Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes

CORC > 水生生物研究所 > 中科院水生所知识产出（2009年前） > 水生生物多样性与资源保护研究中心 > 期刊论文

	Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes
	Wang, Ying 1,2; Yang, Liandong 1,2; Wu, Bo 3; Song, Zhaobin 3; He, Shunping 1
刊名	GENE
	2015-07-10
卷号	565 期号:2 页码:211-220
关键词	Triplophysa dalaica Transcriptome Hypoxic adaptation Positive selection Branch-site model
ISSN号	0378-1119
通讯作者	He, SP (reprint author), Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat, Wuhan 430072, Peoples R China.
英文摘要	Triplophysa 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.
WOS标题词	Science & Technology ; Life Sciences & Biomedicine
类目[WOS]	Genetics & Heredity
研究领域[WOS]	Genetics & Heredity
关键词[WOS]	COMPLETE MITOCHONDRIAL GENOME ; HIGH-ALTITUDE ADAPTATION ; FACTOR-ALPHA SUBUNITS ; PHYLOGENETIC ANALYSIS ; COBITOIDEA TELEOSTEI ; EXPRESSION ANALYSIS ; MAXIMUM-LIKELIHOOD ; REVEALS ADAPTATION ; KYOTO ENCYCLOPEDIA ; CRUCIAN CARP
收录类别	SCI
语种	英语
WOS记录号	WOS:000355711800008
内容类型	期刊论文
源URL	[http://ir.ihb.ac.cn/handle/342005/23819]
专题	水生生物研究所_水生生物多样性与资源保护研究中心_期刊论文
作者单位	1.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
推荐引用方式 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.(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.