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.
2,785
datasets available to search
ShareScore release 0.9.0
Dataset results
2,785 results for “genotyping”
Data from: Analysis-ready datasets for insecticide resistance phenotype and genotype frequency in African malaria vectors
The impact of insecticide resistance in malaria vectors is poorly understood and quantified. Here a series of geospatial datasets for insecticide resistance in malaria vectors are provided so that trends in resistance in time and space can be quantified and the impact of resistance found in wild populations on malaria transmission in Africa can be assessed. Data are also provided for common genetic markers of resistance to support analyses of whether these genetic data can improve the ability to monitor resistance in low resource settings. Specifically, data have been collated and geopositioned for the prevalence of insecticide resistance, as measured by standard bioassays, in representative samples of individual species or species complexes. Data are provided for the Anopheles gambiae species complex, the Anopheles funestus subgroup, and for nine individual vector species. In addition, allele frequencies for known resistance associated markers in the Voltage-gated sodium channel (Vgsc) are provided. In total, eight analysis-ready, standardised, geopositioned datasets encompassing over 20,000 African mosquito collections between 1957 and 2017 are provided.
Data from: Spartina alterniflora genotypic identity affects plant and consumer responses in an experimental marsh community
1. Competition and herbivory are ubiquitous processes known to interactively shape plant performance, distribution and community assembly. Likewise, plant genetic variation and associated trait differences can impact both plant-plant and plant-herbivore interactions individually, yet few studies have explored these interactions simultaneously. 2. Salt marsh communities are an ideal system to study these questions, as they are dominated along the Atlantic and Gulf coasts of the United States by a foundation plant species, Spartina alterniflora, with high levels of genetically-based trait variation. Furthermore, consumer pressure and plant competitors are known to influence both the distribution and production of Spartina. We manipulated Spartina genetic identity, neighbor identity (needlerush, Juncus roemerianus), and consumer presence (snail, Littoraria irrorata) in a one-year field experiment in St. Joseph Bay, FL to test how the strength and direction of neighbor and consumer interactions vary by plant genotype. 3. Consumer effects on Spartina were generally stronger and more variable than those of the plant neighborhood, and these effects were generally consistent across Spartina genotypes. However, genotype-specific variation in morphology, phenology, and palatability significantly influenced both consumer and neighbor responses to Spartina: the consumer Littoraria was more likely to climb palatable Spartina genotypes, and neighboring Juncus had shorter stems in the presence of highly productive Spartina genotypes. 4. Synthesis. Our results add to the growing list of examples highlighting the role of intraspecific variation in species interactions, and suggest that variation in these interactions may promote the maintenance of plant genetic variation and community composition.
Data from: Investigating the production of sexual resting structures in a plant pathogen reveals unexpected self-fertility and genotype-by-environment effects
The sexual stage of pathogens governs recombination patterns and often also provides means of surviving the off-season. Despite its importance for evolutionary potential and between-season epidemiology, sexual systems have not been carefully investigated for many important pathogens, and what generates variation in successful sexual reproduction of pathogens remains unexplored. We surveyed the sexually produced resting structures (chasmothecia) across 86 natural populations of fungal pathogen Podosphaera plantaginis (Ascomycota) naturally infecting Plantago lanceolata in the Åland archipelago, southwest of Finland. For this pathosystem, these resting structures are a key life-history stage, as more than half of the local pathogen populations go extinct every winter. We uncovered substantial variation in the level of chasmothecia produced among populations, ranging from complete absence to presence on all infected leaves. We found that chasmothecia developed within clonal isolates (single strain cultures). Additionally, these clonal isolates all contained both MAT1-1-1 and MAT1-2-1 genes that characterize mating-types in Ascomycetes. Hence, contrary to expectations, we conclude that this species is capable of haploid selfing. In controlled inoculations we discovered that pathogen genotypes varied in their tendency to produce chasmothecia. Production of chasmothecia was also affected by ambient temperature (E), and by the interaction between temperature and pathogen genotype (G × E). These G, E and G × E effects found both at a European scale, as well as within Åland, may partly explain the high variability observed among populations in chasmothecia levels. Consequently, they may be key drivers of the evolutionary potential and epidemiology of this highly dynamic pathosystem.
Data from: Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds
One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.
