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.
2,180
datasets available to search
ShareScore release 0.9.0
Dataset results
2,180 results for “Recombination”
Data from: Hepatitis C virus genotype 1 and 2 recombinant genomes and the phylogeographic history of the 2k/1b lineage
Open the record for dataset details and reuse information.
The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex
Open the record for dataset details and reuse information.
Data from: High-resolution estimates of crossover and noncrossover recombination from a captive baboon colony
Open the record for dataset details and reuse information.
SVXplorer: three-tier approach to identification of structural variants via sequential recombination of discordant cluster signatures
<p>This repository contains the bgzipped variants calls in VCF format for CHM1, NA12878 and AJ trio dataset that are used in the SVXplorer manuscript. The names of the files contain the name of the sample (CHM1/NA12878/HG002/HG003/HG004), the name of the method (SVXplorer/DELLY/LUMPY/TIDDIT/TARDIS/MANTA) used to call the variants. There are three separate files for the DELLY calls which have the deletions, duplications and the inversion calls made by DELLY for each of the samples. For NA12878, there are two sets of calls, one for each of the libraries (ERR194147/SRR505885)</p> <p> </p>
Data and code for project on maternal age and recombination rate in Drosophila pseudoobscura
<p>Github repository containing data files and scripts to reproduce the analysis for the manuscript titled: <strong>"Maternal age alters recombination rate in <em>Drosophila pseudoobscura</em>"</strong>. </p>
SARS-CoV-2 Origins and Evolution: Insights from Coronaviruses Recombination and Phylogenetic Analysis
<p>It is imperative in the midst of a global epidemic to investigate the origins of the infectious agent especially when it has reached parts of the world with either ailing economies or pre-existing political turmoil consistent with non-functional health systems. To explore the possibility of cross species infection, genomic recombination and the emergence of novel coronaviruses in the near future we carried out recombination and phylogenetic analysis to determine the spatio-temporal evolution and origins of the current SARS-CoV-2 virus. Using two robust recombination tools, RDPv4.100 and SimPlot3.5.1 analysis, our findings prove that SARS-CoV-2 is a recombinant of pangolin and bat RaTG13 sequences as been previously shown elsewhere. We also report one novel recombination event between two SARS-CoV-2 sequences (<em>SARS-CoV-2 sequence, MT188341</em>, <em>SARS-CoV-2 sequence, </em><em>MT293183).</em> Bearing in mind that the prerequisite for recombination is the occurrence of two viral sequences in the same reservoir, biological niche or host at the same time we postulate either co-infection with the two viral sequences, or superinfection. The possibility of recombination between the SARS-CoV-2 sequences poses the likelihood of the emergence of new more or less virulent “strains” of the virus. The future of science lies in our ability to be able to use computational based methods to predict the genetic sequences of infectious agents of the next epidemics. Addition of more SARS-CoV-2 sequences has a bearing on our understanding of the origin, evolution and clinical outcome prediction of given viral genomes. More SARS-CoV-2 sequences are needed to elucidate our understanding of this family of viruses.</p>
Genetic architecture of individual variation in recombination rate on the X-chromosome in cattle
<p class="Standard"><span>Meiotic recombination is an essential biological process that ensures proper chromosome segregation and creates genetic diversity. Individual variation in global recombination rates has been shown to be heritable in several species and variants significantly associated with this trait have been identified. Recombination on the sex chromosome has often been ignored in these studies although this trait may be particularly interesting as it may correspond to a biological process distinct from that on autosomes. For instance, recombination in males is restricted to the pseudo-autosomal region (PAR). We herein used a large cattle pedigree with more than 100,000 genotyped animals to improve the genetic map of the X-chromosome and to study the genetic architecture of individual variation in recombination rate on the sex-chromosome (XRR). The length of the genetic map was 46.4 and 121.2 cM in males