Data_Sheet_3_Pinpointing the PRDM9-PRDM7 Gene Duplication Event During Primate Divergence.xlsx

Studies on the function of PRDM9 in model systems and its evolution during vertebrate divergence shed light on the basic molecular mechanisms of hybrid sterility and its evolutionary consequences. However, information regarding PRDM9-homolog, PRDM7, whose origin is placed in the primate evolutionary tree, as well as information about the fast-evolving DNA-binding zinc finger array of strepsirrhine PRDM9 are scarce. Thus, we aimed to narrow down the date of the duplication event leading to the emergence of PRDM7 during primate evolution by comparing the phylogenetic tree reconstructions of representative primate samples of PRDM orthologs and paralogs. To confirm our PRDM7 paralogization pattern, database-deposited sequences were used to test the presence/absence patterns expected from the paralogization timing. In addition, we extended the existing phylogenetic tree of haplorrhine PRDM9 zinc fingers with their strepsirrhine counterparts. The inclusion of strepsirrhine zinc fingers completes the PRDM9 primate phylogeny. Moreover, the updated phylogeny of PRDM9 zinc fingers showed distinct clusters of strepsirrhine, tarsier, and anthropoid degenerated zinc fingers. Here, we show that PRDM7 emerged on the branch leading to the most recent common ancestor of catarrhines; therefore, its origin is more recent than previously expected. A more detailed character evolutionary study suggests that PRDM7 may have evolved differently in Cercopithecoidea as compared to Hominoidea: it lacks the first four exons in Old World monkeys orthologs and exon 10 in Papionini orthologs. Dating the origin of PRDM7 is essential for further studies investigating why Hominoidea representatives need another putative histone methyltransferase in the testis.

针对PRDM9在模式生物中的功能及其在脊椎动物分化过程中的演化开展的研究，已为杂种不育的核心分子机制及其演化后果提供了重要见解。然而，关于起源于灵长类演化谱系的PRDM9同源基因PRDM7的相关信息，以及原猴亚目（Strepsirrhini）PRDM9快速演化的DNA结合锌指阵列的相关资料仍较为匮乏。为此，本研究通过比对PRDM直系同源与旁系同源基因的代表性灵长类样本的系统发育树重构结果，旨在精准缩小导致PRDM7在灵长类演化过程中出现的基因复制事件的发生时间范围。为验证我们推导的PRDM7旁系演化模式，本研究利用数据库中已提交的序列，检验了与旁系复制发生时间相符的基因存在/缺失特征。此外，我们将现有简鼻亚目（Haplorrhini）PRDM9锌指阵列的系统发育树进行了扩展，纳入了原猴亚目对应的同源序列。纳入原猴亚目锌指序列后，灵长类PRDM9的系统发育树得以完整构建。此外，更新后的PRDM9锌指阵列系统发育树显示，原猴亚目、眼镜猴以及类人猿的退化锌指结构各自形成了独立的聚类分支。本研究证实，PRDM7起源于狭鼻小目（Catarrhini）最近共同祖先所在的演化分支，因此其出现时间较此前的预期更为晚近。更为细致的性状演化分析表明，与类人猿总科相比，猕猴总科中PRDM7的演化路径存在显著差异：旧世界猴的同源基因缺失了前四个外显子，而狒狒族的同源基因则缺失了第10号外显子。精准确定PRDM7的起源时间，对于后续探究类人猿总科物种为何需要在睾丸中表达另一种潜在组蛋白甲基转移酶的相关研究至关重要。