Data from: A rapid and cost-effective quantitative microsatellite genotyping protocol to estimate intraspecific competition in protist microcosm experiments
High levels of intra-specific variation are commonly observed in natural microbial populations, yet the consequences of this variation for ecological and evolutionary processes remains poorly understood. Protists are excellent experimental models for investigating fundamental and applied questions in ecology and evolution, but studying intra-specific variation remains a challenge due to a lack of molecular resources to aid in quantifying and distinguishing strains during experiments. Here we present a molecular method, quantitative microsatellite genotyping, to accurately quantify strain specific frequencies from microcosm experiments of the marine flagellate Oxyrrhis marina, both between many pairs of strains and between strains in a multi-strain mixture. We find that for pairs of strains the method is effective for relative frequencies as low as 0.02 and with around 99% accuracy. The method is able to quantify four strains reasonably well, though less accurately than for pairs (range 92%-97% accuracy). This makes accessible a cheap and easy to implement method for quantifying strain (or allele) frequencies, and is suitable for use in a broad range of single celled eukaryotes (Protists) where copy number should correlate well with number of individuals (i.e. cells). This opens up the possibility of examining the role of intra-specific variation using experimental protist microcosms.
Data from: Linking genotype to phenotype in a changing ocean: inferring the genomic architecture of a blue mussel stress response with genome-wide association
A key component to understanding the evolutionary response to a changing climate is linking underlying genetic variation to phenotypic variation in stress response. Here we use a genome-wide association approach (GWAS) to understand the genetic architecture of calcification rates under simulated climate stress. We take advantage of the genomic gradient across the blue mussel hybrid zone (Mytilus edulis and Mytilus trossulus) in the Gulf of Maine (GOM) to link genetic variation with variance in calcification rates in response to simulated climate change. Falling calcium carbonate saturation states are predicted to negatively impact many marine organisms that build calcium carbonate shells - like blue mussels. We sampled wild mussels and measured net calcification phenotypes after exposing mussels to a "climate change" common garden, where we raised temperature 3°C, decreased pH by 0.2 units, and limited food supply by filtering out planktonic particles > 5 μm, compared to ambient GOM conditions in the summer. This climate change exposure greatly increased phenotypic variation in net calcification rates compared to ambient conditions. We then used regression models to link the phenotypic variation with over 170,000 single nucleotide polymorphism loci (SNPs) generated by genotype by sequencing to identify genomic locations associated with calcification phenotype, and estimate heritability and architecture of the trait. We identified at least one of potentially 2-10 genomic regions responsible for 30% of the phenotypic variation in calcification rates that are potential targets of natural selection by climate change. Our simulations suggest a power of 13.7% with our study's average effective sample size of 118 individuals and rare alleles, but a power of > 90% when effective sample size is 900.
Data from: Genotyping-by-sequencing reveals genomic homogeneity among overwintering Pacific Dunlin (Calidris alpina pacifica) aggregations along the Pacific coast of North America
Information on how migratory populations are genetically structured during the overwintering season of the annual cycle can improve our understanding of the strength of migratory connectivity and help identify populations as units for management. Here, we use a genotype-by-sequencing approach to investigate whether population genetic structure exists among overwintering aggregations of the Pacific Dunlin subspecies (Calidris alpina pacifica) sampled at two spatial scales (i.e. within and among overwintering sites) in the eastern Pacific Flyway. Genome-wide analyses of 874 single nucleotide polymorphisms across 80 sampled individuals revealed no evidence for genetic differentiation among aggregations overwintering at three locations within the Fraser River Estuary (FRE) of British Columbia. Similarly, comparisons of aggregations in the FRE and those overwintering in southern sites in California and Mexico indicated no genetic segregation between northern and southern overwintering areas. These results suggest that Pacific Dunlin residing within the FRE, Sacramento Valley (California) and Guerrero Negro (Mexico) are genetically homogeneous, with no evident genetic structure between sampled sites or regions across the overwintering range. Despite no evidence for differentiation among aggregations, we identified a significant effect of geographical distance between sites on the distribution of individual genotypes in a redundancy analysis; however, a small proportion of the total genotypic variance (R2 = 0.036, P = 0.011) was explained by the combined effect of latitude and longitude, suggesting weak genomic patterns of isolation-by-distance that are consistent with chain-like migratory connectivity between breeding and overwintering areas. Our study represents the first genome-scale investigation of population structure for a Dunlin subspecies and provides essential baseline estimates of genomic diversity and differentiation within the Pacific Dunlin.