and females, respectively, but the recombination rate in the PAR was 6 times higher in males. The heritability of CO counts on the X-chromosome was comparable to that of autosomes in males (0.011) but larger than that of autosomes in females (0.024). XRR was highly correlated (0.76) with global recombination rate (GRR) in females, suggesting that both traits might be governed by shared variants. In agreement, a set of eleven previously identified variants associated with GRR had correlated effects on female XRR (0.86). In males, XRR and GRR appeared to be distinct traits, although more accurate CO counts on the PAR would be valuable to confirm these results. </span></p>
Gene Delivery to Neurons in the Auditory Brainstem of Barn Owls using Standard Recombinant Adeno-associated Virus Vectors
<div> <p>Recombinant adeno-associated virus (rAAV) vectors are a commonly used tool for gene delivery. There is a large choice of different serotypes whose transduction efficiency varies for different animal species. In this study, three rAAV vectors were tested for transduction efficiency in the auditory brainstem of adult barn owls (<i>Tyto alba</i>) which are not standard laboratory animals. Injections with rAAV serotypes 2/1 and 2/5 resulted in reliable expression in various nuclei of the auditory brainstem of barn owls. Both vectors showed evidence of being spread by axonal transport. However, only rAAV2/5 also showed expression in regions far distant from the injection site, suggesting long-range axonal transport in connections along the auditory pathway. In contrast, injections with rAAV2/9 resulted in no expression. Our results demonstrate for the first time that commercially available rAAV vectors can be used for reliable gene expression in the barn owl auditory brainstem and pave the way toward optogenetic manipulation of neural activity in this important animal species in neuroethology and auditory physiology.</p> </div>
Figure 1 from: Voynova M, Shkondrov A, Krasteva I, Kondeva-Burdina M (2021) In vitro effects of synthetic muscimol and an extract from Amanita muscaria on human recombinant MAOB enzyme. Pharmacia 68(1): 147-150. https://doi.org/10.3897/pharmacia.68.e60705
Figure 1 Effects of muscimol (M) (at different concentrations) and selegiline (S) on hMAOB activity; * P < 0.05; ** P < 0.01; *** P < 0.001 vs control (pure hMAOB).
Figure 2 from: Voynova M, Shkondrov A, Krasteva I, Kondeva-Burdina M (2021) In vitro effects of synthetic muscimol and an extract from Amanita muscaria on human recombinant MAOB enzyme. Pharmacia 68(1): 147-150. https://doi.org/10.3897/pharmacia.68.e60705
Figure 2 Effects of Amanita muscaria extract (at different concentrations muscimol) and Selegiline (S) on hMAOB activity. ** P < 0.01 vs control (pure hMAOB).
Data from: High throughput sequencing reveals alterations in the recombination signatures with diminishing spo11 activity
Spo11 is the topoisomerase-like enzyme responsible for the induction of the meiosis-specific double strand breaks (DSBs), which initiate the recombination events responsible for proper chromosome segregation. Nineteen PCR-induced alleles of SPO11 were identified and characterized genetically and cytologically. Recombination, spore viability and synaptonemal complex (SC) formation were decreased to varying extents in these mutants. Arrest by ndt80 restored these events in two severe hypomorphic mutants, suggesting that ndt80-arrested nuclei are capable of extended DSB activity. While crossing-over, spore viability and synaptonemal complex (SC) formation defects correlated, the extent of such defects was not predictive of the level of heteroallelic gene conversions (prototrophs) exhibited by each mutant. High throughput sequencing of tetrads from spo11 hypomorphs revealed that gene conversion tracts associated with COs are significantly longer and gene conversion tracts unassociated with COs are significantly shorter than in wild type. By modeling the extent of these tract changes, we could account for the discrepancy in genetic measurements of prototrophy and crossover association. These findings provide an explanation for the unexpectedly low prototroph levels exhibited by spo11 hypomorphs and have important implications for genetic studies that assume an unbiased recovery of prototrophs, such as measurements of CO homeostasis. Our genetic and physical data support previous observations of DSB-limited meioses, in which COs are disproportionally maintained over NCOs (CO homeostasis).
