Data from: Repeated losses of PRDM9-directed recombination despite the conservation of PRDM9 across vertebrates

Studies of highly diverged species have revealed two mechanisms by which meiotic recombination is directed to the genome—through PRDM9 binding or by targeting promoter-like features—that lead to dramatically different evolutionary dynamics of hotspots. Here, we identify PRDM9 orthologs from genome and transcriptome data in 225 species. We find the complete PRDM9 ortholog across distantly related vertebrates but, despite this broad conservation, infer a minimum of six partial and three complete losses. Strikingly, taxa carrying the complete ortholog of PRDM9 are precisely those with rapid evolution of its predicted binding affinity, suggesting that all domains are necessary for directing recombination. Indeed, as we show, swordtail fish carrying only a partial but conserved ortholog share recombination properties with PRDM9 knock-outs.

对高度分化物种的研究已揭示两种可将减数分裂重组（meiotic recombination）定向至基因组（genome）的机制：通过PRDM9结合，或靶向启动子样特征（promoter-like features），这两种机制会使重组热点产生截然不同的进化动力学。本研究从225个物种的基因组与转录组（transcriptome）数据中鉴定出PRDM9直系同源基因（orthologs）。我们在亲缘关系较远的脊椎动物类群中检测到完整的PRDM9直系同源基因；尽管该基因存在广泛的保守性，但推断其至少发生了6次部分功能缺失与3次完全功能缺失。值得注意的是，携带完整PRDM9直系同源基因的类群，恰恰是其预测结合亲和力快速进化的类群，这表明PRDM9的所有结构域对于指导重组均为必需。正如本研究证实的，仅携带部分保守型PRDM9直系同源基因的剑尾鱼，其重组特性与PRDM9基因敲除（knock-outs）个体一致。