Hypoxic and Cold Adaptation Insights from the Himalayan Marmot Genome

Liang Bai; Baoning Liu; Changmian Ji; Sihai Zhao; Siyu Liu; Rong Wang; Weirong Wang; Pu Yao; Xuming Li; Xiaojun Fu; Haiyan Yu; Min Liu; Fengming Han; Ning Guan; Hui Liu; Dongyuan Liu; Yuanqing Tao; Zhongdong Wang; Shunsheng Yan; Greg Florant; Michael T Butcher; Jifeng Zhang; Hongkun Zheng; Jianglin Fan; Enqi Liu

doi:10.1016/j.isci.2018.11.034

Hypoxic and Cold Adaptation Insights from the Himalayan Marmot Genome

iScience. 2019 Jan 25:11:519-530. doi: 10.1016/j.isci.2018.11.034. Epub 2018 Dec 20.

Authors

Liang Bai¹, Baoning Liu¹, Changmian Ji², Sihai Zhao¹, Siyu Liu³, Rong Wang¹, Weirong Wang¹, Pu Yao², Xuming Li², Xiaojun Fu², Haiyan Yu², Min Liu², Fengming Han², Ning Guan², Hui Liu², Dongyuan Liu², Yuanqing Tao⁴, Zhongdong Wang⁴, Shunsheng Yan⁵, Greg Florant⁶, Michael T Butcher⁷, Jifeng Zhang⁸, Hongkun Zheng⁹, Jianglin Fan¹⁰, Enqi Liu¹¹

Affiliations

¹ Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China.
² Biomarker Technologies Corporation, Beijing 101200, China.
³ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
⁴ Qinghai Institute for Endemic Disease Prevention and Control, Xining, Qinghai 811602, China.
⁵ Centers for Disease Control and Prevention, Urumqi, Xinjiang 830054, China.
⁶ Department of Biology, Colorado State University, Ft. Collins, CO 80523, USA.
⁷ Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA.
⁸ Center for Advanced Models for Translational Sciences and Therapeutics, University of Michigan Medical Center, Ann Arbor, MI 48109, USA.
⁹ Biomarker Technologies Corporation, Beijing 101200, China. Electronic address: zhenghk@biomarker.com.cn.
¹⁰ Department of Molecular Pathology, Faculty of Medicine, Interdisciplinary Graduate School of Medicine, University of Yamanashi, 1110, Shimokato, Chuo, Yamanashi 409-3898, Japan. Electronic address: jianglin@yamanashi.ac.jp.
¹¹ Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, No.76, Yanta West Road, Xi'an, Shaanxi 710061, China; Research Institute of Atherosclerotic Disease, Xi'an Jiaotong University Cardiovascular Research Center, Xi'an, Shaanxi 710061, China. Electronic address: liuenqi@mail.xjtu.edu.cn.

Abstract

The Himalayan marmot (Marmota himalayana) is a hibernating mammal that inhabits the high-elevation regions of the Himalayan mountains. Here we present a draft genome of the Himalayan marmot, with a total assembly length of 2.47 Gb. Phylogenetic analyses showed that the Himalayan marmot diverged from the Mongolian marmot approximately 1.98 million years ago. Transcriptional changes during hibernation included genes responsible for fatty acid metabolism in liver and genes involved in complement and coagulation cascades and stem cell pluripotency pathways in brain. Two selective sweep genes, Slc25a14 and ψAamp, showed apparent genotyping differences between low- and high-altitude populations. As a processed pseudogene, ψAamp may be biologically active to influence the stability of Aamp through competitive microRNA binding. These findings shed light on the molecular and genetic basis underlying adaptation to extreme environments in the Himalayan marmot.

Keywords: Bioinformatics; Evolutionary Biology; Genetics; Omics; Physiology.