title: Genetic adaptations of the plateau zokor in high-elevation burrows.
abstract: The plateau zokor (Myospalax baileyi) spends its entire life underground in sealed burrows. Confronting limited oxygen and high carbon dioxide concentrations, and complete darkness, they epitomize a successful physiological adaptation. Here, we employ transcriptome sequencing to explore the genetic underpinnings of their adaptations to this unique habitat. Compared to Rattus norvegicus, genes belonging to GO categories related to energy metabolism (e.g. mitochondrion and fatty acid beta-oxidation) underwent accelerated evolution in the plateau zokor. Furthermore, the numbers of positively selected genes were significantly enriched in the gene categories involved in ATPase activity, blood vessel development and respiratory gaseous exchange, functional categories that are relevant to adaptation to high altitudes. Among the 787 genes with evidence of parallel evolution, and thus identified as candidate genes, several GO categories (e.g. response to hypoxia, oxygen homeostasis and erythrocyte homeostasis) are significantly enriched, are two genes, EPAS1 and AJUBA, involved in the response to hypoxia, where the parallel evolved sites are at positions that are highly conserved in sequence alignments from multiple species. Thus, accelerated evolution of GO categories, positive selection and parallel evolution at the molecular level provide evidences to parse the genetic adaptations of the plateau zokor for living in high-elevation burrows.
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.|Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming 650204, China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Shao
authors.affiliation: Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China.
authors.forename: Jin-Xiu
authors.initials: JX
authors.lastname: Li
authors.affiliation: Key Laboratory for High Altitude Medicine of Ministry of Chinese Education and Research Center for High Altitude Medicine, Qinghai University, Xining 810001, China.
authors.forename: Ri-Li
authors.initials: RL
authors.lastname: Ge
authors.affiliation: Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhong
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.|Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, M5S 1A8, Canada.|Banting and Best Diabetes Centre, University of Toronto, Ontario, M5S 1A8, Canada.
authors.forename: David M
authors.initials: DM
authors.lastname: Irwin
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.|Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, 100 Queen's Park, Toronto, Ont., M5S 2C6, Canada.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Murphy
authors.affiliation: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, the Chinese Academy of Sciences, Kunming 650223, China.|Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming 650091, China.
authors.forename: Ya-Ping
authors.initials: YP
authors.lastname: Zhang
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D000595:Amino Acid Sequence; D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics / Q000378:metabolism; D005075:Biological Evolution; D004734:Energy Metabolism / Q000235:genetics; D000860:Hypoxia; D060588:LIM Domain Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D010100:Oxygen / Q000378:metabolism; D010802:Phylogeny; D060066:Protein Interaction Maps; D051381:Rats; D017207:Rats, Sprague-Dawley; D012377:Rodentia / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D018609:Tibet; D059467:Transcriptome; D000099162:Endothelial PAS Domain-Containing Protein 1
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D060588:LIM Domain Proteins; D010100:Oxygen; D000099162:Endothelial PAS Domain-Containing Protein 1