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.
314
datasets available to search
ShareScore release 0.7.1
Dataset results
314 results for “genome architecture”
Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen
Open the record for dataset details and reuse information.
Data from: Genome-wide association studies across environmental and genetic contexts reveal complex genetic architecture of symbiotic extended phenotypes
Open the record for dataset details and reuse information.
Data from: Genomic architecture drives population structuring in Amazonian birds
Open the record for dataset details and reuse information.
Data from: Genomic and transcriptomic analyses reveal polygenic architecture for ecologically-important functional traits in aspen (Populus tremuloides Michx.)
Open the record for dataset details and reuse information.
Dissecting the genetic architecture of quantitative traits using genome-wide identity-by-descent sharing
Open the record for dataset details and reuse information.
Data from: Genomic architecture and introgression shape a butterfly radiation
Open the record for dataset details and reuse information.
Data from: Dynamic genomic architecture of mutualistic cooperation in a wild population of Mesorhizobium
Open the record for dataset details and reuse information.
Gene flow influences the genomic architecture of local adaptation in six riverine fish species
Open the record for dataset details and reuse information.
Data from: A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture
Open the record for dataset details and reuse information.
A complex genomic architecture underlies reproductive isolation in a North American Oriole hybrid zone
Open the record for dataset details and reuse information.
Data for: Dissecting the genetic architecture of leaf morphology traits in mungbean (Vigna radiata (L.) Wizcek) using genome‐wide association study
Open the record for dataset details and reuse information.
Phenome-to-genome insights for evaluating root system architecture in field studies of maize
Open the record for dataset details and reuse information.
Insights from the timber rattlesnake (<em>Crotalus horridus</em>) genome for MHC gene architecture and evolution in threatened rattlesnakes
Open the record for dataset details and reuse information.
Data from: Genetic and genomic architecture of species-specific cuticular hydrocarbon variation in parasitoid wasps
Open the record for dataset details and reuse information.
Efficient weighting methods for genomic best linear unbiased prediction (BLUP) adaption to the genetic architectures of quantitative traits
<p><a name="_Hlk19877414"></a>Genomic best linear unbiased prediction (GBLUP) assumes equal variance for all marker effects, which is suitable for traits that conform to the infinitesimal model. For traits controlled by major genes, Bayesian methods with shrinkage priors or genome-wide association study (GWAS) methods can be used to identify <a name="_Hlk24974556">causal variants</a> effectively. The information from Bayesian/GWAS methods can be used to construct the weighted genomic relationship matrix (<b>G</b>). However, it remains unclear which methods perform best for traits varying in genetic architecture. Therefore, we developed several methods to <a name="_Hlk23592218">optimize</a> the performance of weighted GBLUP and compare them with other available methods using simulated and real datasets. First, two types of methods (marker effects with local-shrinkage or normal prior) were used to obtain test statistics and estimates for each marker effect. Second, three weighted <b>G</b> matrices were constructed based on the marker information from the first step: (1) the genomic-feature weighted <b>G</b> (GFWG), (2) the estimated marker-variance weighted <b>G</b> (EVWG), and (3) the absolute value of estimated marker-effect weighted <b>G</b> (AEWG). Following the above process, six different weighted GBLUP methods (local-shrinkage/normal prior GF/EV/AE-WGBLUP) were proposed for genomic prediction. Analyses with both simulated and real data demonstrated that these options offer flexibility for optimizing the weighted GBLUP for traits with a broad spectrum of genetic architectures. The advantage of weighting methods over GBLUP in terms of accuracy were trait dependent, ranging from 14.8% to marginal for simulated traits and from 44% to marginal for real traits. Local-shrinkage prior EVWGBLUP is superior for traits mainly controlled by loci of large effect. Normal prior AEWGBLUP performs well for traits mainly controlled by loci of moderate effect. For traits controlled by some loci with large effects (<a name="_Hlk49869847">explain 25%~50% genetic variance</a>) and a range of loci with small effects, GFWGBLUP has advantages. In conclusion, the optimal weighted GBLUP method for genomic selection should take both the genetic architecture and number of QTLs of traits into consideration carefully.</p>
Genomic architecture of a genetically assimilated seasonal color pattern
<p><span><span>Developmental plasticity allows genomes to encode multiple distinct phenotypes that can be differentially manifested in response to environmental cues. Alternative plastic phenotypes can be selected through a process called genetic assimilation; although the mechanisms are still poorly understood. We assimilated a seasonal wing color phenotype in a naturally plastic population of butterflies, and characterized three responsible genes. Combined with endocrine assays, and chromatin accessibility and conformation analyses, we found that the transition of wing coloration from an environmentally determined trait to a predominantly genetic trait occurred through selection for regulatory alleles of downstream wing patterning genes. This mode of genetic evolution is likely favored by selection because it allows tissue- and trait-specific tuning of reaction norms without affecting core cue detection or transduction mechanisms.</span></span></p>
Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted re-sampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principle components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.
