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2,180 results for “Recombination”
Data from: The recombination landscape in Arabidopsis thaliana F2 populations
Recombination during meiosis shapes the complement of alleles segregating in the progeny of hybrids, and has important consequences for phenotypic variation. We examined allele frequencies as well as crossover locations and frequencies in over 7000 plants from 17 F2 populations derived from crosses between 18 Arabidopsis thaliana accessions. We observe segregation distortion between parental alleles in over half of our populations. The potential causes of distortion include variation in seed dormancy and lethal epistatic interactions. Such a high occurrence of distortion was only detected here because of the large sample size of each population, and the number of populations characterized. Most plants carry only one or two crossovers per chromosome pair, and therefore inherit very large, non-recombined genomic fragments from each parent. Recombination frequencies vary between populations but consistently increase adjacent to the centromeres. Importantly, recombination rates do not correlate with whole-genome sequence differences between parental accessions, suggesting that sequence diversity within A. thaliana does not normally reach levels that are high enough to exert a major influence on the formation of crossovers. A global knowledge of the patterns of recombination in F2 populations is crucial to better understand the segregation of phenotypic traits in hybrids, in the laboratory or in the wild.
Data from: Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures
Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.
Data from: Male-mediated effects on female meiotic recombination
Recombination rates vary owing to an individual's genetic composition and/or its environmental condition. Yet, the effects of mating partner on recombination rates have not been considered. Here, I document a previously undescribed male-mediated effect on female recombination rates. After crossing females to males from different genetic backgrounds, I observed a significant difference in proportion of recombinant offspring based on the genetic background of the father (p=0.0292; 3 df; F=3.07). Genetic variation in male ability to affect recombination rate in their mates suggests the potential for sexual conflict on optimal proportion of recombinant offspring, perhaps leading to changes in population-level recombination rates with varying levels of sexual selection.
Data from: First dating of a recombination event in mammalian tick-borne flaviviruses
The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus TBEV. We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window period of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses
Data from: The kinetochore prevents centromere-proximal crossover recombination during meiosis
During meiosis, crossover recombination is essential to link homologous chromosomes and drive 22 faithful chromosome segregation. Crossover recombination is non-random across the genome, 23 and centromere-proximal crossovers are associated with an increased risk of aneuploidy, 24 including Trisomy 21 in humans. Here, we identify the conserved Ctf19/CCAN kinetochore sub- 25 complex as a major factor that minimizes potentially deleterious centromere-proximal crossovers 26 in budding yeast. We uncover multi-layered suppression of pericentromeric recombination by the 27 Ctf19 complex, operating across distinct chromosomal distances. The Ctf19 complex prevents 28 meiotic DNA break formation, the initiating event of recombination, proximal to the centromere. 29 The Ctf19 complex independently drives the enrichment of cohesin throughout the broader 30 pericentromere to suppress crossovers, but not DNA breaks. This non-canonical role of the 31 kinetochore in defining a chromosome domain that is refractory to crossovers adds a new layer 32 of functionality by which the kinetochore prevents the incidence of chromosome segregation 33 errors that generate aneuploid gametes.
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: Mlh3 mutations in baker's yeast alter meiotic recombination outcomes by increasing noncrossover events genome-wide
Mlh1-Mlh3 is an endonuclease hypothesized to act in meiosis to resolve double Holliday junctions into crossovers. It also plays a minor role in eukaryotic DNA mismatch repair (MMR). To understand how Mlh1-Mlh3 functions in both meiosis and MMR, we analyzed in baker's yeast 60 new mlh3 alleles. Five alleles specifically disrupted MMR, whereas one (mlh3-32) specifically disrupted meiotic crossing over. Mlh1-mlh3 representatives for each class were purified and characterized. Both Mlh1-mlh3-32 (MMR+, crossover-) and Mlh1-mlh3-45 (MMR-, crossover+) displayed wild-type endonuclease activities in vitro. Msh2-Msh3, an MSH complex that acts with Mlh1-Mlh3 in MMR, stimulated the endonuclease activity of Mlh1-mlh3-32 but not Mlh1-mlh3-45, suggesting that Mlh1-mlh3-45 is defective in MSH interactions. Whole genome recombination maps were constructed for wild-type and MMR+ crossover-, MMR- crossover+, endonuclease defective and null mlh3 mutants in an S288c/YJM789 hybrid background. Compared to wild-type, all of the mlh3 mutants showed increases in the number of noncrossover events, consistent with recombination intermediates being resolved through alternative recombination pathways. Our observations provide a structure-function map for Mlh3 that reveals the importance of protein-protein interactions in regulating Mlh1-Mlh3's enzymatic activity. They also illustrate how defective meiotic components can alter the fate of meiotic recombination intermediates, providing new insights for how meiotic recombination pathways are regulated.