Age, tissue, genotype and virus infection regulate Wolbachia levels in Drosophila
The bacterial symbiont Wolbachia can protect insects against viral pathogens, and the varying levels of antiviral protection are correlated with the endosymbiont load within the insects. To understand why Wolbachia strains differ in their antiviral effects, we investigated the factors controlling Wolbachia density in five closely related strains in their natural Drosophila hosts. We found that Wolbachia density varied greatly across different tissues and between flies of different ages, and these effects depended on the host-symbiont association. Some endosymbionts maintained largely stable densities as flies aged while others increased, and these effects in turn depended on the tissue being examined. Measuring Wolbachia rRNA levels in response to viral infection, we found that viral infection itself also altered Wolbachia levels, with FHV causing substantial reductions in symbiont loads late in the infection. This effect, however, was virus-specific as DCV had little impact on Wolbachia in all of the five host systems. Since viruses have strong tissue tropisms and antiviral protection is thought to be cell autonomous, these effects are likely to affect the virus-blocking phenomenon. However, we were unable to find any evidence of a correlation between Wolbachia and viral titers within the same tissues. We conclude that Wolbachia levels within flies are regulated in a complex host-symbiont-virus dependent manner and this trinity is likely to influence the antiviral effects of Wolbachia.
Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements
Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27–43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.
Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak
<p>Leaves interact with a wealth of microorganisms. Among these, fungi are highly diverse, and are known to contribute to plant health, leaf senescence and early decomposition. However, patterns and drivers of the seasonal dynamics of foliar fungal communities are poorly understood.</p> <p>We used a multi-factorial experiment to investigate the influence of warming and tree genotype on the foliar fungal community on the pedunculate oak <i>Quercus robur</i> across one growing season.</p> <p>Fungal species richness increased, evenness tended to decrease, and community composition strongly shifted during the growing season. Yeasts increased in relative abundance as the season progressed, while putative fungal pathogens decreased. Warming decreased species richness, reduced evenness and changed community composition, especially in the end of the growing season. Warming also negatively affected putative fungal pathogens. We only detected a minor imprint of tree genotype and warming-by-genotype interactions on species richness and community composition.</p> <p>Overall, our findings demonstrate that warming plays a larger role than plant genotype in shaping the seasonal dynamics of the foliar fungal community on oak. These warming-induced shifts in the foliar fungal community may have a pronounced impact on plant health, plant-fungal interactions and ecosystem functions.</p>
SNP genotyping of North Head and northern Sydney Long-nosed bandicoots (Perameles nasuta)
<p>Wildlife species impacted by habitat loss and fragmentation often require conservation efforts to maintain populations. Long-nosed bandicoots (<i>Perameles nasuta</i>) still persist within the highly urbanised matrix of northern Sydney (Australia). These data are from a conservation genetics project investigating population structure and genetic diversity of the North Head Long-nosed bandicoot (<em>Perameles nasuta) </em>population and individuals from surrounding suburbs throughout northern Sydney.</p> <p>The population at North Head, Sydney, is currently listed as an <i>Endangered</i> population due to its small size, apparent isolation and other threats. To support future management, we used 1,446 single nucleotide polymorphism markers (SNPs) from 167 bandicoots to: i) assess the assumption of isolation and determine if genetic structuring is present between North Head and individuals from 11 other localities in northern Sydney, and ii) investigate genetic diversity over time in the North Head population from 2002 to 2018. Analyses confirmed population structuring and genetic divergence between North Head and greater northern Sydney. Three distinct populations were identified that corresponded to geographic localities (North Head, northern Sydney and Mosman). All populations were significantly differentiated (<i>F</i><sub>ST</sub> = 0.171–0.345), suggesting local genetic drift between localities. North Head genetic diversity indices estimated between 2002 to 2018 showed relatively constant levels of allelic richness (1.90–2.00) and observed heterozygosity (<i>H</i><sub>O</sub> = 0.231–0.310) along with minor levels of inbreeding (<i>F</i><sub>IS</sub> 0.020–0.052). The identification of some individuals sampled on North Head that were assigned to other populations suggests some sporadic geneflow into the population has occurred and may have assisted with maintaining genetic diversity.</p> <p>These data were used to suggest that the North Head population is distinct from other northern Sydney populations and has relatively constant levels of genetic diversity.</p>
FIG. 3. Conchological diOEerentiation among the homozygous genotypes Aat 1 in Selection and habitat-speci®c allozyme variation in the self-fertilizing land snail Cochlicopa lubrica (O. F. MuÈller)
FIG. 3. Conchological diOEerentiation among the homozygous genotypes Aat 1`20 ' and Aat 1`80' of Cochlicopa lubrica. The two groups are very similar with respect to the four shell dimensions. Discriminant scores are extracted with`shell height',`shell diameter',`diameter of the last whorl' and`diameter of the penultimate shell whorl'. Data of 316 shells are incorporated.
