Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish

	Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish
	Tong, Chao 1,2,3; Zhang, Cunfang 1,2; Zhang, Renyi 1,2,3; Zhao, Kai 1,2
刊名	fish & shellfish immunology
	2015-10-01
卷号	46 期号:2 页码:366-377
关键词	Gymnocypris przewalskii Gill and kidney Transcriptome Immune-related gene Gene family SSR mark
中文摘要	the naked carp, gymnocypris przewalskii, is one of the dominant aquaculture fish species in qinghai province, china. its wild stocks have severely suffered from overfishing, and the farming species are vulnerable to various pathogens infections. here we report the first immune-related tissues transcriptome of a wild naked carp using a deep sequencing approach. a total of 158,087 unigenes are generated, 2687 gill-specific gene and 3215 kidney-specific genes are identified, respectively. gene ontology analysis shows that 51,671 unigenes are involved in three major functional categories: biological process, cellular component, and molecular function. further analysis shows that numerous consensus sequences are homologous to known immune-related genes. pathways mapping annotate 56,270 unigenes and identify a large number of immune-related pathways. in addition, we focus on the immune-related genes and gene family in toll-like receptor signaling pathway involved in innate immunity, including toll-like receptors (tlrs), interferon regulatory factors (irfs), interleukins (ils) and tumor necrosis factors (tnfs). eventually, we identify 5 tlrs, 4 irfs, 3 ils and 2 tnfs with a completed coding sequence though mining the transcriptome data. phylogeny analysis shows these genes of naked carp are mostly close to zebrafish. protein domain and selection pressure analyses together show that all these genes are highly conserved in gene sequence and protein domain structure with other species, and purifying selection underwent in these genes, implied functionally important features are conserved in the genes above. intriguingly, we detect positive selection signals in naked carp tlr4, and significant divergence occurred among tested species tlr4, suggested that naked carp tlr4 function may be affected. finally, we identify 23,867 simple sequence repeat (ssr) marks in this transcriptome. taken together, this study not only contributes a large number of candidate genes in naked carp immunity, and also helps improve current understanding of immunogenetics basis and evolutionary history of immune related genes and gene family in highland fish species. (c) 2015 elsevier ltd. all rights reserved.
英文摘要	the naked carp, gymnocypris przewalskii, is one of the dominant aquaculture fish species in qinghai province, china. its wild stocks have severely suffered from overfishing, and the farming species are vulnerable to various pathogens infections. here we report the first immune-related tissues transcriptome of a wild naked carp using a deep sequencing approach. a total of 158,087 unigenes are generated, 2687 gill-specific gene and 3215 kidney-specific genes are identified, respectively. gene ontology analysis shows that 51,671 unigenes are involved in three major functional categories: biological process, cellular component, and molecular function. further analysis shows that numerous consensus sequences are homologous to known immune-related genes. pathways mapping annotate 56,270 unigenes and identify a large number of immune-related pathways. in addition, we focus on the immune-related genes and gene family in toll-like receptor signaling pathway involved in innate immunity, including toll-like receptors (tlrs), interferon regulatory factors (irfs), interleukins (ils) and tumor necrosis factors (tnfs). eventually, we identify 5 tlrs, 4 irfs, 3 ils and 2 tnfs with a completed coding sequence though mining the transcriptome data. phylogeny analysis shows these genes of naked carp are mostly close to zebrafish. protein domain and selection pressure analyses together show that all these genes are highly conserved in gene sequence and protein domain structure with other species, and purifying selection underwent in these genes, implied functionally important features are conserved in the genes above. intriguingly, we detect positive selection signals in naked carp tlr4, and significant divergence occurred among tested species tlr4, suggested that naked carp tlr4 function may be affected. finally, we identify 23,867 simple sequence repeat (ssr) marks in this transcriptome. taken together, this study not only contributes a large number of candidate genes in naked carp immunity, and also helps improve current understanding of immunogenetics basis and evolutionary history of immune related genes and gene family in highland fish species. (c) 2015 elsevier ltd. all rights reserved.
WOS标题词	science & technology ; life sciences & biomedicine
类目[WOS]	fisheries ; immunology ; marine & freshwater biology ; veterinary sciences
研究领域[WOS]	fisheries ; immunology ; marine & freshwater biology ; veterinary sciences
关键词[WOS]	toll-like receptors ; interferon regulatory factors ; genome sequence ; cynoglossus-semilaevis ; expression analysis ; cyprinus-carpio ; teleost fish ; common carp ; innate ; infection
收录类别	SCI
语种	英语
WOS记录号	WOS:000363071200024
内容类型	期刊论文
源URL	[http://ir.nwipb.ac.cn/handle/363003/5499]
专题	西北高原生物研究所_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 810001, Qinghai, Peoples R China 2.Chinese Acad Sci, Northwest Inst Plateau Biol, Lab Plateau Fish Evolutionary & Funct Genom, Xining 810001, Qinghai, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Tong, Chao,Zhang, Cunfang,Zhang, Renyi,et al. Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish[J]. fish & shellfish immunology,2015,46(2):366-377.
APA	Tong, Chao,Zhang, Cunfang,Zhang, Renyi,&Zhao, Kai.(2015).Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish.fish & shellfish immunology,46(2),366-377.
MLA	Tong, Chao,et al."Transcriptome profiling analysis of naked carp (Gymnocypris przewalskii) provides insights into the immune-related genes in highland fish".fish & shellfish immunology 46.2(2015):366-377.