Meiotic recombination is a prominent force shaping genome evolution, and understanding why recombination rates vary within and between species has remained a central, though challenging, question. Variation in recombination is widely thought to influence the efficacy of selection in purging transposable elements (TEs), prevalent selfish genetic elements, leading to widely observed negative correlations between TE abundance and recombination rates across taxa. However, accumulating evidence suggests that TEs could instead be the cause rather than the consequence of this relationship. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked an approach that uses PacBio long-read sequencing to efficiently, accurately, and cost-effectively identify crossovers (COs), a key recombination product, among large numbers of pooled recombinant individuals. By applying this approach to Drosophila strains with distinct TE insertion profiles, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, reduce the occurrence of COs. Such an effect leads to different CO frequencies between homologous sequences with and without TEs, contributing to varying CO maps between individuals. The suppressive effect of TEs on CO is further supported by two orthogonal approaches–analyzing the distributions of COs in panels of recombinant inbred lines in relation to TE polymorphism and applying marker-assisted estimations of CO frequencies to isogenic strains with and without transgenically inserted TEs. Our investigations reveal how the constantly changing TE landscape can actively modify recombination, shaping genome evolution within and between species.

中文翻译：

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多态性转座因子导致重组景观的变化


减数分裂重组是塑造基因组进化的重要力量，理解为什么物种内部和物种之间的重组率不同仍然是一个核心问题，尽管具有挑战性。重组的变异被广泛认为会影响清除转座因子 （TE）（普遍的自私遗传元件）的选择功效，导致广泛观察到的 TE 丰度与分类群重组率之间的负相关。然而，越来越多的证据表明，TE 可能是这种关系的原因而不是结果。为了验证这一预测，我们正式研究了多态性、假定活性 TE 对重组率的影响。我们开发了一种方法并进行了基准测试，该方法使用 PacBio 长读长测序来高效、准确和经济地识别大量混合重组个体中的交叉 （CO），这是一种关键的重组产物。通过将这种方法应用于具有不同 TE 插入曲线的果蝇菌株，我们发现多态性 TE，尤其是基于 RNA 的 TE 和具有抑制标记局部富集的 TE，减少了 CO 的发生。这种效应导致有和没有 TE 的同源序列之间的 CO 频率不同，从而导致个体之间的 CO 图谱不同。两种正交方法进一步支持 TE 对 CO 的抑制作用——分析与 TE 多态性相关的重组自交系面板中 COs 的分布，并将 CO 频率的标记辅助估计应用于有和没有转基因插入的 TE 的同基因菌株。我们的研究揭示了不断变化的 TE 景观如何主动改变重组，塑造物种内部和物种之间的基因组进化。