Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants
文献类型：期刊论文
| 作者 | Shi, Tao2,3; Rahmani, Razgar Seyed4; Gugger, Paul F.5; Wang, Muhua6; Li, Hui2,3,7; Zhang, Yue2,3,7; Li, Zhizhong2,3,7; Wang, Qingfeng2,3,8; Van de Peer, Yves1,4,9,10; Marchal, Kathleen4,11 |
| 刊名 | MOLECULAR BIOLOGY AND EVOLUTION
 |
| 出版日期 | 2020-08-01 |
| 卷号 | 37期号:8页码:2394-2413 |
| 关键词 | whole-genome duplication gene expression methylation gene balance subgenome dominance |
| ISSN号 | 0737-4038 |
| DOI | 10.1093/molbev/msaa105 |
| 英文摘要 | For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K-pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein-protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein-protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant. |
| 资助项目 | Strategic Priority Research Program of Chinese Academy of Sciences[XDB31000000] ; National Natural Science Foundation of China[31570220] ; National Natural Science Foundation of China[31870208] ; National Natural Science Foundation of China[31700197] ; Youth Innovation Promotion Association of Chinese Academy of Sciences[2019335] ; Hubei Provincial Natural Science Foundation of China[2019CFB275] ; Hubei Chenguang Talented Youth Development Foundation ; European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program[833522] ; Ministry of Science, Research and Technology (Iran) |
| WOS研究方向 | Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:000574381000020 |
| 出版者 | OXFORD UNIV PRESS |
| 源URL | [http://202.127.146.157/handle/2RYDP1HH/15840]  |
| 专题 | 中国科学院武汉植物园 |
| 通讯作者 | Wang, Qingfeng; Van de Peer, Yves; Marchal, Kathleen; Chen, Jinming |
| 作者单位 | 1.Nanjing Agr Univ, Coll Hort, Nanjing, Peoples R China 2.Chinese Acad Sci, CAS Key Lab Aquat Bot & Watershed Ecol, Wuhan Bot Garden, Wuhan, Peoples R China 3.Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Wuhan, Peoples R China 4.Univ Ghent, Dept Plant Biotechnol & Bioinformat, Ghent, Belgium 5.Univ Maryland, Appalachian Lab, Ctr Environm Sci, Frostburg, MD USA 6.Sun Yat Sen Univ, Sch Marine Sci, Guangzhou, Peoples R China 7.Univ Chinese Acad Sci, Beijing, Peoples R China 8.Chinese Acad Sci, Sino African Joint Res Ctr, Wuhan, Peoples R China 9.VIB, Ctr Plant Syst Biol, Ghent, Belgium 10.Univ Pretoria, Dept Biochem Genet & Microbiol, Pretoria, South Africa |
| 推荐引用方式 GB/T 7714 | Shi, Tao,Rahmani, Razgar Seyed,Gugger, Paul F.,et al. Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants[J]. MOLECULAR BIOLOGY AND EVOLUTION,2020,37(8):2394-2413. |
| APA | Shi, Tao.,Rahmani, Razgar Seyed.,Gugger, Paul F..,Wang, Muhua.,Li, Hui.,...&Chen, Jinming.(2020).Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants.MOLECULAR BIOLOGY AND EVOLUTION,37(8),2394-2413. |
| MLA | Shi, Tao,et al."Distinct Expression and Methylation Patterns for Genes with Different Fates following a Single Whole-Genome Duplication in Flowering Plants".MOLECULAR BIOLOGY AND EVOLUTION 37.8(2020):2394-2413. |
入库方式： OAI收割
来源：武汉植物园
浏览0
下载0
收藏0
其他版本
除非特别说明，本系统中所有内容都受版权保护，并保留所有权利。