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.
281
datasets available to search
ShareScore release 0.9.0
Dataset results
281 results for “genetic sequence”
Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing
Open the record for dataset details and reuse information.
Data from: Genetic incompatibilities in reciprocal hybrids between populations of Tigriopus californicus with low to moderate mitochondrial sequence divergence
Open the record for dataset details and reuse information.
Datasets of "Whole genome sequencing of European autochthonous and commercial pig breeds provides selection signatures of adaptation of genetic resources to different breeding and production systems"
<p>Results of the F<sub>ST</sub> and H<sub>P</sub> analyses.</p>
standard with together) corner left bottom (analysis genetic the in included species among bold gene in shown oxidase-I are SE cytochrome and species the within at) % (divergence divergence sequence average The . pairwise) corner showing right upper (Matrix) %;. SE 4 ABLE (T error in Description of a new species of the Rhinolophus trifoliatus-group (Chiroptera: Rhinolophidae) from Southeast Asia
standard with together) corner left bottom (analysis genetic the in included species among bold gene in shown oxidase-I are SE cytochrome and species the within at) % (divergence divergence sequence average The . pairwise) corner showing right upper (Matrix) %;. SE 4 ABLE (T error
Whole genome sequence analysis of porcine astroviruses reveals novel genetically diverse genotypes circulating in East African smallholder pig farms
<p>Supplementary materials for the porcine astrovirus study in East Africa.</p> <p><strong>Table S1</strong>: Pairwise comparison of nucleotide sequence identities of the complete (near complete, U460) genomes of the seven (7) astrovirus field strains (bold) and with sequences of other astroviruses available in GenBank </p> <p><strong>Table S2</strong>. Summary of nucleotide sequence identity matrix of the capsid protein (ORF2) among the seven (7) astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S3</strong>. Summary of amino acid sequence identity matrix of the capsid protein (ORF2) among the 7 astroviruses field strains (bold) and the known reference strains in the GenBank using Clustal Omega</p> <p><strong>Table S4</strong>: Estimates of evolutionary divergence between the East African PoAstVs and selected known AstV in the GenBank based on the amino acid sequences of complete ORF2 protein. The number of amino acid differences per site from between sequences is shown. Standard error estimate(s) are shown above the diagonal for our strains.</p> <p><strong>Table S5</strong>. Recommended potential linear antigenic epitopes predicted inside capsid protein (ORF2) of our field strains by SVMTriP web-based tool and corresponding antigenicity predicted by VaxiJen software</p>
Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences
Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed "mosaic" group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.
Data from: Seascape genetics along environmental gradients in the Arabian Peninsula: insights from ddRAD sequencing of anemonefishes
Understanding the processes that shape patterns of genetic structure across space is a central aim of landscape genetics. However, it remains unclear how geographic features and environmental variables shape gene flow, particularly for marine species in large complex seascapes. Here, we evaluated the genomic composition of the two-band anemonefish Amphiprion bicinctus across its entire geographic range in the Red Sea and Gulf of Aden, as well as its close relative, Amphiprion omanensis endemic to the southern coast of Oman. Both the Red Sea and the Arabian Sea are complex and environmentally heterogeneous marine systems that provide an ideal scenario to address these questions. Our findings confirm the presence of two genetic clusters previously reported for A. bicinctus in the Red Sea. Genetic structure analyses suggest a complex seascape configuration, with evidence of both Isolation by Distance (IBD) and Isolation by Environment (IBE). In addition to IBD and IBE, genetic structure among sites was best explained when two barriers to gene flow were also accounted for. One of these coincides with a strong oligotrophic-eutrophic gradient at around 16-20˚N in the Red Sea. The other agrees with an historical bathymetric barrier at the straight of Bab al Mandab. Finally, these data support the presence of inter-specific hybrids at an intermediate suture zone at Socotra and indicate complex patterns of genomic admixture in the Gulf of Aden with evidence of introgression between species. Our findings highlight the power of recent genomic approaches to resolve subtle patterns of gene flow in marine seascapes.
