Meiotic recombination is a prominent force shaping genome evolution, and understanding the causes for varying recombination landscapes within and between species has remained a central, though challenging, question. Recombination rates are widely observed to negatively associate with the abundance of transposable elements (TEs), selfish genetic elements that move between genomic locations. While such associations are usually interpreted as recombination influencing the efficacy of selection at removing TEs, accumulating findings suggest that TEs could instead be the cause rather than the consequence. To test this prediction, we formally investigated the influence of polymorphic, putatively active TEs on recombination rates. We developed and benchmarked a novel 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 mobilome can actively modify recombination landscapes, shaping genome evolution within and between species.

减数重组是塑造基因组进化的重要力量，而理解种内和种间重组图谱变化的原因始终是一个核心但极具挑战性的问题。重组率通常被观察到与转座元件（TEs）的丰度呈负相关，这些自私的遗传元素可以在基因组位置之间移动。尽管这种关联通常被解释为重组影响了移除TE的有效选择压力，但积累的研究结果表明，TE可能是原因而不是结果。为了检验这一预测，我们正式研究了多态性、可能活跃的TE对重组率的影响。我们开发并评估了一种新的方法，该方法利用PacBio长读测序技术有效地、准确地和经济地在大量混合的重组个体中识别交换（CO），这是重组的一个关键产物。通过将这种方法应用于具有不同TE插入谱系的果蝇品系，我们发现多态性TEs（尤其是基于RNA的TEs和富含抑制标记的局部TE）会减少CO的发生率。这种效应导致同源序列中有无TE之间CO频率的不同，从而在个体间产生不同的CO图谱。TE对CO的抑制作用进一步得到了两种正交方法的支持：分析重组近交系面板中与TE多态性相关的CO分布，并应用标记辅助估计等基因品系中和转基因插入TE中的CO频率。我们的研究揭示了不断变化的动员体如何主动修改重组景观，从而在种内和种间塑造基因组进化。