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44 results for “recombination rate”
Raw Genotyping data from: Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets
<p>Data supporting :</p> <p><strong>Variation in recombination rate and its genetic determinism in sheep populations from combining multiple genomewide datasets</strong></p> <p>Morgane Petit, Jean-Michel Astruc, Julien Sarry, Laurence Drouilhet, Stephane Fabre, Carole Moreno, Bertrand Servin</p> <p>http://doi.org/10.1534/genetics.117.300123</p> <p><strong>Abstract</strong></p> <p>Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the <em>RNF212</em> and<em> HEI10</em> genes and possibly 2 other loci of smaller effects including the <em>KCNJ15</em> and <em>FSHR</em> genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.</p> <p> </p> <p>Data files are provided in Plink format ( https://www.cog-genomics.org/plink2 ).</p> <p> </p>
Fine-scale map reveals highly variable recombination rates associated with genomic features in the Eurasian blackcap
<p>This project estimates historical recombination rates of the Eurasian blackcap (<em>Sylvia atricapilla</em>) and the garden warbler (<em>Sylvia borin)</em> using a linkage disequilibrium-based approach. The population-scaled recombination rates were inferred using 'pyrho' considering the population's demographic information and mutation rates. The mutation rate was taken from a closely related species (flycatcher, <em>Ficedula albicollis</em>).</p> <p>Here we report the recombination rate per site per generation (r, output of pyrho) for all the chromosomes along the genome for both species. </p> <p>Blackcap dataset file: WholeGenome_chromosomes_blackap_n38_Pen20_W50.gz</p> <p>Garden warbler dataset file: WholeGenome_chromosomes_SylBor_n10_Pen20W50.gz</p> <p> </p> <p>Additionally, we annotated the blackcap genome to evaluate the association between recombination rates and specific annotation features (e.g., genes, transcription start sites, promoters, 5'UTR, and 3'UTR regions). The annotation of the genome was based on RNA-seq and Iso-Seq data. It can be found with the name bSylAtr1.1.gff.</p>
Constructing a high-density linkage map to infer the genomic landscape of recombination rate variation in European Aspen (Populus tremula)
<p>Data sets and files for linkage map construction and for inferring recombination rate variation in <em>Populus tremula</em>. Associated scripts for analyses can be found at <a href="https://github.com/parkingvarsson/Recombination_rate_variation">https://github.com/parkingvarsson/Recombination_rate_variation</a> </p>
Data and code relating to Becher, Jackson & Charlesworth. Patterns of genetic variability in genomic regions with low rates of recombination.
<p>Data and code relating to Becher, Jackson & Charlesworth. Patterns of genetic variability in genomic regions with low rates of recombination.</p> <p>Contains genotype data, R code for analysis and visualisation, a SLiM simulation script, README, etc.</p>
Data from: The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)
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Data from: The effect of parasite infection on the recombination rate of the yellow fever mosquito Aedes aegyti
Sexual reproduction and meiotic recombination generate new genetic combinations and may thereby help an individual infected by a parasite to protect its offspring from being infected. While this idea is often used to understand the evolutionary forces underlying the maintenance of sex and recombination, it also suggests that infected individuals should increase plastically their rate of recombination. We tested the latter idea with the mosquito Aedes aegypti and asked whether females infected by the microsporidian Vavraia culicis were more likely to have recombinant offspring than uninfected females. To measure the rate of recombination over a chromosome we analysed combinations of microsatellites on chromosome 3 in infected and uninfected females, in the (uninfected) males they copulated with and in their offspring. As predicted, the infected females were more likely to have recombinant offspring than the uninfected ones. These results show the ability of a female to diversify her offspring in response to parasitic infection by plastically increasing her recombination rate.
Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers
<p><span>Understanding the mechanisms underlying heterogeneous genomic divergence is of particular interest in evolutionary biology. Highly differentiated genomic regions, known as genomic islands, often evolve between diverging lineages. These genomic islands may be related to selection promoting adaptation or reproductive isolation. Based on whole genome assembly and genome-wide RAD sequencing in a pair of yellow croakers (genus: <em>Larimichthys</em>), we investigated the evolutionary processes shaping genomic landscapes of divergence. Demographic modelling indicated that the two species diverged following a secondary contact scenario, where differential introgression and linked selection were suggested to be involved in heterogeneous genomic divergence. We identified reduced recombination rate in genomic islands and a relatively good conservation of both genetic diversity and recombination landscapes between species, which highlight the roles of linked selection and recombination rate variation in promoting heterogeneous divergence in the common ancestral lineage of the two species. In addition, we found a positive correlation between differentiation (F<sub>ST</sub>) and absolute sequence divergence (<em>D</em><sub>xy</sub>), and elevated </span><span><span><em>D</em><sub>xy</sub></span> in genomic islands, which were different from the patterns under linked selection. Restricted gene flow in highly differentiated regions has likely remodeled the landscape of heterogeneous genomic divergence. Moreover, genomic islands showed little evidence of overlapping within and between species, implying that high gene flow and divergent selection when colonizing new habitats have reshaped the patterns of intraspecific divergence. This study highlights that highly differentiated genomic regions can also be from linked selection and variation of recombination rate, and thus are not necessarily related to speciation islands or local adaptation. </span></p>
Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
<p>While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of <i>Drosophila pseudoobscura</i> from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a Q<sub>ST</sub>-F<sub>ST</sub> analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short and long read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400kb scale, recombination rate appears to vary largely genome wide, rather than in specific intervals and (3) interpopulation differences in recombination rate may be the result of local adaptation.</p>
Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly
<p>Genetic recombination is a key molecular mechanism that has profound implications on both micro- and macro-evolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly (<em>Leptidea</em> <em>sinapis</em>) shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially due to interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a negligible influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements (TEs), most notably a significant enrichment of SINEs in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination cold-spots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and has particular implications for forthcoming research in population genetics, molecular/genome evolution and speciation.</p>
The code used to simulate range expansion in "The effect of the recombination rate between adaptive loci on the capacity of a population to expand its range"
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Natural selection shapes variation in genome-wide recombination rate in Drosophila pseudoobscura
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Linked selection, differential introgression and recombination rate variation promote heterogeneous divergence in a pair of yellow croakers
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Data from: The effect of parasite infection on the recombination rate of the yellow fever mosquito Aedes aegyti
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Chromosome VCF files and 1Mb recombination rate estimations for: Fine-scale recombination rate variation and association with genomic features in a butterfly
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Data from: Recombination rate variation shapes barriers to introgression across butterfly genomes
Hybridisation and introgression can dramatically alter the relationships among groups of species, leading to phylogenetic discordance across the genome and between populations. Introgression can also erode species differences over time, but selection against introgression at certain loci acts to maintain post-mating species barriers. Theory predicts that species barriers made up of many loci throughout the genome should lead to a broad correlation between introgression and recombination rate, which determines the extent to which selection on deleterious foreign alleles will affect neutral alleles at physically linked loci. Here we describe the variation in genealogical relationships across the genome among three species of Heliconius butterflies: H. melpomene, H. cydno and H. timareta, using whole genomes of 92 individuals, and ask whether this variation can be explained by heterogeneous barriers to introgression. We find that species relationships vary predictably at the chromosomal scale. By quantifying recombination rate and admixture proportions, we then show that rates of introgression are predicted by variation in recombination rate. This implies that species barriers are highly polygenic, with selection acting against introgressed alleles across most of the genome. In addition, long chromosomes, which have lower recombination rates, produce stronger barriers on average than short chromosomes. Finally, we find a consistent difference between two species pairs on either side of the Andes, which suggests differences in the architecture of the species barriers. Our findings illustrate how the combined effects of hybridisation, recombination and natural selection, acting at multitudes of loci over long periods, can dramatically sculpt the phylogenetic relationships among species.
Data from: Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds
Recombination rate is heterogeneous across the genome of various species, and so are genetic diversity and differentiation as a consequence of linked selection. However, we still lack a clear picture of the underlying mechanisms for regulating recombination. Here we estimated fine-scale population recombination rate based on the patterns of linkage disequilibrium (LD) across the genomes of multiple populations of two closely related flycatcher species (Ficedula albicollis and F. hypoleuca). This revealed an overall conservation of the recombination landscape between these species at the scale of 200-kb, but we also identified differences in the local rate of recombination despite their recent divergence (<1 million years). Genetic diversity and differentiation were associated with recombination rate in a lineage-specific manner, indicating differences in the extent of linked selection between species. We detected 400-3,085 recombination hotspots per population. Location of hotspots was conserved between species, but the intensity of hotspot activity varied between species. Recombination hotspots were primarily associated with CpG islands (CGIs), regardless of whether CGIs were at promoter regions or away from genes. Recombination hotspots were also associated with specific transposable elements (TEs), but this association appears indirect due to shared preferences of the transposition machinery and the recombination machinery for accessible open chromatin regions. Our results suggest that CGIs are a major determinant of the localization of recombination hotspots, and we propose that both the distribution of TEs and fine-scale variation in recombination rate may be associated with the evolution of the epigenetic landscape.
