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Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus
Yang, Liandong1,2; Wang, Ying1,2; Zhang, Zhaolei3,4; He, Shunping1; He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China.
2015
Source PublicationGENOME BIOLOGY AND EVOLUTION
ISSN1759-6653
Volume7Issue:1Pages:251-261
AbstractElucidating the genetic mechanisms of organismal adaptation to the Tibetan Plateau at a genomic scale can provide insights into the process of adaptive evolution. Many highland species have been investigated and various candidate genes that may be responsible for highland adaptation have been identified. However, we know little about the genomic basis of adaptation to Tibet in fishes. Here, we performed transcriptome sequencing of a schizothoracine fish (Gymnodiptychus pachycheilus) and used it to identify potential genetic mechanisms of highland adaptation. We obtained totally 66,105 assembled unigenes, of which 7,232 were assigned as putative one-to-one orthologs in zebrafish. Comparative gene annotations from several species indicated that at least 350 genes lost and 41 gained since the divergence between G. pachycheilus and zebrafish. An analysis of 6,324 orthologs among zebrafish, fugu, medaka, and spotted gar identified consistent evidence for genome-wide accelerated evolution in G. pachycheilus and only the terminal branch of G. pachycheilus had an elevated Ka/Ks ratio than the ancestral branch. Many functional categories related to hypoxia and energy metabolism exhibited rapid evolution in G. pachycheilus relative to zebrafish. Genes showing signature of rapid evolution and positive selection in the G. pachycheilus lineage were also enriched in functions associated with energy metabolism and hypoxia. The first genomic resources for fish in the Tibetan Plateau and evolutionary analyses provided some novel insights into highland adaptation in fishes and served as a foundation for future studies aiming to identify candidate genes underlying the genetic bases of adaptation to Tibet in fishes.
SubtypeArticle
KeywordTibetan Plateau Adaptation Positive Selection Schizothoracine Fish Transcriptome
Department[Yang, Liandong ; Wang, Ying ; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China ; [Yang, Liandong ; Wang, Ying] Univ Chinese Acad Sci, Beijing, Peoples R China ; [Zhang, Zhaolei] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada ; [Zhang, Zhaolei] Univ Toronto, Donnelly Ctr Cellular & Biomol Res, Toronto, ON M5S 1A1, Canada
DOI10.1093/gbe/evu279
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaEvolutionary Biology ; Genetics & Heredity
WOS SubjectEvolutionary Biology ; Genetics & Heredity
WOS KeywordHIGH-ALTITUDE ADAPTATION ; PHYLOGENETIC ANALYSIS ; MOLECULAR PHYLOGENY ; POSITIVE SELECTION ; ADAPTIVE EVOLUTION ; GENOMIC LANDSCAPE ; UP-REGULATION ; KINASE YES ; HYPOXIA ; EXPRESSION
WOS IDWOS:000350036100018
Citation statistics
Cited Times:31[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/23837
Collection水生生物多样性与资源保护研究中心
Corresponding AuthorHe, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China
2.Univ Chinese Acad Sci, Beijing, Peoples R China
3.Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A1, Canada
4.Univ Toronto, Donnelly Ctr Cellular & Biomol Res, Toronto, ON M5S 1A1, Canada
Recommended Citation
GB/T 7714
Yang, Liandong,Wang, Ying,Zhang, Zhaolei,et al. Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus[J]. GENOME BIOLOGY AND EVOLUTION,2015,7(1):251-261.
APA Yang, Liandong,Wang, Ying,Zhang, Zhaolei,He, Shunping,&He, SP .(2015).Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus.GENOME BIOLOGY AND EVOLUTION,7(1),251-261.
MLA Yang, Liandong,et al."Comprehensive Transcriptome Analysis Reveals Accelerated Genic Evolution in a Tibet Fish, Gymnodiptychus pachycheilus".GENOME BIOLOGY AND EVOLUTION 7.1(2015):251-261.
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