Construction of genetic linkage map based on SNP markers, QTL mapping and detection of candidate genes of growth-related traits in Pacific abalone using genotyping-by-sequencing
<p><a name="_Hlk72585736"><span>Pacific abalone (<i>Haliotis discus hannai</i>) is a commercially important high valued molluscan species. Its wild population has decreased in recent years. Pacific abalone is widely cultured in Korea. Traditional breeding programs have been implemented for hatchery production of abalone seeds. To obtain more genetic information for the molecular breeding program, a high-density linkage map and quantitative trait locus (QTL) for three growth-related traits was constructed for Pacific abalone. F1 cross population with two parents were sampled to construct the linkage map using genotyping by sequencing (GBS). A total of 664,630,534 clean reads and 56,686 SNPs were generated. In sum, 3,345 segregating SNPs were used to construct a consensus linkage map. The map spanned 1,747.023 cM with 18 linkage groups and an average interval of 0.55 cM. QTL analysis revealed two significant QTL in LG10 on the consensus linkage map in each growth-related trait. Both the QTLs are located in the telomere region of the chromosome. Moreover, four potential candidate genes for growth-related traits were identified in the QTL region. Expression analysis revealed that identified genes are involved in growth regulation of abalone. The newly constructed genetic linkage map, growth-related QTLs and potential candidate genes identified in the present study can be used as valuable genetic resources and will be useful for marker-assisted selection (MAS) of Pacific abalone in molecular breeding program.</span></a></p>
Data from: Parallel tagged next-generation sequencing on pooled samples – a new approach for population genetics in ecology and conservation
Next-generation sequencing (NGS) on pooled samples has already been broadly applied in human medical diagnostics and plant and animal breeding. However, thus far it has been only sparingly employed in ecology and conservation, where it may serve as a useful diagnostic tool for rapid assessment of species genetic diversity and structure at the population level. Here we undertake a comprehensive evaluation of the accuracy, practicality and limitations of parallel tagged amplicon NGS on pooled population samples for estimating species population diversity and structure. We obtained 16S and Cyt b data from 20 populations of Leiopelma hochstetteri, a frog species of conservation concern in New Zealand, using two approaches – parallel tagged NGS on pooled population samples and individual Sanger sequenced samples. Data from each approach were then used to estimate two standard population genetic parameters, nucleotide diversity (π) and population differentiation (FST), that enable population genetic inference in a species conservation context. We found a positive correlation between our two approaches for population genetic estimates, showing that the pooled population NGS approach is a reliable, rapid and appropriate method for population genetic inference in an ecological and conservation context. Our experimental design also allowed us to identify both the strengths and weaknesses of the pooled population NGS approach and outline some guidelines and suggestions that might be considered when planning future projects.
Data from: The genetic architecture of reproductive isolation during speciation-with-gene-flow in lake whitefish species pairs assessed by RAD sequencing
During speciation-with-gene-flow, effective migration varies across the genome as a function of several factors, including proximity of selected loci, recombination rate, strength of selection, and number of selected loci. Genome scans may provide better empirical understanding of the genome-wide patterns of genetic differentiation, especially if the variance due to the previously mentioned factors is partitioned. In North American lake whitefish (Coregonus clupeaformis), glacial lineages that diverged in allopatry about 60,000 years ago and came into contact 12,000 years ago have independently evolved in several lakes into two sympatric species pairs (a normal benthic and a dwarf limnetic). Variable degrees of reproductive isolation between species pairs across lakes offer a continuum of genetic and phenotypic divergence associated with adaptation to distinct ecological niches. To disentangle the complex array of genetically based barriers that locally reduce the effective migration rate between whitefish species pairs, we compared genome-wide patterns of divergence across five lakes distributed along this divergence continuum. Using restriction site associated DNA (RAD) sequencing, we combined genetic mapping and population genetics approaches to identify genomic regions resistant to introgression and derive empirical measures of the barrier strength as a function of recombination distance. We found that the size of the genomic islands of differentiation was influenced by the joint effects of linkage disequilibrium maintained by selection on many loci, the strength of ecological niche divergence, as well as demographic characteristics unique to each lake. Partial parallelism in divergent genomic regions likely reflected the combined effects of polygenic adaptation from standing variation and independent changes in the genetic architecture of postzygotic isolation. This study illustrates how integrating genetic mapping and population genomics of multiple sympatric species pairs provide a window on the speciation-with-gene-flow mechanism.
