The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau

doi:10.1371/journal.pone.0174534

NWIPB OpenIR

	The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau
	Tong, Chao 1,2,3,4; Tian, Fei 1,2,3; Zhang, Cunfang 1,2,3; Zhao, Kai 1,2,3
	2017-03-30
发表期刊	PLOS ONE
卷号	12 期号:3
文章类型	Article
摘要	Tibetan naked carp Gymnocypris przewalskii is an ideal model system to study highland adaptation of fish, because it evolved specific genetic and phenotypic characteristics to adapt to chronic cold and alkaline environments in Lake Qinghai. MicroRNAs (miRNAs) are small noncoding RNAs that regulating gene expression post-transcriptionally in a wide range of biological processes. In this study, we focus on the role of miRNAs in adaptation of G. przewalskii to extreme conditions in Lake Qinghai. We generate the first miRNAome of G. przewalskii in Schizothoracinae fish. Using several genomic resources, we inferred 341 conserved miRNAs belonged to 152 miRNA families and 43 novel miRNAs in G. przewalskii, and also identified 15 teleost-specific miRNAs. Using a large scale of conserved miRNAs, we constructed a high-confidence phylogenetic tree between teleost and mammals than mitochondria and nuclear genes. In addition, we found that several miRNA family (e.g. miR-10 and let-7) members highly expressed in G. przewalskii, which may function in multiple biological processes. Finally, we predicted a total of 34,258 miRNA targets genes. Conserved miRNAs target genes participating in signal transduction, cell differentiation and biosynthetic process, and showed signature of functional constraint. While novel miRNAs in a species displayed species-specific targets and involved in ion binding, transport and oxidoreductase activity, may affect the expression patterns of targets with signature of gene family expansion or positive selection under extreme environment. Taken together, this study demonstrated that miRNAs may involve into roles of adaptation of G. przewalskiito highland aquatic environment, and also provide insights into miRNA regulatory network in Schizothoracinae fish as a case study.
WOS标题词	Science & Technology
DOI	10.1371/journal.pone.0174534
关键词[WOS]	WIDE IDENTIFICATION ; EVOLUTION ; SELECTION ; CYPRINIDAE ; REVEALS ; GENES ; ADAPTATION ; ZEBRAFISH ; SEQUENCES ; GENOMICS
收录类别	SCI
语种	英语
项目资助者	Natural Science Foundation of Qinghai Province, China(2016-ZJ-939Q) ; National Natural Science Foundation of China(31572258 ; Key Innovation Plan from Chinese Academy of Sciences(KSCX2-EW-N-004) ; Open Foundation from the Qinghai Key Laboratory of Tibetan Medicine Pharmacology and Safety Evaluation(2014-ZY-03) ; 31500306)
WOS研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000399174800050
引用统计	被引频次：13[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/6821
专题	中国科学院西北高原生物研究所
作者单位	1.Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining, Peoples R China 2.Chinese Acad Sci, Northwest Inst Plateau Biol, Lab Plateau Fish Evolutionary & Funct Genom, Xining, Peoples R China 3.Chinese Acad Sci, Northwest Inst Plateau Biol, Qinghai Key Lab Anim Ecol Genom, Xining, Peoples R China 4.Univ Chinese Acad Sci, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Tong, Chao,Tian, Fei,Zhang, Cunfang,et al. The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau[J]. PLOS ONE,2017,12(3).
APA	Tong, Chao,Tian, Fei,Zhang, Cunfang,&Zhao, Kai.(2017).The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau.PLOS ONE,12(3).
MLA	Tong, Chao,et al."The microRNA repertoire of Tibetan naked carp Gymnocypris przewalskii: A case study in Schizothoracinae fish on the Tibetan Plateau".PLOS ONE 12.3(2017).