Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises
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Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises. / Li, Ming Li; Wang, Sheng; Xu, Penghui; Tian, Hang Yu; Bai, Mixue; Zhang, Ya Ping; Shao, Yong; Xiong, Zi Jun; Qi, Xiao Guang; Cooper, David N.; Zhang, Guojie; Zhu, He Helen; Wu, Dong Dong.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 119, No. 40, e2123030119, 2022.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises
AU - Li, Ming Li
AU - Wang, Sheng
AU - Xu, Penghui
AU - Tian, Hang Yu
AU - Bai, Mixue
AU - Zhang, Ya Ping
AU - Shao, Yong
AU - Xiong, Zi Jun
AU - Qi, Xiao Guang
AU - Cooper, David N.
AU - Zhang, Guojie
AU - Zhu, He Helen
AU - Wu, Dong Dong
N1 - Publisher Copyright: © 2022 National Academy of Sciences. All rights reserved.
PY - 2022
Y1 - 2022
N2 - 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.
AB - 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.
KW - adaptive evolution
KW - demographic history
KW - slow lorises
U2 - 10.1073/pnas.2123030119
DO - 10.1073/pnas.2123030119
M3 - Journal article
C2 - 36161902
AN - SCOPUS:85138661207
VL - 119
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
IS - 40
M1 - e2123030119
ER -
ID: 329193250