Meiotic recombination in vertebrates is concentrated in hotspots throughout the genome. The location and stability of hotspots have been linked to the presence or absence of PRDM9, leading to two primary models for hotspot evolution derived from mammals and birds. Species with PRDM9-directed recombination have rapid turnover of hotspots concentrated in intergenic regions (i.e., mammals), whereas hotspots in species lacking PRDM9 are concentrated in functional regions and have greater stability over time (i.e., birds). Snakes possess PRDM9, yet virtually nothing is known about snake recombination. Here, we examine the recombination landscape and test hypotheses about the roles of PRDM9 in rattlesnakes. We find substantial variation in recombination rate within and among snake chromosomes, and positive correlations between recombination rate and gene density, GC content, and genetic diversity. Like mammals, snakes appear to have a functional and active PRDM9, but rather than being directed away from genes, snake hotspots are concentrated in promoters and functional regions-a pattern previously associated only with species that lack a functional PRDM9. Snakes therefore provide a unique example of recombination landscapes in which PRDM9 is functional, yet recombination hotspots are associated with functional genic regions-a combination of features that defy existing paradigms for recombination landscapes in vertebrates. Our findings also provide evidence that high recombination rates are a shared feature of vertebrate microchromosomes. Our results challenge previous assumptions about the adaptive role of PRDM9 and highlight the diversity of recombination landscape features among vertebrate lineages.

中文翻译：

---

尽管有PRDM9，但蛇的重组景观仍集中在功能区域中。

脊椎动物的减数分裂重组集中在整个基因组的热点中。热点的位置和稳定性与PRDM9的存在与否有关，从而导致了两个主要的哺乳动物和鸟类热点进化模型。具有PRDM9指导重组的物种热点集中在基因间区域（即哺乳动物）中，其快速更新，而缺乏PRDM9物种中的热点聚集在功能区域中，并且随着时间的推移具有更高的稳定性（即鸟类）。蛇拥有PRDM9，但实际上对蛇重组一无所知。在这里，我们检查重组格局，并测试有关PRDM9在响尾蛇中的作用的假设。我们发现蛇染色体内和蛇染色体之间的重组率存在很大差异，重组率与基因密度，GC含量和遗传多样性之间呈正相关。像哺乳动物一样，蛇似乎具有功能性和活动性的PRDM9，但是蛇的热点并没有远离基因，而是集中在启动子和功能区中-这种模式以前仅与缺少功能性PRDM9的物种有关。因此，蛇提供了PRDM9在其中起作用的重组格局的独特示例，而重组热点却与功能性基因区域相关联-这些特征的组合违背了脊椎动物中重组格局的现有范例。我们的发现还提供证据表明高重组率是脊椎动物微染色体的一个共同特征。