Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster

CORC > 海洋研究所 > 中国科学院海洋研究所 > 实验海洋生物学重点实验室

	Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster
	Gao, Dahai 1; Ko, Dennis C.2; Tian, Xinmin 3; Yang, Guang 4; Wang, Liuyang 2
刊名	EVOLUTIONARY BIOINFORMATICS
	2015
卷号	11 期号:2015 页码:57-65
关键词	duplicate genes Pacific oyster RNA-seq protein kinase superfamily
英文摘要	Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster.
收录类别	SCI
语种	英语
WOS记录号	WOS:000366735800006
内容类型	期刊论文
源URL	[http://ir.qdio.ac.cn/handle/337002/86623]
专题	海洋研究所_实验海洋生物学重点实验室
作者单位	1.Chinese Acad Sci, Inst Oceanol, Key Lab Expt Marine Biol, Qingdao, Shandong, Peoples R China 2.Duke Univ, Dept Mol Genet & Microbiol, Med Ctr, Durham, NC 27706 USA 3.Chinese Acad Trop Agr Sci, Trop Crops Genet Resources Res Inst, Danzhou, Hainan, Peoples R China 4.Chinese Acad Sci, Inst Oceanol, Key Lab Marine Ecol & Environm Sci, Qingdao, Shandong, Peoples R China
推荐引用方式 GB/T 7714	Gao, Dahai,Ko, Dennis C.,Tian, Xinmin,et al. Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster[J]. EVOLUTIONARY BIOINFORMATICS,2015,11(2015):57-65.
APA	Gao, Dahai,Ko, Dennis C.,Tian, Xinmin,Yang, Guang,&Wang, Liuyang.(2015).Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster.EVOLUTIONARY BIOINFORMATICS,11(2015),57-65.
MLA	Gao, Dahai,et al."Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster".EVOLUTIONARY BIOINFORMATICS 11.2015(2015):57-65.