Data from: Genetic and evolutionary correlates of fine-scale recombination rate variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed “recombinational neighborhoods,” where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5–7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.重组（Recombination）是众多物种减数分裂的核心过程，可为自然选择提供可作用的遗传变异，但精细连锁图谱的构建却颇为繁琐。我们利用覆盖5条主要染色体臂中2条的181个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，构建了拟暗果蝇（Drosophila persimilis）两条主要染色体的精细重组率图谱。借助该图谱，我们发现局部重组率存在显著的精细尺度异质性。然而在排除着丝粒与端粒附近区域后，我们还观察到了“重组邻域”现象：相邻区间的重组率较为相似。我们进一步发现，精细尺度的重组率与重复元件丰度、以及已知与人类重组率相关的13bp序列基序存在显著正相关。我们还观察到，初始交叉事件可引发长达5-7 Mb的强交叉干涉（crossover interference）。此外，我们发现拟暗果蝇的精细重组率与其姊妹物种伪暗果蝇（Drosophila pseudoobscura）的同类研究所得结果存在极强相关性。我们证实，物种内核苷酸序列多样性与重组率存在显著关联，但物种间内含子序列分化与重组率并无关联。上述结果契合选择模型（即搭车效应与背景选择），而非诱变重组模型，可用于解释重组与物种内核苷酸多样性之间的关联。最后，我们发现重组率与GC含量存在显著相关性，这支持了GC偏向性基因转换（GC-biased gene conversion, BGC）模型以及选择驱动的密码子偏好性模型。总体而言，这份基于基因组学的精细重组率图谱不仅验证了大规模研究的结论，还鉴定出多项值得深入探究的全新特征。