Abstract
BackgroundAlthough homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. Recombination can reduce genome size by enabling the removal of LTR retrotransposons, alter codon usage by GC biased gene conversion, contribute to complex histories of gene duplication and loss through tandem duplication, and enhance purifying selection on genes. Therefore, variation in recombination rate across species may explain some of the variation in genomic architecture as well as rates of molecular evolution. We used phylogenetic comparative methods to investigate the evolution of global meiotic recombination rate in angiosperms and its effects on genome architecture and selection at the molecular level using genetic maps and genome sequences from thirty angiosperm species.ResultsRecombination rate is negatively correlated with genome size, which is likely caused by the removal of LTR retrotransposons. After correcting recombination rates for euchromatin content, we also found an association between global recombination rate and average gene family size. This suggests a role for recombination in the preservation of duplicate genes or expansion of gene families. An analysis of the correlation between the ratio of nonsynonymous to synonymous substitution rates (dN/dS) and recombination rate in 3748 genes indicates that higher recombination rates are associated with an increased efficacy of purifying selection, suggesting that global recombination rates affect variation in rates of molecular evolution across distantly related angiosperm species, not just between populations. We also identified shifts in dN/dS for recombination proteins that are associated with shifts in global recombination rate across our sample of angiosperms.ConclusionsAlthough our analyses only reveal correlations, not mechanisms, and do not include potential covariates of recombination rate, like effective population size, they suggest that global recombination rates may play an important role in shaping the macroevolutionary patterns of gene and genome evolution in plants. Interspecific recombination rate variation is tightly correlated with genome size as well as variation in overall LTR retrotransposon abundances. Recombination may shape gene-to-gene variation in dN/dS between species, which might impact the overall gene duplication and loss rates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0473-3) contains supplementary material, which is available to authorized users.
Highlights
Homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown
We examined the relationship between global recombination rate and total genome size, genome size without long terminal repeat (LTR) retrotransposon content, the relative abundance of LTR retrotransposons, gene density, and gene family size
Euchromatin corrected recombination rate, genome size, the proportion of the genome that consists of LTR retrotransposons, and average gene family size do not deviate significantly from Brownian motion
Summary
Homologous recombination affects the efficacy of selection in populations, the pattern of recombination rate evolution and its effects on genome evolution across plants are largely unknown. We take advantage of these new data to explore the relationship between recombination rate, genome structure, and patterns of molecular evolution throughout angiosperms in order to better characterize the broad macroevolutionary patterns of recombination rate variation and its possible consequences for genome evolution. Recombination affects both genome architecture and evolutionary rates. Rees and Durrant [7] corroborated this result in a study of the genera Lathyrus, Lolium, and Petunia and by Narayan and McIntyre [8] in Lathyrus Both of these studies estimated nuclear genome size in picograms per haploid genome (C-values) and recombination rates based on observable chiasma from pachytene chromosomes. The number of crossovers per chromosome arm is variable [9], and Ross-Ibarra [10] demonstrated a positive correlation between genome size and the number of chiasmata per chromosome arm across 279 angiosperm species from 22 families
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