Data from: Nuclear and mitochondrial sequence data reveal and conceal different demographic histories and population genetic processes in Caribbean reef fishes
Mitochondrial and nuclear sequence data should recover historical demographic events at different temporal scales due to differences in their effective population sizes and substitution rates. This expectation was tested for two closely related coral reef fish, the tube blennies Acanthemblemaria aspera and A. spinosa. These two have similar life histories and dispersal potentials, and co-occur throughout the Caribbean. Sequence data for one mitochondrial and two nuclear markers were collected for 168 individuals across the species' Caribbean ranges. While both species shared a similar pattern of genetic subdivision, A. spinosa had 20-25-times greater nucleotide sequence divergence among populations than A. aspera at all three markers. Substitution rates estimated using a relaxed clock approach revealed that mitochondrial COI is evolving at 11.2% pairwise sequence divergence per million years. This rapid mitochondrial rate had obscured the signal of old population expansions for both species, which were only recovered using the more slowly evolving nuclear markers. However, the rapid COI rate allowed the recovery of a recent expansion in A. aspera corresponding to a period of increased habitat availability. Only by combining both nuclear and mitochondrial data were we able to recover the complex demographic history of these fishes.
Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci
Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.
Data from: Extending RAD tag analysis to microbial ecology: a comparison between multi locus sequence typing (MLST) and 2b-RAD to investigate Listeria monocytogenes genetic structure
The advent of next-generation sequencing (NGS) has dramatically changed bacterial typing technologies, increasing our ability to differentiate bacterial isolates. Despite it is now possible to sequence a bacterial genome in a few days and at reasonable costs, most genetic analyses do not require whole-genome sequencing, which also remains impractical for large population samples due to the cost of individual library preparation and bioinformatics. More traditional sequencing approaches, however, such as MultiLocus Sequence Typing (mlst) are quite laborious and time-consuming, especially for large-scale analyses. In this study, a genotyping approach based on restriction site-associated (RAD) tag sequencing, 2b-RAD, was applied to characterize Listeria monocytogenes strains. To verify the feasibility of the method, an in silico analysis was performed on 30 available complete genomes. For the same set of strains, in silico mlst analysis was conducted as well. Subsequently, 2b-RAD and mlst analyses were experimentally carried out on 58 isolates collected from food samples or food-processing sites. The obtained results demonstrate that 2b-RAD predicts mlst types and often provides more detailed information on population structure than mlst. Moreover, the majority of variants differentiating identical sequence type isolates mapped against accessory fragments, thus providing additional information to characterize strains. Although mlst still represents a reliable typing method, large-scale studies on molecular epidemiology and public health, as well as bacterial phylogenetics, population genetics and biosafety could benefit of a low cost and fast turnaround time approach such as the 2b-RAD analysis proposed here.
Fig. 3 in Genetic variation in the spotted seal (Phoca largha Pallas, 1811) from the Rimsky-Korsakov Archipelago (Peter the Great Bay, western sea of Japan) as inferred from mitochondrial DNA control region sequences
Fig. 3. Consensus maximum likelihood tree demonstrating the matrilineal genealogy of some Phocidae species generated from the 460 bp mtDNA control region sequences. The numbers at branch nodes represent bootstrap support of 1000 replications for the maximum likelihood trees and posterior probabilities of 2,000,000 generations for the Bayesian trees with the same topology, respectively. The accession numbers of Phoca largha from Liaodong Bay are highlighted in bold. Scale bar indicates the relative branch lengths.
