TE impacts recombination

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 influences the efficacy of selection removing TEs, accumulating findings suggest TEs could instead be the cause rather than the consequence. To test this prediction, we formally investigated the influence of polymorphic, putatively still active TEs on recombination rates. We achieved this by comparing the distribution of crossovers (COs), a key recombination product, between homologous alleles with and without TEs of two Drosophila strains with distinct TE insertion profiles. We developed a novel approach that uses PacBio long-read sequencing to efficiently and accurately identify COs among large numbers of pooled recombinant individuals. Supporting our prediction that TEs can directly influence recombination, we found that polymorphic TEs, especially RNA-based TEs and TEs with local enrichment of repressive marks, negatively impact the occurrence of COs, which contributes to varying CO maps between individuals.