High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

Smeds, Linnéa; Mugal, Carina F.; Qvarnström, Anna; Ellegren, Hans

doi:10.1371/journal.pgen.1006044

Cited by 85 publications

(92 citation statements)

References 112 publications

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“…This resolution has never been reached in wheat before and was close to the one observed for the four hotspots described in rice (Wu et al 2003). In the collared flycatcher, a songbird species, 279 COs were localized within intervals of ,10 kb (Smeds et al 2016) which was only 1.8 times more compared to our analysis (156 COs) while the wheat genome is 17 times larger. Similarly in human, genome-wide sperm sequencing allowed mapping of 13-45% of COs in 30-kb intervals (Lu et al 2012;Wang et al 2012) showing that even in a highly documented genome sixfold smaller than that of wheat, reaching a resolution lower than 30 kb is difficult.…”

Section: Discussionsupporting

confidence: 86%

“…At the whole-genome level, similar results were found with 2/3 of COs overlapping genes, as this is the case for most COs in plants (reviewed in Mercier et al 2015). Our COs were found in the gene body and slightly more frequently in promoters and terminators, confirming the results observed in Arabidopsis (Choi et al 2013) as well as in avian (Singhal et al 2015;Smeds et al 2016) and in Saccharomyces species (Lam and Keeney 2015), where recombination pattern is highly conserved and localized to the promoter (TSS) and terminator (TTS) regions.…”

Section: Retrotransposons Associate With Reduced Recombination Ratesupporting

confidence: 89%

“…In avian (Singhal et al 2015;Smeds et al 2016) and in Saccharomyces species (Lam and Keeney 2015), recombination patterns are highly conserved during evolution. This led us to assay using another approach to reveal historical recombination using LD and coalescent theory (r-map) (Li and Stephens 2003;Crawford et al 2004) in wheat.…”

Section: Discussionmentioning

confidence: 99%

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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry 60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F 6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (,26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. KEYWORDS recombination; meiosis; bread wheat; linkage disequilibrium; transposon; hotspot; sequence motif M EIOTIC recombination is a process that allows reshuffling of diversity by the reciprocal exchange of DNA called a crossover (CO). This phenomenon is conserved in most eukaryotes (for a review see Mercier et al. 2015) and follows the formation of a double-strand break (DSB) of DNA generated by the topoisomerase SPO11 complex. However, the number of DSBs is at least 10-to 50-fold greater than the number of COs which rarely exceeds three per bivalent chromosome per meiosis (Mercier et al. 2015). This paucity of COs per meiosis with regards to the number of DSBs suggests the existence of a tight control and regulation of recombination in plants that promote DSB repair in a manner that does not lead to COs. For example, the study of the two helicases AtFANCM and RECQ4 (AtRECQ4A and AtRECQ4B) (Crismani et al. 2012;Knoll et al. 2012;Girard et al. 2014;Séguéla-Arnaud et al. 2015) revealed three-and sixfold CO frequency increases in the Atfancm single mutant and the Atrecq4a/Atrecq4b double mutant, respectively, compared to the wild type. These increases result from additional COs from the class-II pathway which suggests that FANCM and RECQ4 prevent CO formation and direct recombination intermediates towar...

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Section: Discussionsupporting

confidence: 86%

Section: Retrotransposons Associate With Reduced Recombination Ratesupporting

confidence: 89%

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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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“…For practical reasons cultivated species have been chosen but we only sampled wild individuals over the species range, except for palm tree for which cultivated individuals were sampled (See S1 Table for sampling details). In this species cultivation is very recent without real domestication process (19 th century [45]). For each species, we used RNA-seq techniques to sequence the transcriptome of about ten individuals plus two individuals from two outgroup species, giving a total of 130 individual transcriptomes.…”

Section: Resultsmentioning

confidence: 99%

“…A phylogeny of these species is shown in Fig 1. For practical reasons, we chose diploid cultivated species but focused our analysis on wild populations except in Elaeis guineensis where domestication is very recent and limited (19 th century [45]). Using the same methodology as [48], we sequenced for each species the transcriptome of ten individuals (12 in the case of C. canephora and V. vinifera, nine in the case of S. bicolor and five in the case of D. abyssinica) plus two individuals coming from two outgroup species, using RNA-seq (see S3 Text for details).…”

Section: Datasetmentioning

confidence: 99%

Evolutionary forces affecting synonymous variations in plant genomes

Clément

Sarah

Homa

et al. 2016

Preprint

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Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.PLOS Genetics | https://doi.org/10.1371/journal.pgen

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Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds

et al. 2018

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Heterogeneous patterns of genomic differentiation are commonly documented between closely related populations and there is considerable interest in identifying factors that contribute to their formation. These factors could include genomic features (e.g., areas of low recombination) that promote processes like linked selection (positive or purifying selection that affects linked neutral sites) at specific genomic regions. Examinations of repeatable patterns of differentiation across population pairs can provide insight into the role of these factors. Birds are well suited for this work, as genome structure is conserved across this group. Accordingly, we reestimated relative (FST) and absolute (dXY) differentiation between eight sister pairs of birds that span a broad taxonomic range using a common pipeline. Across pairs, there were modest but significant correlations in window‐based estimates of differentiation (up to 3% of variation explained for FST and 26% for dXY), supporting a role for processes at conserved genomic features in generating heterogeneous patterns of differentiation; processes specific to each episode of population divergence likely explain the remaining variation. The role genomic features play was reinforced by linear models identifying several genomic variables (e.g., gene densities) as significant predictors of FST and dXY repeatability. FST repeatability was higher among pairs that were further along the speciation continuum (i.e., more reproductively isolated) providing further insight into how genomic differentiation changes with population divergence; early stages of speciation may be dominated by positive selection that is different between pairs but becomes integrated with processes acting according to shared genomic features as speciation proceeds.

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High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree

Cited by 85 publications

References 112 publications

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

Evolutionary forces affecting synonymous variations in plant genomes

Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds

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