Data from: Reduced crossover interference and increased ZMM-independent recombination in the absence of Tel1/ATM
Meiotic recombination involves the repair of double-strand break (DSB) precursors as crossovers (COs) or noncrossovers (NCOs). The proper number and distribution of COs is critical for successful chromosome segregation and formation of viable gametes. In budding yeast the majority of COs occurs through a pathway dependent on the ZMM proteins (Zip2-Zip3-Zip4-Spo16, Msh4-Msh5, Mer3), which form foci at CO-committed sites. Here we show that the DNA-damage-response kinase Tel1/ATM limits ZMM-independent recombination. By whole-genome mapping of recombination products, we find that lack of Tel1 results in higher recombination and reduced CO interference. Yet the number of Zip3 foci in tel1Δ cells is similar to wild type, and these foci show normal interference. Analysis of recombination in a tel1Δ zip3Δ double mutant indicates that COs are less dependent on Zip3 in the absence of Tel1. Together these results reveal that in the absence of Tel1, a significant proportion of COs occurs through a non-ZMM-dependent pathway, contributing to a CO landscape with poor interference. We also see a significant change in the distribution of all detectable recombination products in the absence of Tel1, Sgs1, Zip3, or Msh4, providing evidence for altered DSB distribution. These results support the previous finding that DSB interference depends on Tel1, and further suggest an additional level of DSB interference created through local repression of DSBs around CO-designated sites.
Data from: Recombination and hitchhiking of deleterious alleles
When new advantageous alleles arise and spread within a population, deleterious alleles at neighbouring loci can hitchhike alongside them and spread to fixation in areas of low recombination, introducing a fixed mutation load. We use branching processes and diffusion equations to calculate the probability that a deleterious allele hitchhikes and fixes alongside an advantageous mutant. As expected, the probability of fixation of a deleterious hitchhiker rises with the selective advantage of the sweeping allele and declines with the selective disadvantage of the deleterious hitchhiker. We then use computer simulations of a genome with an infinite number of loci to investigate the increase in load after an advantageous mutant is introduced. We show that the appearance of advantageous alleles on genetic backgrounds loaded with deleterious alleles has two potential effects: it can fix deleterious alleles and also facilitate the persistence of recombinant lineages that happen to occur. The latter is expected to reduce the signals of selection in the surrounding region. We consider these results in light of human genetic data to infer how likely it is that such deleterious hitchhikers have occurred in our recent evolutionary past.
Data from: Plastome mutations and recombination events in barley chloroplast mutator seedlings
The barley chloroplast mutator (cpm) is an allele of a nuclear gene that when homozygous induces several types of cytoplasmically inherited chlorophyll deficiencies. In this work, a plastome TILLING (Targeting Induced Local Lesions in Genomes) strategy based on mismatch digestion was used on families that carried the cpm genotype through many generations. Extensive scanning of 33 plastome genes and a few intergenic regions was conducted. Numerous polymorphisms were detected on both genic and intergenic regions. The detected polymorphisms can be accounted for by at least 61 independent mutational events. The vast majority of the polymorphisms originated in substitutions and small indels (insertions/deletions) in microsatellites. The rpl23 and the rps16 genes were the most polymorphic. Interestingly, the variation observed in the rpl23 gene consisted of several combinations of five different one nucleotide polymorphisms. Besides, four large indels that have direct repeats at both ends were also observed, which appear to be originated from recombinational events. The cpm mutation spectrum suggests that the CPM gene product is probably involved in plastome mismatch repair. The numerous subtle molecular changes that were localized in a wide range of plastome sites show the cpm as a valuable source of plastome variability for plant research and/or plant breeding. Moreover, the cpm mutant appears to be as an interesting experimental material for investigating the mechanisms responsible for maintaining the stability of plant organelles DNA.
