Prevalent Role of Gene Features in Determining Evolutionary Fates of Whole-Genome Duplication Duplicated Genes in Flowering Plants
文献类型：期刊论文
| 作者 | Jiang, Wen-kai1,2; Liu, Yun-long2,3; Xia, En-hua2,3 ; Gao, Li-zhi2
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| 刊名 | PLANT PHYSIOLOGY
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| 出版日期 | 2013-04-01 |
| 卷号 | 161期号:4页码:1844-1861 |
| 关键词 | ARABIDOPSIS-THALIANA SACCHAROMYCES-CEREVISIAE PHYLOGENETIC ANALYSIS CYTOSINE METHYLATION DOSAGE SENSITIVITY BALANCE HYPOTHESIS YEAST GENOME PROBE LEVEL POLYPLOIDY DUPLICABILITY |
| ISSN号 | 0032-0889 |
| 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 |
| 英文摘要 | 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. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 学科主题 | Plant Sciences |
| 类目[WOS] | Plant Sciences |
| 研究领域[WOS] | Plant Sciences |
| 关键词[WOS] | ARABIDOPSIS-THALIANA ; SACCHAROMYCES-CEREVISIAE ; PHYLOGENETIC ANALYSIS ; CYTOSINE METHYLATION ; DOSAGE SENSITIVITY ; BALANCE HYPOTHESIS ; YEAST GENOME ; PROBE LEVEL ; POLYPLOIDY ; DUPLICABILITY |
| 收录类别 | SCI |
| 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 |
| 语种 | 英语 |
| WOS记录号 | WOS:000316987900021 |
| 公开日期 | 2013-06-08 |
| 源URL | [http://ir.kib.ac.cn:8080/handle/151853/16489]  |
| 专题 | 昆明植物研究所_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. |
入库方式： OAI收割
来源：昆明植物研究所
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