Fig. 2 in Genetic variation in the spotted seal (Phoca largha Pallas, 1811) from the Rimsky-Korsakov Archipelago (Peter the Great Bay, western sea of Japan) as inferred from mitochondrial DNA control region sequences
Fig. 2. Minimum spanning network showing the mutational relationships among Phoca largha haplotypes detected in a sample of 32 spotted seal underyearlings. The tick marks on the branches indicate mutational changes. The circle sizes correspond to the number of haplotypes. The haplotypes of groups (A) and (B) are shown in gray and white circles, respectively. The median vectors are indicated by dark dots.
Obovaria olivaria maf filtered vcf file from: RAD-tag and mitochondrial DNA sequencing reveal the genetic structure of a widespread and regionally imperiled freshwater mussel, Obovaria olivaria (Bivalvia: Unionidae)
<p><em>Obovaria olivaria</em> is a species of freshwater mussel native to the Mississippi River and Laurentian Great Lakes-St. Lawrence River drainages of North America. This mussel has experienced population declines across large parts of its distribution and is imperiled in many jurisdictions. <em>Obovaria olivaria </em>uses the similarly imperiled <em>Acipenser fulvescens</em> (Lake Sturgeon) as a host for its glochidia. We employed mitochondrial DNA sequencing and Restriction-site Associated DNA sequencing (RAD-seq) to assess patterns of genetic diversity and population structure of <em>O. olivaria</em> from 19 collection locations including the St. Lawrence River drainage, the Great Lakes drainage, the Upper Mississippi River drainage, the Ohioan River drainage and the Mississippi Embayment. Heterozygosity was highest in Upper Mississippi and Great Lakes populations, followed by a reduction in diversity and relative effective population size in the St. Lawrence populations. Pairwise <em>F</em><sub>ST</sub> ranged from 0.00 to 0.20, and analyses of genetic structure revealed two major ancestral populations, one including all St. Lawrence River/Ottawa River sites and the other including remaining sites; however, significant admixture and isolation by river distance across the range were evident. The genetic diversity and structure of <em>O. olivaria</em> is consistent with the existing literature on <em>Acipenser fulvescens</em> and suggest that, although northern and southern <em>O. olivaria</em> populations are genetically distinct, genetic structure in <em>O. olivaria</em> is largely clinal rather than discrete across its range. Conservation and restoration efforts of <em>O. olivaria</em> should prioritize the maintenance and restoration of locations where <em>O. olivaria </em>remain, especially in northern rivers, and to ensure connectivity that will facilitate dispersal of <em>Acipenser fulvescens</em> and movement of encysted glochidia.</p>
Fig. 3 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 3. Likelihood phylogeny of concatenated supermatrix of Pogonolepis and outgroups. Numbers above branches indicate UltraFast Bootstrap values, gene Concordance Factors, and site Concordance Factors. The dashed branch was shortened for the figure. Western Australian specimens of P. muelleriana are marked with (WA), all others are from eastern states. A and B indicate informally named clades inside P. stricta.
Fig. 2 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 2. Geographic spread of the specimens of Pogonolepis at CANB sampled for molecular analysis (large, pale circles) and ranges of species according to the Australasian Virtual Herbarium (dots; see https://doi.org/10.26197/ala.6556e234- 7160-49de-bf63-5123af624e94, accessed 31 May 2022). Red: P. muelleriana; blue: P. stricta. Note that specimens of P. muel-leriana geocoded in Canberra and Hobart were likely cultivated.
Fig. 1 in Sequence capture data support the taxonomy of Pogonolepis (Asteraceae: Gnaphalieae) and show unexpected genetic structure
Fig. 1. (a) Pogonolepis muelleriana, New South Wales, SchmidtLebuhn 1633 (CANB); (b) Pogonolepis stricta, Western Australia, Schmidt-Lebuhn 1474 (CANB).
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.