Data from: Inter-locus sexually antagonistic coevolution creates indirect selection for increased recombination
The ubiquity of recombination in nature is a paradox because it breaks up combinations of alleles favored by natural selection. Theoretical work has shown that antagonistic coevolution between hosts and parasites can result in rapid fluctuations in epistasis, which can create a short-term advantage to recombination. Here we show that another kind of antagonistic coevolution, inter-locus sexually antagonistic coevolution (SAC), can also create indirect selection for modifiers that increase the rate of recombination, and that it can lead to very high levels of recombination at equilibrium. Recombination is favored because inter-locus SAC creates heterogeneity in the strength and direction of selection, both within and between generations, which maintains an excess of disadvantageous haplotypes in the population. This result is similar to and consistent with dynamics of fluctuating epistasis produced in models of host-parasite coevolution. However, the conditions under which inter-locus SAC provides an advantage to recombination are more permissive.
Data from: Is recombination a problem for species-tree analyses?
As the field of phylogenetics transitions into phylogenomics it has spurred a shift in the general paradigm for data analysis whereby specific dataset attributes can now be considered in a model-based framework. Much effort has been put in to modeling the effects of nucleotide substitution within a genealogy (i.e., modeling mutations; Felsenstein 2005) and the sorting genes between lineages (i.e., coalescence; Knowles and Kubatko 2010), both of which are inherent properties of all species histories. Improvements in accuracy of species-tree estimation related to using models that account for these two sources of uncertainty have been well documented (Carstens and Knowles 2007; Edwards et al. 2007; Kubatko and Degnan 2007), but these are clearly not the only sources of gene tree species-tree discordance. As the field transitions towards using multilocus data, the role of other inherent dataset properties that may be sources of uncertainty, such as intralocus recombination needs to be examined and quantified. As all species-tree methods in current use rely on the simplifying assumption that recombination occurs between but not within loci, ignoring the presence of recombination represents a widespread and ubiquitous violation of species-tree models. Recombination within a locus may be a greater problem for species-tree methodologies than for concatenation because species-tree methods more accurately model the patterns arising from coalescent stochasticity. Concatenation assumes all genes share a common underlying tree, a model violated by most multilocus data (Knowles and Carstens 2007; Cranston 2010; Linnen 2010; Wiens et al. 2010). Relative to the presence of such a gross model violation, errors introduced by within-locus recombination are likely to be minor for datasets analyzed by concatenation. Coalescent methods for species-tree estimation explicitly model each gene tree separately, making the relative contribution of recombination to the uncertainty of the estimated species tree greater. Challenges posed by recombination may also be greatest for species-tree methods that rely on estimating parameters related to the scaled mutation rate (Liu 2008; Liu et al. 2008; Heled and Drummond 2010) because recombination-introduced heterogeneity may interfere with branch length estimates. Lastly, recombination may interact with other aspects of the speciation history, such as time to divergence, population size, and the length of time between speciation events, and sampling effort (McCormack et al. 2009). For example, recombination events occurring in recently speciated groups may not have accumulated a sufficient number of mutations for the effects to be problematic (see Fig. 1).
Data from: Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex
Background: Determining the presence or absence of gene flow between populations is the target of some statistical methods in population genetics. Until recently, these methods either avoided the use of recombining genes, or treated recombination as a nuisance parameter. However, genes with recombination contribute additional information for the detection of gene flow (i.e. through linkage disequilibrium). Methods: We present three summary statistics based on the spatial arrangement of fixed differences, and shared and exclusive polymorphisms that are sensitive to the presence and direction of gene flow. Power and false positive rate for tests based on these statistics are studied by simulation. Results: The application of these tests to populations from the Drosophila simulans species complex yielded results consistent with migration between D. simulans and its two endemic sister species D. mauritiana and D. sechellia, and between populations D. mauritiana on the islands of the Mauritius and Rodrigues. Conclusions: We demonstrate the sensitivity of the developed statistics to the presence and direction of gene flow, and characterize their power as a function of differentiation level and recombination rate. The properties of these statistics make them especially suitable for analyzing high-throughput sequencing data or for their integration within the approximate Bayesian computation framework.
