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Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes
Wang, Ying1,2; Yang, Liandong1,2; Wu, Bo3; Song, Zhaobin3; He, Shunping1; He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China.
2015-07-10
Source PublicationGENE
ISSN0378-1119
Volume565Issue:2Pages:211-220
AbstractTriplophysa dalaica, endemic species of Qinghai-Tibetan Plateau, is informative for understanding the genetic basis of adaptation to hypoxic conditions of high altitude habitats. Here, a comprehensive gene repertoire for this plateau fish was generated using the Illumina deep paired-end high-throughput sequencing technology. De novo assembly yielded 145,256 unigenes with an average length of 1632 bp. Blast searches against GenBank non-redundant database annotated 74,594(51.4%) unigenes encoding for 30,047 gene descriptions in T. dalaica. Functional annotation and classification of assembled sequences were performed using Gene Ontology (GO), clusters of euKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (ICEGG) analysis. After comparison with other fish transcriptomes, including silver carp (Hypophthalmichthys molitrix) and mud loach (Misgurnus anguillicaudatus), 2621 high-quality orthologous gene alignments were constructed among these species. 61 (2.3%) of the genes were identified as having undergone positive selection in the T. dalaica lineage. Within the positively selected genes, 13 genes were involved in hypoxia response, of which 11 were listed in HypoxiaDB. Furthermore, duplicated hif-alpha (hif-1 alpha A/B and hif-2 alpha A/B), EGLN1 and PPARA candidate genes involved in adaptation to hypoxia were identified in T. dalaica transcriptome. Branch-site model in PAML validated that hif-1 alpha B and hif-2 alpha A genes have undergone positive selection in T.dalaica. Finally, 37,501 simple sequence repeats (SSRs) and 19,497 high-quality single nucleotide polymorphisms (SNPs) were identified in T. dalaica. The identified SSR and SNP markers will facilitate the genetic structure, population geography and ecological studies of Triplophysa fishes. (C) 2015 Elsevier B.V. All rights reserved.
SubtypeArticle
KeywordTriplophysa Dalaica Transcriptome Hypoxic Adaptation Positive Selection Branch-site Model
Department[Wang, Ying ; Yang, Liandong ; He, Shunping] Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China ; [Wang, Ying ; Yang, Liandong] Univ Chinese Acad Sci, Beijing 100049, Peoples R China ; [Wu, Bo ; Song, Zhaobin] Sichuan Univ, Coll Life Sci, Sichuan Key Lab Conservat Biol Endangered Wildlif, Chengdu 610065, Peoples R China
DOI10.1016/j.gene.2015.04.023
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000355711800008
WOS KeywordCOMPLETE MITOCHONDRIAL GENOME ; HIGH-ALTITUDE ADAPTATION ; FACTOR-ALPHA SUBUNITS ; PHYLOGENETIC ANALYSIS ; COBITOIDEA TELEOSTEI ; EXPRESSION ANALYSIS ; MAXIMUM-LIKELIHOOD ; REVEALS ADAPTATION ; KYOTO ENCYCLOPEDIA ; CRUCIAN CARP
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Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/23819
Collection水生生物多样性与资源保护研究中心_期刊论文
Corresponding AuthorHe, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China.
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
3.Sichuan Univ, Coll Life Sci, Sichuan Key Lab Conservat Biol Endangered Wildlif, Chengdu 610065, Peoples R China
Recommended Citation
GB/T 7714
Wang, Ying,Yang, Liandong,Wu, Bo,et al. Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes[J]. GENE,2015,565(2):211-220.
APA Wang, Ying,Yang, Liandong,Wu, Bo,Song, Zhaobin,He, Shunping,&He, SP .(2015).Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes.GENE,565(2),211-220.
MLA Wang, Ying,et al."Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes".GENE 565.2(2015):211-220.
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