Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
537
datasets available to search
ShareScore release 0.9.0
Dataset results
537 results for “Structural Genomics”
Fig. 1 in The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications
Fig. 1. Genetic map of the complete mitochondrial genome of Platygaster robiniae. Notes: the blue arrow represents the direction of gene transcription; the black peak represents the deviation of GC%; the purple and green peaks represent the deviation in GC skew; green refers to positive skew, and purple indicates negative skew. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Conservation of animal genome structure is the exception not the rule
<p>Species from diverse animal lineages, including molluscs, annelids, echinoderms, hemichordates, and cephalochordates, have retained groups of orthologous genes on the same chromosomes for over half a billion years since the last common ancestor of bilaterians. Though there are notable exceptions, it has been proposed that the conservation of chromosome-scale gene linkages is the norm among animals. Here, by examining interchromosomal rearrangements in 64 chromosome-level genomes across 15 bilaterian phyla and at least 52 classes, we show that, though striking, cases of genome structure conservation are exceptionally rare. The ubiquity of massive genome rearrangements suggests that, in general, chromosome-scale gene linkages are of minimal importance to animal genome function.</p> <p>This project includes gene models for 14 genome assemblies annotated in this study, with files available for coding sequences (*.fasta), protein sequences (*.faa), and gene annotations in GTF format (*.gtf), as detailed below. Additionally, a spreadsheet containing all accession numbers and genome metadata for 64 bilaterian genomes and 3 cnidarian genomes is provided as a Supplemental Dataset.</p> <p>- Amphiscolops sp. MND2022 (acoel worm; phylum Xenacoelomorpha)<br>- Antedon bifida (crinoid; phylum Echinodermata)<br>- Carcinoscorpius rotundicauda (horseshoe crab; phylum Arthropoda)<br>- Convolutriloba macropyga (acoel worm; phylum Xenacoelomorpha)<br>- Emplectonema gracile (ribbon worm; phylum Nemertea)<br>- Gordius sp. MW1 (horsehair worm; phylum Nematomorpha)<br>- Hypsibius dujardini (water bear; phylum Tardigrada)<br>- Ophiura sarsii (brittle star; phylum Echinodermata)<br>- Schizocardium californicum (acorn worm, phylum Hemichordata)<br>- Schmidtea mediterranea (planarian; phylum Platyhelminthes)<br>- Strigamia acuminata (centipede; phylum Arthropoda)<br>- Styela plicata (tunicate; phylum Chordata)<br>- Trichinella spiralis (nematode; phylum Nematoda)<br>- Trididemnum miniatum (tunicate; phylum Chordata)</p> <p>Custom R scripts are available at our GitHub repository (https://github.com/symgenoevolab/animal_genome_structure) under the MIT License.</p>
Data from: Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea
<p>In oceanic ecosystems, the nature of barriers to gene flow, and the processes by which populations may become isolated are different from the terrestrial environment, and less well understood. In this study, we investigate a highly mobile species (the sperm whale, <em>Physeter macrocephalus</em>) that is genetically differentiated between an open North Atlantic population and the populations in the Mediterranean Sea. We apply high-resolution single nucleotide polymorphisms (SNP) analysis to study the nature of barriers to gene flow in this system, comparing gene flow across the putative boundary into the Mediterranean (Strait of Gibraltar and Alboran Sea region) with novel analyses on structuring among sperm whale populations within the Mediterranean basin. Our data support a recent founding of the Mediterranean, around the time of the last glacial maximum, and shows concerted historical demographic profiles in both the Atlantic and the Mediterranean. In each region, there is evidence for a population decline around the time of the founder event, more extreme within the Mediterranean Sea where effective population size is substantially lower. While differentiation is strongest at the Atlantic/Mediterranean boundary, there is also significant differentiation between the Eastern and Western basins of the Mediterranean Sea. We propose, however, that the mechanisms are different. While post-founding gene flow was reduced between the Mediterranean and Atlantic populations, within the Mediterranean an important factor differentiating the basins is likely a greater degree of admixture between the Western basin and the North Atlantic.</p>
Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years
<p>Radiocarbon dating is the gold standard in archeology to estimate the age of skeletons, a key to studying their origins. Many published ancient genomes lack reliable and direct dates, which results in obscure and contradictory reports. Here, we developed the Temporal Population Structure (TPS), the first DNA-based dating method for ancient genomes ranging from the Late Mesolithic to modern-days, and applied it to 3,591 ancient and 1,307 modern Eurasians. We show that TPS predictions align with their known dates and correctly account for kin relationships. TPS dating of poorly dated Eurasian samples resolved conflicting reports in the literature, as illustrated by one test case. We demonstrated how TPS improved the ability to study phenotypic traits over time.</p>
Population genomic evidence that stream networks structure genetic diversity in the narrowly endemic patch-nosed salamander (Urspelerpes brucei)
<p>Described in 2009, the Patch-nosed Salamander (<em>Urspelerpes brucei</em>) is a miniature species of lungless salamander with a geographic range of only ~45 km<sup>2</sup>. This species is endemic to the foothills of the Appalachian Mountains in extreme northeastern Georgia and northwestern South Carolina. The Tugaloo River—a waterway of some 50 m in width that forms the political boundary between the two states—bisects the tiny range of <em>U. brucei</em> and likely acts as a barrier to gene flow. Using RADcap data and a suite of complementary population genomic analyses, we evaluated the role that this river and its tributaries may play in enabling and/or interrupting gene flow among populations of <em>U. brucei</em>, and we investigated patterns of within-population and between-population genetic variation. Our results revealed a general pattern of isolation-by-stream distance and indicated that a population separated by the Tugaloo River is moderately more differentiated than what is explainable by stream distance alone. Unique in both its physiography and geologic history, this region in which <em>U. brucei</em> lives also harbors more than a dozen other species of lungless salamanders. Therefore, the genetic patterns that we have elucidated may have larger implications for differentiation among populations of other species with similar dispersal abilities.</p>
Structural genomic variation in the inbred Scandinavian wolf population contributes to the realized genetic load but is positively affected by immigration
Open the record for dataset details and reuse information.