Data from: Sex-antagonistic genes, XY recombination, and feminized Y chromosomes
The canonical model of sex-chromosome evolution predicts that sex-antagonistic (SA) genes play an instrumental role in the arrest of XY recombination and ensuing Y-chromosome degeneration. Although this model might account for the highly differentiated sex chromosomes of birds and mammals, it does not fit the situation of many lineages of fish, amphibians or non-avian reptiles, where sex chromosomes are maintained homomorphic through occasional XY recombination and/or high turnover rates. Such situations call for alternative explanatory frameworks. A crucial issue at stake is the effect of XY recombination on the dynamics of SA genes and deleterious mutations. Using individual-based simulations, we show that a complete arrest of XY recombination actually benefits females, not males. Male fitness is maximized at different XY-recombination rates depending on SA selection, but never at zero XY recombination. This should consistently favor some level of XY recombination, which in turn generates a recombination load at sex-linked SA genes. Hill-Robertson interferences with deleterious mutations also impede the differentiation of sex-linked SA genes, to the point that males may actually fix feminized phenotypes when SA selection and XY recombination are low. We argue that sex chromosomes might not be a good localization for SA genes, and sex conflicts seem better solved through the differential expression of autosomal genes.
Data from: Extensive recombination of a yeast diploid hybrid through meiotic reversion
In somatic cells, recombination between the homologous chromosomes followed by equational segregation leads to loss of heterozygosity events (LOH), allowing the expression of recessive alleles and the production of novel allele combinations that are potentially beneficial upon Darwinian selection. However, inter-homolog recombination in somatic cells is rare, thus reducing potential genetic variation. Here, we explored the property of S. cerevisiae to enter the meiotic developmental program, induce meiotic Spo11-dependent double-strand breaks genome-wide and return to mitotic growth, a process known as Return To Growth (RTG). Whole genome sequencing of 36 RTG strains derived from the hybrid S288c/SK1 diploid strain demonstrates that the RTGs are bona fide diploids with mosaic recombined genome, derived from either parental origin. Individual RTG genome-wide genotypes are comprised of 5 to 87 homozygous regions due to the loss of heterozygous (LOH) events of various lengths, varying between a few nucleotides up to several hundred kilobases. Furthermore, we show that reiteration of the RTG process shows incremental increases of homozygosity. Phenotype/genotype analysis of the RTG strains for the auxotrophic and arsenate resistance traits validates the potential of this procedure of genome diversification to rapidly map complex traits loci (QTLs) in diploid strains without undergoing sexual reproduction.
Data from: A recombination suppressor contributes to ecological speciation in Ostrinia moths
Despite unparalleled access to species' genomes in our post-genomic age, we often lack adequate biological explanations for a major hallmark of the speciation process—genetic divergence. In the presence of gene flow, chromosomal rearrangements such as inversions are thought to promote divergence and facilitate speciation by suppressing recombination. Using a combination of genetic crosses, phenotyping of a trait underlying ecological isolation, and population genetic analysis of wild populations, we set out to determine whether evidence supports a role for recombination suppressors during speciation between the Z and E strains of European corn borer moth (Ostrinia nubilalis). Our results are consistent with the presence of an inversion that has contributed to accumulation of ecologically adaptive alleles and genetic differentiation across roughly 20% of the Ostrinia sex chromosome (~4 Mb). Patterns in Ostrinia suggest that chromosomal divergence may involve two separate phases—one driving its transient origin through local adaptation and one determining its stable persistence through differential introgression. As the evolutionary rate of rearrangements in lepidopteran genomes appears to be one of the fastest among eukaryotes, structural mutations may have had a disproportionate role during adaptive divergence and speciation in Ostrinia and in other moths and butterflies.
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.