| 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 Publication | GENOME BIOLOGY AND EVOLUTION
 |
| ISSN | 1759-6653 |
| Volume | 7Issue:1Pages:251-261 |
| Abstract | Elucidating 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. |
| Subtype | Article |
| Keyword | Tibetan 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 |
| DOI | 10.1093/gbe/evu279 |
| WOS Headings | Science & Technology ; Life Sciences & Biomedicine |
| Indexed By | SCI |
| Language | 英语 |
| WOS Research Area | Evolutionary Biology ; Genetics & Heredity |
| WOS Subject | Evolutionary Biology ; Genetics & Heredity |
| WOS Keyword | HIGH-ALTITUDE ADAPTATION ; PHYLOGENETIC ANALYSIS ; MOLECULAR PHYLOGENY ; POSITIVE SELECTION ; ADAPTIVE EVOLUTION ; GENOMIC LANDSCAPE ; UP-REGULATION ; KINASE YES ; HYPOXIA ; EXPRESSION |
| WOS ID | WOS:000350036100018 |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://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 Author | He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan, Hubei, Peoples R China. |
| Affiliation | 1.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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| Comprehensive Transc（424KB） | 开放获取 | CC BY-NC-SA | View Application Full Text | |||
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