Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises

作者：Mingli Li, Sheng Wang, Penghui Xu, Hang-Yu Tian, Mixue Bai, Ya‐Ping Zhang, Yong Shao, Zijun Xiong, Xiao‐Guang Qi, D.N. Cooper, Guojie Zhang, He Helen Zhu, Dong‐Dong Wu · 发表于：Proceedings of the National Academy of Sciences · 年份：2022 · DOI：10.1073/pnas.2123030119 · 被引用次数：12 · 研究领域：Primate Behavior and Ecology、Bat Biology and Ecology Studies、Genomics and Phylogenetic Studies

Lorises are a group of globally threatened strepsirrhine primates that exhibit many unusual physiological and behavioral features, including a low metabolic rate, slow movement, and hibernation. Here, we assembled a chromosome-level genome sequence of the pygmy loris ( Xanthonycticebus pygmaeus ) and resequenced whole genomes from 50 pygmy lorises and 6 Bengal slow lorises ( Nycticebus bengalensis ). We found that many gene families involved in detoxification have been specifically expanded in the pygmy loris, including the GSTA gene family, with many newly derived copies functioning specifically in the liver. We detected many genes displaying evolutionary convergence between pygmy loris and koala, including PITRM1. Significant decreases in PITRM1 enzymatic activity in these two species may have contributed to their characteristic low rate of metabolism. We also detected many evolutionarily convergent genes and positively selected genes in the pygmy loris that are involved in muscle development. Functional assays demonstrated the decreased ability of one positively selected gene, MYOF, to up-regulate the fast-type muscle fiber, consistent with the lower proportion of fast-twitch muscle fibers in the pygmy loris. The protein product of another positively selected gene in the pygmy loris, PER2 , exhibited weaker binding to the key circadian core protein CRY, a finding that may be related to this species’ unusual circadian rhythm. Finally, population genomics analysis revealed t...