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Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants
Jiang, Wen-kai1,2; Liu, Yun-long2,3; Xia, En-hua2,3; Gao, Li-zhi2
2013-04-01
发表期刊PLANT PHYSIOLOGY
ISSN0032-0889
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
资助信息Natural Science Foundation of Yunnan Province [2010CC011]; Top Talents Program of Yunnan Province [20080A009]; Hundreds Oversea Talents Program of Yunnan Province; Hundreds Talents Program of the Chinese Academy of Sciences; Chinese Academy of Sciences [KSCX2-YW-N-029]; Chinese Department of Science and Technology (973 Program) [2007CB815703]; startup grant of the Kunming Institute of Botany, Chinese Academy of Sciences
学科领域Plant Sciences
DOI10.1104/pp.112.200147
收录类别SCI
语种英语
WOS研究方向Plant Sciences
WOS类目Plant Sciences
WOS记录号WOS:000316987900021
引用统计
被引频次:35[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
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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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