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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
Corresponding AuthorGao, 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
Source PublicationPLANT PHYSIOLOGY
ISSN0032-0889
Volume161Issue:4Pages:1844-1861
AbstractThe 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.
KeywordArabidopsis-thaliana Saccharomyces-cerevisiae Phylogenetic Analysis Cytosine Methylation Dosage Sensitivity Balance Hypothesis Yeast Genome Probe Level Polyploidy Duplicability
Subject AreaPlant Sciences
DOI10.1104/pp.112.200147
Indexed BySCI
Language英语
WOS Research AreaPlant Sciences
WOS SubjectPlant Sciences
WOS IDWOS:000316987900021
Citation statistics
Cited Times:42[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/16489
Collection中国西南野生生物种质资源库
Affiliation1.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
Recommended Citation
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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