Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises
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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 that these two extant loris species, which coexist in the same habitat, have exhibited an inverse relationship in terms of their demography over the past 1 million years, implying strong interspecies competition after speciation.
Originalsprog | Engelsk |
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Artikelnummer | e2123030119 |
Tidsskrift | Proceedings of the National Academy of Sciences of the United States of America |
Vol/bind | 119 |
Udgave nummer | 40 |
Antal sider | 10 |
ISSN | 0027-8424 |
DOI | |
Status | Udgivet - 2022 |
Bibliografisk note
Funding Information:
ACKNOWLEDGMENTS. We thank the Primate Laboratory Animal Center from the Kunming Institute of Zoology, Chinese Academy of Sciences; Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences; and Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (the Large Research Infrastructure Funding) for providing the sample of slow loris. This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB17); the National Natural Science Foundation of China (31822048, 81901300, and 82101637); Yunnan Fundamental Research Project (2019FI010); and the Animal Branch of the Germplasm Bank of Wild Species of Chinese Academy of Science (the Large Research Infrastructure Funding).
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© 2022 National Academy of Sciences. All rights reserved.
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