Data from: The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms

Background: Although 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. Results: Recombination 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. Conclusions: Although 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.

背景：尽管同源重组（homologous recombination）会影响种群内选择的效率，但被子植物（angiosperms）的重组率进化模式及其对基因组进化的影响目前仍未得到充分解析。重组可通过清除长末端重复序列逆转录转座子（LTR retrotransposons）缩小基因组大小，通过GC偏向性基因转换改变密码子使用偏好，通过串联重复参与基因重复与丢失的复杂演化历程，并强化对基因的纯化选择（purifying selection）。因此，物种间重组率的差异或许可以解释基因组结构与分子进化速率的部分变异。本研究采用系统发育比较方法（phylogenetic comparative methods），利用30种被子植物的遗传图谱与基因组序列，探究了全局减数分裂重组率（meiotic recombination rate）的演化规律及其对基因组结构和分子水平选择的影响。
结果：重组率与基因组大小呈负相关，这一现象可能由长末端重复序列逆转录转座子的清除所导致。在校正常染色质（euchromatin）含量对重组率的影响后，本研究还发现全局重组率与平均基因家族大小存在显著关联，这表明重组可能在保留重复基因或扩张基因家族的过程中发挥作用。对3748个基因的非同义替换率与同义替换率之比（dN/dS）与重组率的相关性分析显示，更高的重组率与更强的纯化选择效率相关，这表明全局重组率会影响远缘被子植物类群间的分子进化速率变异，而非仅局限于种群内部。此外，本研究还鉴定到，在本次研究的被子植物类群中，与全局重组率转变相关的重组蛋白编码基因的dN/dS发生了显著改变。
结论：尽管本研究仅揭示了相关性而非作用机制，且未纳入重组率的潜在协变量（如有效种群大小（effective population size）），但研究结果表明，全局重组率可能在塑造植物基因与基因组进化的宏观进化模式方面发挥重要作用。种间重组率变异与基因组大小以及整体长末端重复序列逆转录转座子的丰度变异均呈显著相关。重组或许会塑造物种间基因间的dN/dS变异，这可能会影响整体的基因重复与丢失速率。