Genotyping-by-sequencing data for a Haitian sorghum breeding program
<p>Rapid environmental change can lead to extinction of populations or evolutionary rescue via genetic adaptation. In the past several years, smallholder and commercial cultivation of sorghum (Sorghum bicolor), a global cereal and forage crop, has been threatened by a global outbreak of an aggressive new biotype of sugarcane aphid (SCA; Melanaphis sacchari). Here we characterized genomic signatures of adaptation in a Haitian sorghum breeding population, which had been recently founded from admixed global germplasm, extensively intercrossed, and subjected to intense selection under SCA infestation. We conducted evolutionary population genomics analyses of 296 post-selection Haitian lines compared to 767 global accessions at 159,683 single nucleotide polymorphisms. Despite intense selection, the Haitian population retains high nucleotide diversity through much of the genome due to diverse founders and an intercrossing strategy. A genome-wide fixation (FST) scan and geographic analyses suggests that adaptation to SCA in Haiti is conferred by a globally-rare East African allele of RMES1, which has also spread to other breeding programs in Africa, Asia, and the Americas. De novo genome sequencing data for SCA resistant and susceptible lines revealed putative causative variants at RMES1. Convenient low-cost markers were developed from the RMES1 selective sweep and successfully predicted resistance in independent U.S. × African breeding lines and eight U.S. commercial and public breeding programs, demonstrating the global relevance of the findings. Together, the findings highlight the potential of evolutionary genomics to develop adaptive trait breeding technology and the value of global germplasm exchange to facilitate evolutionary rescue.</p>
Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 4. Individual multilocus genotype clustering analysis for Podarcis carbonelli. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 4 (chosen by the previous method) for each locality.
Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A in Recent evolutionary history of the Iberian endemic lizards Podarcis bocagei (Seoane, 1884) and Podarcis carbonelli Pérez-Mellado, 1981 (Squamata: Lacertidae) revealed by allozyme and microsatellite markers
Figure 3. Individual multilocus genotype clustering analysis for Podarcis bocagei. A, inferred population structure from the number of clusters (K) = 2 to 5. These plots were obtained from the runs producing the highest values of Ln probability for each value of K, assuming correlated allele frequencies. In these plots, each individual is represented by a column divided into K segments, the size of each corresponding to the individual's estimated membership fraction in each of the K clusters. See Table 1 for locality name abbreviations. B, variation of the value of DK with the number of clusters, following Evanno et al. (2005). C, pie charts representing the mean proportion of membership for K = 3 and 5 (chosen by the previous method) for each locality.
Genotypes for herring samples collected from Chinook salmon gut contents
<p>Dynamic prey resources influence foraging opportunities for consumers. In coastal food webs, forage fish abundance and seasonal reproduction mediate foraging opportunities for mobile consumers. Recent declines in Chinook salmon productivity have prompted efforts to determine whether poormarine survival is caused by limited feeding opportunities. To establish the importance of phenological diversity in Pacific herring for Chinook salmon, we used genetic stock identification to assign individual herring collected from the guts of juvenile and adult Chinook salmon to populations with distinct spawning phenologies. The majority of herring in the guts of adult Chinook salmon across seasons and geographic areas were dominated by the March–April herring spawn group, but juvenile Chinook salmon diets varied seasonally, with a higher proportion of January–February spawners in summer than in spring. Our results suggest that (1) population diversity of Pacific herring is used by juvenile Chinook salmon and thus contributes to their growth, and (2) stock-specific distribution of Pacific herring extends well beyond documented spawning grounds. Herring population diversity may therefore support foraging opportunities for Chinook salmon during a critical period and highlights the need for future research to quantify seasonal distribution and abundance of phenologically distinct groups of Pacific herring within Salish Sea.</p>
Trachymyrmex ant and Leucocoprinus fungus genotypes
<p>Over the past few decades, large-scale phylogenetic analyses of fungus-gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is widespread among unrelated ant lineages. Sharing has been explained using a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange were indeed due to symbiont sharing or the result of employing relatively uninformative molecular markers, samples of <i>Trachymyrmex arizonensis</i> and <i>Trachymyrmex pomonae</i> and their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome-wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence between <i>Trachymyrmex</i> species and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange. These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.</p>
New incidence or recurrence hepatocellular carcinoma (HCC) in genotype 4 hepatitis C virus treated with sofosbuvir/daclatasvir with or without ribavirin
