Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants

doi:10.1104/pp.112.200147

	Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants
	Jiang, Wen-kai 1,2; Liu, Yun-long 2,3; Xia, En-hua2,3 ; Gao, Li-zhi2
通讯作者	Gao, LZ (reprint author), Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species Southwest China, Kunming 650201, Peoples R China. ; lgao@mail.kib.ac.cn
	2013-04-01
发表期刊	PLANT PHYSIOLOGY
ISSN	0032-0889
卷号	161 期号:4 页码:1844-1861
摘要	The evolution of genes and genomes after polyploidization has been the subject of extensive studies in evolutionary biology and plant sciences. While a significant number of duplicated genes are rapidly removed during a process called fractionation, which operates after the whole-genome duplication (WGD), another considerable number of genes are retained preferentially, leading to the phenomenon of biased gene retention. However, the evolutionary mechanisms underlying gene retention after WGD remain largely unknown. Through genome-wide analyses of sequence and functional data, we comprehensively investigated the relationships between gene features and the retention probability of duplicated genes after WGDs in six plant genomes, Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa), soybean (Glycine max), rice (Oryza sativa), sorghum (Sorghum bicolor), and maize (Zea mays). The results showed that multiple gene features were correlated with the probability of gene retention. Using a logistic regression model based on principal component analysis, we resolved evolutionary rate, structural complexity, and GC3 content as the three major contributors to gene retention. Cluster analysis of these features further classified retained genes into three distinct groups in terms of gene features and evolutionary behaviors. Type I genes are more prone to be selected by dosage balance; type II genes are possibly subject to subfunctionalization; and type III genes may serve as potential targets for neofunctionalization. This study highlights that gene features are able to act jointly as primary forces when determining the retention and evolution of WGD-derived duplicated genes in flowering plants. These findings thus may help to provide a resolution to the debate on different evolutionary models of gene fates after WGDs.
关键词	Arabidopsis-thaliana Saccharomyces-cerevisiae Phylogenetic Analysis Cytosine Methylation Dosage Sensitivity Balance Hypothesis Yeast Genome Probe Level Polyploidy Duplicability
学科领域	Plant Sciences
DOI	10.1104/pp.112.200147
收录类别	SCI
语种	英语
WOS记录号	WOS:000316987900021
引用统计	被引频次：75[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/16489
专题	中国西南野生生物种质资源库
作者单位	1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming 650201, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species Southwest China, Kunming 650201, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100039, Peoples R China
推荐引用方式 GB/T 7714	Jiang, Wen-kai,Liu, Yun-long,Xia, En-hua,et al. Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants[J]. PLANT PHYSIOLOGY,2013,161(4):1844-1861.
APA	Jiang, Wen-kai,Liu, Yun-long,Xia, En-hua,&Gao, Li-zhi.(2013).Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants.PLANT PHYSIOLOGY,161(4),1844-1861.
MLA	Jiang, Wen-kai,et al."Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants".PLANT PHYSIOLOGY 161.4(2013):1844-1861.

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