Data from: Conservation of the genome-wide recombination rate in white-footed mice
Despite being linked to the fundamental processes of chromosome segregation and offspring diversification, meiotic recombination rates vary within and between species. Recent years have seen progress in quantifying recombination rate evolution across multiple temporal and genomic scales. Nevertheless, the level of variation in recombination rate within wild populations – a key determinant of evolution in this trait – remains poorly documented on the genomic scale. To address this notable gap, we used immunofluorescent cytology to quantify genome-wide recombination rates in a wild population of male white-footed mouse, Peromyscus leucopus. For comparison, we measured recombination rates in a second population of male P. leucopus raised in the laboratory and in a lab strain of deer mouse, Peromyscus maniculatus bairdii. Although we found differences between individuals in the genome-wide recombination rate, levels of variation were low – within populations, between populations, and between species. Quantification of synaptonemal complex length and crossover positions along chromosome 1 using a novel automated approach also revealed conservation in broad-scale crossover patterning, including strong crossover interference. We propose stabilizing selection targeting recombination or correlated processes as the explanation for these patterns.
Supplemental Data to: Variation in recombination rate and its genetic determinism in sheep populations
<p>Supplemental Data to reproduce the analysis of</p> <p><strong>Variation in recombination rate and its genetic determinism in sheep (Ovis Aries) populations from combining multiple genome-wide datasets.</strong></p> <p>Morgane Petit*, Jean-Michel Astruc✝, Julien Sarry*, Laurence Drouilhet*, Stéphane Fabre*, Carole Moreno*, Bertrand Servin*</p> <p>*INRA, Génétique, Physiologie et Systèmes d’Elevage, F-31326 Castanet-Tolosan, France</p> <p>✝Institut de l’Elevage, F-31326 Castanet-Tolosan, France</p> <p><strong>Abstract</strong></p> <p>Recombination is a complex biological process that results from a cascade of multiple events during meiosis. Understanding the genetic determinism of recombination can help to understand if and how these events are interacting. To tackle this question, we studied the patterns of recombination in sheep, using multiple approaches and datasets. We constructed male recombination maps in a dairy breed from the south of France (the Lacaune breed) at a fine scale by combining meiotic recombination rates from a large pedigree genotyped with a 50K SNP array and historical recombination rates from a sample of unrelated individuals genotyped with a 600K SNP array. This analysis revealed recombination patterns in sheep similar to other mammals but also genome regions that have likely been affected by directional and diversifying selection. We estimated the average recombination rate of Lacaune sheep at 1.5 cM/Mb, identified about 50,000 crossover hotspots on the genome and found a high correlation between historical and meiotic recombination rate estimates. A genome-wide association study revealed two major loci affecting inter-individual variation in recombination rate in Lacaune, including the <em>RNF212</em> and<em> HEI10</em> genes and possibly 2 other loci of smaller effects including the <em>KCNJ15</em> and <em>FSHR</em> genes. Finally, we compared our results to those obtained previously in a distantly related population of domestic sheep, the Soay. This comparison revealed that Soay and Lacaune males have a very similar distribution of recombination along the genome and that the two datasets can be combined to create more precise male meiotic recombination maps in sheep. Despite their similar recombination maps, we show that Soay and Lacaune males exhibit different heritabilities and QTL effects for inter-individual variation in genome-wide recombination rates.</p> <p> </p>
Rhometa: Population recombination rate estimation from metagenomic read datasets
<p>Rhometa provides a suite of pipelines for calculating the recombination rate in metagenomic datasets. The tool is developed using Nextflow, a workflow management tool, and the Python programming language. The repository contains all results generated using Rhometa for the manuscript. During the development of Rhometa, various pipelines were employed, including our Nextflow LDhat pipeline. The scripts and results for all pipelines are included. The Github repositories for the pipelines are referenced in the accompanying manuscript. Files named "figure" pertain to the evaluation of simulated data, the simulations themselves have not been included to save space. However, the scripts used to generate the simulations and the final results are included. The file "Lookup_tables.zip" contains lookup tables used in the analysis. The lookup tables are too large to include, but the scripts used to create them are included. Where applicable, experiment accession codes are provided.</p>
Comparison of Radiographic Fusion Rate and Clinical Outcome of ALIF and XLIF Performed With Either Recombinant Human Bone Morphogenetic Protein-2 or ViviGen®
ClinicalTrials.gov study NCT05238740. IPD Sharing: NO. Countries: 1. Publications: 7.
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