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: Controlling meiotic recombinational repair: specifying the roles of ZMMs, Sgs1 and Mus81/Mms4 in crossover formation
Crossovers (COs) play a critical role in ensuring proper alignment and segregation of homologous chromosomes during meiosis. How the cell balances recombination between CO vs. noncrossover (NCO) outcomes is not completely understood. Further lacking is what constrains the extent of DNA repair such that multiple events do not arise from a single double-strand break (DSB). Here, by interpreting signatures that result from recombination genome-wide, we find that synaptonemal complex proteins promote crossing over in distinct ways. Our results suggest that Zip3 (RNF212) promotes biased cutting of the double Holliday-junction (dHJ) intermediate whereas surprisingly Msh4 does not. Moreover, detailed examination of conversion tracts in sgs1 and mms4-md mutants reveal distinct aberrant recombination events involving multiple chromatid invasions. In sgs1 mutants, these multiple invasions are generally multichromatid involving 3–4 chromatids; in mms4-md mutants the multiple invasions preferentially resolve into one or two chromatids. Our analysis suggests that Mus81/Mms4 (Eme1), rather than just being a minor resolvase for COs is crucial for both COs and NCOs in preventing chromosome entanglements by removing 3′- flaps to promote second-end capture. Together our results force a reevaluation of how key recombination enzymes collaborate to specify the outcome of meiotic DNA repair.
Data from: The effect of deleterious mutations and age on recombination in Drosophila melanogaster
At the population level, recombination mediates the efficiency with which selection can eliminate deleterious mutations. At the individual level, deleterious alleles may influence recombination, which would change the rate at which linkage disequilibrium is eroded and thereby alter the efficiency with which deleterious alleles are purged. Here we test whether the presence of a deleterious allele on one autosome affects recombination on another autosome. We find that deleterious alleles not only alter the rate but also the pattern of recombination. However, there is little support that different deleterious alleles affect recombination in a consistent manner. Because we have detailed information on individual females across their life times, we are able to examine how recombination patterns change with age and find that these patterns are also affected by the presence of deleterious alleles. The differences among genotypes or among age classes is large enough to add substantial noise to genetic mapping experiments that do not consider these sources of variation.
Data from: Construction of ultra-dense linkage maps with Lep-MAP2: stickleback F2 recombinant crosses as an example
High-density linkage maps are important tools for genome biology and evolutionary genetics by quantifying the extent of recombination, linkage disequilibrium and chromosomal rearrangements across chromosomes, sexes and populations. They provide one of the best ways to validate and refine de novo genome assemblies, with the power to identify errors in assemblies increasing with marker density. However, assembly of high-density linkage maps is still challenging due to software limitations. We describe Lep-MAP2, a software for ultra-dense genome-wide linkage map construction. Lep-MAP2 can handle various family structures and can account for achiasmatic meiosis to gain linkage map accuracy. Simulations show that Lep-MAP2 outperforms other available mapping software both in computational efficiency and accuracy. When applied to two large F2-generation recombinant crosses between two nine-spined stickleback (Pungitius pungitius) populations, it produced two high-density (~6 markers/cM) linkage maps containing 18 691 and 20 054 SNPs. The two maps showed a high degree of synteny, but female maps were 1.5 to 2 times longer than male maps in all linkage groups, suggesting genome-wide recombination suppression in males. Comparison with the genome sequence of the three-spined stickleback (Gasterosteus aculeatus) revealed a high degree of interspecific synteny with a low frequency (<5%) of interchromosomal re-arrangements. However, a fairly large (ca. 10Mb) translocation from autosome to sex chromosome was detected in both maps. These results illustrate the utility and novel features of Lep-MAP2 in assembling high-density linkage maps, and their usefulness in revealing evolutionarily interesting properties of genomes, such as strong genome-wide sex-bias in recombination rates.
mTORC1 in thymic epithelial cells is critical for thymopoiesis, T-cell generation, and temporal control of gdT17 development and TCRg/d recombination
<p>FCS Files for Fig 1 to Fig 11</p>
Script and data for "rec-1 loss of function increases recombination in the central gene clusters at the expense of autosomal pairing centers"
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High prevalence of Prdm9-independent recombination hotspots in placental mammals
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Figure 4 from: Shkondrov A, Kondeva-Burdina M, Stambolov I, Krasteva I (2024) Activity of an oleanane-type tritrepenoid saponin from A. glycyphyllos on human recombinant MAO enzymes. Pharmacia 71: 1-6. https://doi.org/10.3897/pharmacia.71.e114786
Figure 4 Effect of Sg and Selegiline (at concentrations of 0.050, 0.250, 0.500, 0.750, and 1 μM) on human recombinant MAOA enzyme (hMAOB) activity. ** P < 0.01; *** P < 0.001 vs. control (pure hMAOB).
Figure 3 from: Shkondrov A, Kondeva-Burdina M, Stambolov I, Krasteva I (2024) Activity of an oleanane-type tritrepenoid saponin from A. glycyphyllos on human recombinant MAO enzymes. Pharmacia 71: 1-6. https://doi.org/10.3897/pharmacia.71.e114786
Figure 3 Effect of Sg and Chlorgyline (at concentrations of 0.050, 0.250, 0.500, 0.750, and 1 μM) on the activity (%) of human recombinant MAOA enzyme (hMAOA). * P < 0.05; ** P < 0.01; *** P < 0.001 vs. control (pure hMAOA).
Generation and Recombination of a carrier
<p>Generation and Recombination of a carrier</p>
Patterns of recombination in snakes reveal a tug of war between PRDM9 and promoter-like features
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Figure 1 in Placebo-Controlled Phase 3 Trial of a Recombinant Glycoprotein 120 Vaccine to Prevent HIV-1 Infection
Figure 1. Flow of study participants in the present trial (VAX004). rgp, recombinant glycoprotein.
Technical evaluation of recombinant-Ag-based InBios ELISA for the diagnosis of S Stercoralis
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