<p><span><b>Background</b>: Several studies have resulted in controversial data about the recurrence or new incidence of hepatocellular carcinoma (HCC) in patients with hepatitis C who were treated with direct-acting antivirals (DAAs). </span></p> <p><span><b>Aim:</b> This observational study aimed to assess the occurrence rate of HCC in patients who developed a sustained virological response (SVR).. </span></p> <p><span><b>Methods</b>: A six-month prospective study was done at the National Hepatology and Tropical Medicine Research Institute [NHTMRI] in Cairo, Egypt on 150 chronic hepatitis C (CHC) patients treated with sofosbuvir and daclatasvir with or without ribavirin. Patients were assigned into two groups according to their laboratory values to either receive sofosbuvir/daclatasvir and ribavirin (S/D/R) or receive only sofosbuvir/daclatasvir (S/D). The main outcome measure was the occurrence of HCC.</span></p> <p><span><b>Results</b>: SVR-12 was 100%. 8.5% of patients developed HCC in the S/D/R group, while 0% in the S/D group.</span></p> <p><span><b>Conclusion:</b> New incidence or recurrence of HCC may occur in CHC genotype 4 cirrhotic patients receiving sofosbuvir/daclatasvir and ribavirin (difficult to treat) although achieving SVR. The cause of HCC development in this study is cirrhosis, not the administered DAAs.</span></p>
A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations
<p>An optimized, high-throughput and cost-effective genotyping method applicable to various crop breeding populations is very important in this genomic era. We have developed an optimized Nextera skim-sequencing (skim-seq) approach to genotype different populations that can be used for genetics studies and genomics-assisted breeding. We performed skim-seq on a variety of populations developed through doubled haploid (DH) technology, inter-specific recombinants developed through introgression, amphidiploid developed through wide crosses, and on known monosomic samples.</p> <p>1. A doubled haploid (DH) population consisting of 48 lines from the cross of spring wheat (<i>Triticum</i> <i>aestivum</i>) cultivars CDC Stanley and CDC Landmark developed by the Crop Development Centre at the University of Saskatchewan. We genotyped these DH with skim-seq and identified the genomic segments contributed by each of the two parental lines.</p> <p>2. A population of 335 back cross generation 1 (BC1) skim-seq samples for wheat-barley recombinants with group 7 translocations and 839 F1 wheat 5D monosomic lines (TA3059) along with 16 standard Chinese Spring lines as internal control.</p> <p>3. A panel of 144 <i>Thinopyrum</i> <i>intermedium</i> x <i>Triticum</i> <i>durum</i> (IWG--durum) lines and 141 <i>Thinopyrum</i> <i>intermedium</i> (IWG) lines were evaluated to assess skim-seq genome coverage as well as amphiploidy levels.</p> <p>The demultiplexed FASTQ files for all samples tested in the experiment are available at NCBI SRA public repository with respective BioProject accessions; DH lines [PRJNA729723], 5D monosomic line [PRJNA742385], wheat-barley recombinants [PRJNA738484], IWG-durum and IWG [PRJNA736976]. An example key file for the 5D monosomic line is also attached. </p> <p>This study indicated that skim-seq is an efficient approach for genomic evaluation of a range of different populations and applications. The scripts have been provided to implement skim-seq data for variant calling, identification of genomic segment dosage and alien introgression. Each step of the pipeline is described and implemented with similar sequencing data from skim-seq libraries.</p>
Genotyping-by-Sequencing data of weedy and domesticated Brassica rapa L.
<p>The study of domestication contributes to our knowledge of evolution and crop genetic resources. Human selection has shaped wild <em>Brassica rapa</em> into diverse turnip, leafy, and oilseed crops. Despite its worldwide economic importance and potential as a model for understanding diversification under domestication, insights into the number of domestication events and initial crop(s) domesticated in <em>B. rapa</em> have been limited due to a lack of clarity about the wild or feral status of conspecific non-crop relatives. To address this gap and reconstruct the domestication history of <em>B. rapa</em>, we analyzed 68,468 genotyping-by-sequencing-derived SNPs for 416 samples in the largest diversity panel of domesticated and weedy <em>B. rapa</em> to date. To further understand the center of origin, we modeled the potential range of wild <em>B. rapa</em> during the mid-Holocene. Our analyses of genetic diversity across <em>B. rapa</em> morphotypes suggest that non-crop samples from the Caucasus, Siberia, and Italy may be truly wild, while those occurring in the Americas and much of Europe are feral. Clustering, tree-based analyses, and parameterized demographic inference further indicate that turnips were likely the first crop type domesticated, from which leafy types in East Asia and Europe were selected from distinct lineages. These findings clarify the domestication history and nature of wild crop genetic resources for <em>B. rapa</em>, which provides the first step toward investigating cases of possible parallel selection, the domestication and feralization syndrome, and novel germplasm for <em>Brassica</em> crop improvement.</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.