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题名: Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes
作者: Wang, Ying1, 2; Yang, Liandong1, 2; Zhou, Kun3; Zhang, Yanping4; Song, Zhaobin5; He, Shunping1
关键词: Tibetan Plateau ; adaptation ; transcriptome ; accelerated evolution ; Triplophysa fishes
刊名: GENOME BIOLOGY AND EVOLUTION
发表日期: 2015-11-01
DOI: 10.1093/gbe/evv192
卷: 7, 期:11, 页:2970-2982
收录类别: SCI
文章类型: Article
WOS标题词: Science & Technology ; Life Sciences & Biomedicine
类目[WOS]: Evolutionary Biology ; Genetics & Heredity
研究领域[WOS]: Evolutionary Biology ; Genetics & Heredity
英文摘要: Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.
关键词[WOS]: HIGH-ALTITUDE ADAPTATION ; DEER MOUSE HEMOGLOBIN ; PHYLOGENETIC ANALYSES ; MAXIMUM-LIKELIHOOD ; POSITIVE SELECTION ; GENOME SEQUENCE ; HYPOXIA ; EVOLUTION ; PROTEIN ; FISH
语种: 英语
项目资助者: (XDB13020100)
WOS记录号: WOS:000364951500002
ISSN号: 1759-6653
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内容类型: 期刊论文
URI标识: http://ir.ihb.ac.cn/handle/342005/27362
Appears in Collections:水生生物多样性与资源保护研究中心_期刊论文

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作者单位: 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
3.Cent China Normal Univ, Hubei Key Lab Genet Regulat & Integrat Biol, Coll Life Sci, Wuhan, Peoples R China
4.Gansu Fishers Res Inst, Gansu Key Lab Cold Water Fishes Germplasm Resourc, Lanzhou, Peoples R China
5.Sichuan Univ, Coll Life Sci, Sichuan Key Lab Conservat Biol Endangered Wildlif, Chengdu 610064, Peoples R China
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