this reference genome will be a door-opening dataset for many future research applications, and we demonstrated its utility in a phylogenetic analysis that provides new insights into the evolution of this group of living fossils.</p>
Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics
<p><strong>Background</strong></p> <p><em>Hydrangea petiolaris</em> Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in <em>Hydrangea</em> breeding and interest in germplasm conservation, relatively little is known about the relationships between <em>Hydrangea</em> species.</p> <p><strong>Results</strong></p> <p>We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the <em>restorer of fertility</em> (<em>Rf</em>) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations.</p> <p><strong>Conclusions</strong></p> <p>The <em>H</em>. <em>petiolaris</em> transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for <em>H</em>. <em>petiolaris</em>. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.</p>
Genomic Resources for BIC@MSKCC Mouse Variant Pipeline
<p>Custom genomic resource files for Mouse Variant pipeline. Details and code are here: https://github.com/soccin/MusVar</p>
Data and code to reproduce analyses in Heinken et al, "A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites"
<p>This datasets archives the GitHub version found at https://github.com/ThieleLab/CodeBase to reproduce simulations for the article Heinken et al, "A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites", Cell Systems, in press.</p>
ATAC-seq processing resources for the GRCm38 (mm10) assembly of the mouse genome
<p>A collection of publicly available, but preprocessed, reference data for the analysis of ATAC-seq samples using the GRCm38 (mm10) assembly of the mouse genome using the <a href="https://doi.org/10.5281/zenodo.6323634">Ultimate ATAC-seq Data Processing & Analysis Pipeline</a> (details in the documentation on GitHub).</p>
Genomic resources for Macadamia tetraphylla and an examination of its historic use as a crop resource in Hawaii
<p><em>Macadamia tetraphylla </em>is a wild relative of the economically valuable crop <em>Macadamia integrifolia. </em>Genomic knowledge of crop wild relatives is central to determining their possible role in breeding programs to mitigate biotic and abiotic stress in the future. The data stored here represent SNP files for material found on Oahu and assembled transcriptomes from different tissue types. </p>
Fine-scale subpopulation detection via SNP-based unsupervised method: A case study on the 1000 Genomes Project Resources
<p>Here are the supplementary files to the paper "Fine-scale subpopulation detection via SNP-based unsupervised method:<br> A case study on the 1000 Genomes Project Resources".<br> <br> The repository is organized as:</p> <ol> <li><strong>Supplementary information</strong>: the additional detailed information for the experiments in the paper <ul> <li>Supplementary_information_IPCAPS_Chaichoompu_v1.pdf</li> </ul> </li> <li><strong>Real-life dataset</strong>: the 1000 genome dataset, which is referred to in the paper and is filtered with the parameters explained in the paper. Reference: https://www.internationalgenome.org/ <ul> <li>1000genomes_with_filtering.zip</li> </ul> </li> </ol>
Genome sequence resources from three isolates of the apple canker pathogen Neonectria ditissima infecting forest trees
<p><em>Neonectria ditissima</em> is a generalist ascomycete plant pathogen causing canker diseases on a variety of hardwood tree species and can cross-infect many of them. The fungus enters the plants through wounds throughout the year. <em>N. ditissima</em> is considered a major threat to apple production responsible for the fruit tree canker disease which damages trees and causes rotting of fruits in storage. Nearby forests and shelter belts can serve as source of inoculum for well-managed apple orchards. Thus, knowledge about the <em>N. ditissima</em> isolates infecting different host species is essential for designing integrated pest management strategies. Here, we describe the genomes of three <em>N. ditissima</em> isolates, Nd_iso34, Nd_iso35, and Nd_iso36, infecting European beech, American tulip tree, and American beech, respectively. We obtained genome assemblies of ca. 45 megabases for all isolates, covering 94% of the <em>N. ditissima</em> reference annotation, and 97% of the universal single-copy orthologs (BUSCOs). We conclude that these genome assemblies are a highly relevant resource considering the scarcity of genomic data available for <em>N. ditissima</em>.</p>
Genetic admixture and evolutionary history of Han Chinese in the Shandong Peninsula inferred from integrative modern and ancient genomic resources
<p>The allele frequency data of 264 individuals from Shandong Province and supplementary table.</p>
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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.