Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden;
Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, SE-752 36 Uppsala, Sweden.
Genome Res. 2023 May;33(5):810-823. doi: 10.1101/gr.277414.122. Epub 2023 Jun 12.
Recombination is a key molecular mechanism that has profound implications on both micro- and macroevolutionary processes. However, the determinants of recombination rate variation in holocentric organisms are poorly understood, in particular in Lepidoptera (moths and butterflies). The wood white butterfly () shows considerable intraspecific variation in chromosome numbers and is a suitable system for studying regional recombination rate variation and its potential molecular underpinnings. Here, we developed a large whole-genome resequencing data set from a population of wood whites to obtain high-resolution recombination maps using linkage disequilibrium information. The analyses revealed that larger chromosomes had a bimodal recombination landscape, potentially caused by interference between simultaneous chiasmata. The recombination rate was significantly lower in subtelomeric regions, with exceptions associated with segregating chromosome rearrangements, showing that fissions and fusions can have considerable effects on the recombination landscape. There was no association between the inferred recombination rate and base composition, supporting a limited influence of GC-biased gene conversion in butterflies. We found significant but variable associations between the recombination rate and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity in recombination coldspots, potentially indicating that expression of transferases can inhibit formation of chiasmata during meiotic division. Our results provide novel information about recombination rate variation in holocentric organisms and have particular implications for forthcoming research in population genetics, molecular/genome evolution, and speciation.
重组是一个关键的分子机制，对微观和宏观进化过程都有深远的影响。然而，在全着丝粒生物中，重组率变化的决定因素还了解甚少，尤其是在鳞翅目（蛾和蝴蝶）中。木白蝶（）在染色体数目上表现出相当大的种内变异，是研究区域重组率变化及其潜在分子基础的合适系统。在这里，我们从木白蝶种群中开发了一个大型全基因组重测序数据集，利用连锁不平衡信息获得了高分辨率的重组图谱。分析表明，较大的染色体具有双峰重组景观，可能是由于同时发生的交叉干扰所致。在端粒区域，重组率显著降低，但与分离的染色体重排相关的区域除外，这表明分裂和融合对重组景观有相当大的影响。推断的重组率与碱基组成之间没有关联，支持了 GC 偏向性基因转换在蝴蝶中影响有限的观点。我们发现重组率与不同类别的转座元件密度之间存在显著但可变的关联，最显著的是在重组率较高的基因组区域中短散布核元件的显著富集。最后，分析揭示了重组率冷点中与法呢基转移酶活性相关的基因显著富集，这可能表明转移酶的表达可以在减数分裂过程中抑制交叉的形成。我们的研究结果提供了全着丝粒生物中重组率变化的新信息，对即将进行的种群遗传学、分子/基因组进化和物种形成研究具有特殊意义。
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