Data from: Genomic and phenotypic architecture of a spruce hybrid zone (Picea sitchensis x P. glauca)
Interspecific hybridization may enhance the capacity of populations to adapt to changing environments, and has practical implications for reforestation. We use genomewide estimates of admixture and phenotypic traits for trees in a common garden to examine the extent and direction of gene flow across a Picea hybrid zone, testing assumptions of the bounded hybrid superiority and tension zone models of hybrid zone maintenance. Seeds were collected from the ecological transition zone spanning from maritime to continental climates across the Picea sitchensis-P. glauca contact zone, and 721 trees were planted in a common garden experiment within the hybrid zone. Individuals were genotyped using a panel of 384 candidate-gene single nucleotide polymorphisms (SNPs) putatively associated with adaptive traits in Picea, and phenotyped at age ten for height and autumn cold hardiness. Low interspecific heterozygosity in hybrids indicated intrinsic reproductive barriers were too weak to prevent widespread recombination, although introgression appeared asymmetric with P. sitchensis dominating the zone. While marker-based hybrid index was strongly correlated with climate and geography, phenotypic traits exhibited weak or no significant clines. Our results indicated that exogenous selection appeared to play a strong role in the distribution and structure of this hybrid zone, indicative of an environmentally determined bounded hybrid superiority model of hybrid zone maintenance, although endogenous mechanisms could not be ruled out. This study provides insight into the mechanisms underlying adaptation across ecologically transitional hybrid zones that will ultimately provide an additional tool in managing these economically important tree species.
Data from: Rapid divergence of genome architectures following the origin of an ectomycorrhizal symbiosis in the genus Amanita
Fungi are evolutionary shape shifters and adapt quickly to new environments. Ectomycorrhizal (EM) symbioses are mutualistic associations between fungi and plants and have evolved repeatedly and independently across the fungal tree of life, suggesting lineages frequently reconfigure genome content to take advantage of open ecological niches. To date analyses of genomic mechanisms facilitating EM symbioses have involved comparisons of distantly related species, but here, we use the genomes of three EM and two asymbiotic (AS) fungi from the genus Amanita as well as an AS outgroup to study genome evolution following a single origin of symbiosis. Our aim was to identify the defining features of EM genomes, but our analyses suggest no clear differentiation of genome size, gene repertoire size or transposable element content between EM and AS species. Phylogenetic inference of gene gains and losses suggests the transition to symbiosis was dominated by the loss of plant cell wall decomposition genes, a confirmation of previous findings. However, the same dynamic defines the AS species A. inopinata, suggesting loss is not strictly associated with origin of symbiosis. Gene expansions in the common ancestor of EM Amanita were modest, but lineage specific and large gene family expansions are found in two of the three EM extant species. Even closely related EM genomes appear to share few common features. The genetic toolkit required for symbiosis appears already encoded in the genomes of saprotrophic species, and this dynamic may explain the pervasive, recurrent evolution of ectomycorrhizal associations.
Data from: Genomic architecture of habitat-related divergence and signature of directional selection in the body shapes of Gnathopogon fishes
Evolution of ecomorphologically relevant traits such as body shapes is important to colonize and persist in a novel environment. Habitat-related adaptive divergence of these traits is therefore common among animals. We studied the genomic architecture of habitat-related divergence in the body shape of Gnathopogon fishes, a novel example of lake–stream ecomorphological divergence, and tested for the action of directional selection on body shape differentiation. Compared to stream-dwelling Gnathopogon elongatus, the sister species Gnathopogon caerulescens, exclusively inhabiting a large ancient lake, had an elongated body, increased proportion of the caudal region and small head, which would be advantageous in the limnetic environment. Using an F2 interspecific cross between the two Gnathopogon species (195 individuals), quantitative trait locus (QTL) analysis with geometric morphometric quantification of body shape and restriction-site associated DNA sequencing-derived markers (1622 loci) identified 26 significant QTLs associated with the interspecific differences of body shape-related traits. These QTLs had small to moderate effects, supporting polygenic inheritance of the body shape-related traits. Each QTL was mostly located on different genomic regions, while colocalized QTLs were detected for some ecomorphologically relevant traits that are proxy of body and caudal peduncle depths, suggesting different degree of modularity among traits. The directions of the body shape QTLs were mostly consistent with the interspecific difference, and QTL sign test suggested a genetic signature of directional selection in the body shape divergence. Thus, we successfully elucidated the genomic architecture underlying the adaptive changes of the quantitative and complex morphological trait in a novel system.
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.