Data from: Genomic data reveal deep genetic structure but no support for current taxonomic designation in a grasshopper species complex
Open the record for dataset details and reuse information.
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion
Open the record for dataset details and reuse information.
The chloroplast genomes of Sanicula (Apiaceae): plastome structure, comparative analyses, and phylogenetic relationships
Open the record for dataset details and reuse information.
Population genomic evidence that stream networks structure genetic diversity in the narrowly endemic patch-nosed salamander (Urspelerpes brucei)
Open the record for dataset details and reuse information.
Data and code from: Evaluating genomic offset predictions in a forest tree with high population genetic structure
Open the record for dataset details and reuse information.
Data from: Genomics reveals the role of admixture in the evolution of structure among sperm whale populations within the Mediterranean Sea
Open the record for dataset details and reuse information.
Analysis of copy number variation in dogs implicates genomic structural variation in the development of anterior cruciate ligament rupture
Open the record for dataset details and reuse information.
Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years
Open the record for dataset details and reuse information.
Discordant population structure among rhizobium divided genomes and their legume hosts
Open the record for dataset details and reuse information.
Detection and analysis of complex structural variation in human genomes across populations and in brains of donors with psychiatric disorders
Open the record for dataset details and reuse information.
Data from: Seascape genomics of red abalone: Limited range-wide population structure and evidence for local adaptation
Open the record for dataset details and reuse information.
Source code for StrVCTVRE: a supervised learning method to predict the pathogenicity of human genome structural variants
Open the record for dataset details and reuse information.
Data from: Population genomic diversity and structure at the discontinuous southern range of the Great Gray Owl in North America
<p>Species' distributions are often discontinuous near the edge of the range where the environment may be more variable than the core of the range. Range discontinuity can reduce or cut off gene flow to small peripheral populations and lead to genetic drift and subsequent loss of genetic diversity. The southern extent of the Great Gray Owl ( Strixnebulosa) range in North America is discontinuous, unlike their northern core range across the boreal forests. We sampled owls from five different locations on the periphery of the range across the western US (Wyoming, Idaho, California, northern Oregon, and southern Oregon) to investigate genetic population structure and genetic diversity. Using a reduced-representation genomic sequencing approach to genotype 123 individuals at 4,817 single nucleotide polymorphic loci, we identified four genetically differentiated populations: California, southern Oregon, northern Oregon, and Wyoming and Idaho grouped together as a single Rocky Mountain population. The four genetically differentiated populations of Great Gray Owls identified in this study display high differentiation and low genetic variation, which is suggestive of long-term isolation and lack of connectivity, potentially caused by range discontinuity. The populations that lack habitat connectivity to the rest of the breeding range (i.e. those in California and Oregon) had lower genetic diversity than the Rocky Mountain population that is connected to the core of the range. These factors and other risks (such as disease and human-caused mortality) heighten susceptibility of these range-edge populations to future habitat and climate changes, genetic diversity erosion, and potential extinction vortex. For these reasons, protecting and monitoring this species on the southern edge of their range is vital.</p>
Data from: NOVOWrap: an automated solution for plastid genome assembly and structure standardization
<p>Plastid genomes play an important role in genomics and evolutionary biology. Next-generation sequencing has revolutionized plastid genomic data acquisition to the point that genome assembly has become a bottlenecks for widespread utilization of plastid genome data. To solve this problem, we developed an open-source, cross-platform tool known as, NOVOWrap, which includes both command-line and graphical interfaces for automatically assembling plastid genomes on personal computers. With minimal inputs, settings, and user intervention, NOVOWrap can automatically assemble plastid genomes, validate results and standardize the structure using affordable computer resources. The performance of this software has been successfully benchmarked against the plastid genomes of 11 species belonging to lycopods, gymnosperms, and angiosperms. This program is expected to liberate researchers from laborious and cumbersome computer manipulations and create reliable and standardized genomic data.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.