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44 results for “recombination rate”
Data from: Evidence for structure and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus
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Data from: Conservation of the genome-wide recombination rate in white-footed mice
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Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds
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Data from: Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
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Data from: Recombination rate variation shapes barriers to introgression across butterfly genomes
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Data from: A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution
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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>
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>
Data from: Fine-Scale Mapping of Recombination Rate in Drosophila Refines its Correlation to Diversity and Divergence
Regional rates of recombination often correlate with levels of nucleotide diversity, and either selective or neutral hypotheses can explain this relationship. Regional recombination rates also correlate with nucleotide differences between human and chimpanzee, consistent with models where recombination is mutagenic; however, a lack of correlation is observed in the Drosophila melanogaster group, consistent with models invoking natural selection. Here, we revisit the relationship among recombination, diversity, and interspecies difference by generating empirical estimates of these parameters in Drosophila pseudoobscura. To measure recombination rate, we genotyped 1,294 backcross hybrids at 50 markers across the largest assembled linkage group in this species. Genome-wide diversity was estimated by sequencing a second isolate of D. pseudoobscura at shallow coverage. Alignment to the sequenced genome of the closely related species, Drosophila persimilis, provided nucleotide site orthology. Our findings demonstrate that scale is critical in determining correlates to recombination rate: fine-scale cross-over rate estimates are far stronger predictors of both diversity and interspecies difference than broad-scale estimates. The correlation of fine-scale recombination rate to diversity and interspecies difference appears to be genome-wide, evidenced by examination of an X-linked region in greater detail. Because we observe a strong correlation of cross-over rate with interspecies difference, even after correcting for segregating ancestral variation, we suggest that both mutagenic and selective forces generate these correlations, the latter in regions of low crossing over. We propose that it is not cross-overs per se that are mutagenic, but rather repair of DNA double-strand break precursors via crossing over and gene conversion.
Data from: Conserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries)
Meiotic recombination breaks down linkage disequilibrium and forms new haplotypes, meaning that it is an important driver of diversity in eukaryotic genomes. Understanding the causes of variation in recombination rate is important in interpreting and predicting evolutionary phenomena and for understanding the potential of a population to respond to selection. However, despite attention in model systems, there remains little data on how recombination rate varies at the individual level in natural populations. Here, we used extensive pedigree and high-density SNP information in a wild population of Soay sheep (Ovis aries) to investigate the genetic architecture of individual autosomal recombination rate. Individual rates were high relative to other mammal systems, and were higher in males than in females (autosomal map lengths of 3748 cM and 2860 cM, respectively). The heritability of autosomal recombination rate was low but significant in both sexes (h2 = 0.16 & 0.12 in females and males, respectively). In females, 46.7% of the heritable variation was explained by a sub-telomeric region on chromosome 6; a genome-wide association study showed the strongest associations at the locus RNF212, with further associations observed at a nearby ~374kb region of complete linkage disequilibrium containing three additional candidate loci, CPLX1, GAK and PCGF3. A second region on chromosome 7 containing REC8 and RNF212B explained 26.2% of the heritable variation in recombination rate in both sexes. Comparative analyses with 40 other sheep breeds showed that haplotypes associated with recombination rates are both old and globally distributed. Both regions have been implicated in rate variation in mice, cattle and humans, suggesting a common genetic architecture of recombination rate variation in mammals.
Data from: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms
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Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis
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Data from: How hot are Drosophila hotspots? Examining recombination rate variation and associations with nucleotide diversity, divergence, and maternal age in Drosophila pseudoobscura
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Data from: Fine-Scale Mapping of Recombination Rate in Drosophila Refines its Correlation to Diversity and Divergence
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Genetic architecture of individual variation in recombination rate on the X-chromosome in cattle
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Data from: Hybrid sterility locus on Chromosome X controls meiotic recombination rate in mouse
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Data from: Conserved genetic architecture underlying recombination rate variation in a wild population of Soay sheep (Ovis aries)
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Data from: Recombinant DNA modification of gibberellin metabolism alters growth rate and biomass allocation in Populus
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The theory and applications of measuring broad-range and chromosome-wide recombination rate from allele frequency decay around a selected locus
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Metabolomic and transcriptomic analysis for rate-limiting metabolic steps in xylose utilization by recombinant Candida utilis
GEO Series GSE43514. Cyberlindnera jadinii. 8 samples. Type: Expression profiling by array.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.