GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Mugal, Carina F.; Weber, Claudia; Ellegren, Hans

doi:10.1002/bies.201500058

Cited by 71 publications

(42 citation statements)

References 124 publications

(187 reference statements)

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“…vinifera ). Recalling that B = 4 N e rb 0 (see Introduction), this could be explained by changes in effective population size ( N e ) recombination rate ( r ), gBGC intensity per recombination event ( b 0 ) and also conversion tract length, which might also vary among species [60]. To date, we do not know anything about the stability of b 0 across generations and how fast it can evolve.…”

Section: Discussionmentioning

confidence: 99%

Evolutionary forces affecting synonymous variations in plant genomes

et al. 2017

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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.

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Section: Discussionmentioning

confidence: 99%

Evolutionary forces affecting synonymous variations in plant genomes

et al. 2017

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“…Preferential fixation of "strong" bases (S) over "weak" bases (W) by gBGC leaves footprints mimicking directional selection by skewing the site frequency spectrum at sites with S-W polymorphisms (Duret & Galtier, 2009;Glemin et al, 2015;Mugal, Weber, & Ellegren, 2015).…”

Section: Strength Of Gbgcmentioning

confidence: 99%

Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

et al. 2017

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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 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.

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“…GC-biased gene conversion (gBGC) belongs to widely evidenced hypotheses and states that regions with higher recombination rates contain higher local GC content (Lartillot 2013;Mugal et al, 2013Mugal et al, , 2015b. In gars, the centromeres, the majority of very small chromosomes, and some short chromosomal arms (all anticipated high-recombining regions), together with a number of other regions, are distinctly GC-rich ( Fig.…”

Section: Gc-biased Gene Conversionmentioning

confidence: 99%

Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray‐Finned Fish

et al. 2016

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Genomic GC content can vary locally, and GC-rich regions are usually associated with increased DNA thermostability in thermophilic prokaryotes and warm-blooded eukaryotes. Among vertebrates, fish and amphibians appeared to possess a distinctly less heterogeneous AT/GC organization in their genomes, whereas cytogenetically detectable GC heterogeneity has so far only been documented in mammals and birds. The subject of our study is the gar, an ancient "living fossil" of a basal ray-finned fish lineage, known from the Cretaceous period. We carried out cytogenomic analysis in two gar genera (Atractosteus and Lepisosteus) uncovering a GC chromosomal pattern uncharacteristic for fish. Bioinformatic analysis of the spotted gar (Lepisosteus oculatus) confirmed a GC compartmentalization on GC profiles of linkage groups. This indicates a rather mammalian mode of compositional organization on gar chromosomes. Gars are thus the only analyzed extant ray-finned fishes with a GC compartmentalized genome. Since gars are cold-blooded anamniotes, our results contradict the generally accepted hypothesis that the phylogenomic onset of GC compartmentalization occurred near the origin of amniotes. Ecophysiological findings of other authors indicate a metabolic similarity of gars with mammals. We hypothesize that gars might have undergone convergent evolution with the tetrapod lineages leading to mammals on both metabolic and genomic levels. Their metabolic adaptations might have left footprints in their compositional genome evolution, as proposed by the metabolic rate hypothesis. The genome organization described here in gars sheds new light on the compositional genome evolution in vertebrates generally and contributes to better understanding of the complexities of the mechanisms involved in this process.

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GC‐biased gene conversion links the recombination landscape and demography to genomic base composition

Cited by 71 publications

References 124 publications

Evolutionary forces affecting synonymous variations in plant genomes

Evolutionary forces affecting synonymous variations in plant genomes

Whole‐genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine‐scale recombination rate variation in birds

Genome Compositional Organization in Gars Shows More Similarities to Mammals than to Other Ray‐Finned Fish

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