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| Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence | |
| Wei, Chendan1; Wang, Zhenyi1; Wang, Jianyu1; Teng, Jia1; Shen, Shaoqi1; Xiao, Qimeng1; Bao, Shoutong1; Feng, Yishan1; Zhang, Yan1; Li, Yuxian1; Sun, Sangrong1; Yue, Yuanshuai1; Wu, Chunyang1; Wang, Yanli1; Zhou, Tianning1; Xu, Wenbo1; Yu, Jigao2,3; Wang, Li1; Wang, Jinpeng1,2,3 | |
| 2021 | |
| 发表期刊 | BMC GENOMICS
 |
| ISSN | 1471-2164 |
| 卷号 | 22期号:1 |
| 摘要 | BackgroundDuplicated gene pairs produced by ancient polyploidy maintain high sequence similarity over a long period of time and may result from illegitimate recombination between homeologous chromosomes. The genomes of Asian cultivated rice Oryza sativa ssp. indica (XI) and Oryza sativa ssp. japonica (GJ) have recently been updated, providing new opportunities for investigating ongoing gene conversion events and their impact on genome evolution.ResultsUsing comparative genomics and phylogenetic analyses, we evaluated gene conversion rates between duplicated genes produced by polyploidization 100 million years ago (mya) in GJ and XI. At least 5.19-5.77% of genes duplicated across the three rice genomes were affected by whole-gene conversion after the divergence of GJ and XI at similar to 0.4 mya, with more (7.77-9.53%) showing conversion of only portions of genes. Independently converted duplicates surviving in the genomes of different subspecies often use the same donor genes. The ongoing gene conversion frequency was higher near chromosome termini, with a single pair of homoeologous chromosomes, 11 and 12, in each rice genome being most affected. Notably, ongoing gene conversion has maintained similarity between very ancient duplicates, provided opportunities for further gene conversion, and accelerated rice divergence. Chromosome rearrangements after polyploidization are associated with ongoing gene conversion events, and they directly restrict recombination and inhibit duplicated gene conversion between homeologous regions. Furthermore, we found that the converted genes tended to have more similar expression patterns than nonconverted duplicates. Gene conversion affects biological functions associated with multiple genes, such as catalytic activity, implying opportunities for interaction among members of large gene families, such as NBS-LRR disease-resistance genes, contributing to the occurrence of the gene conversion.ConclusionDuplicated genes in rice subspecies generated by grass polyploidization similar to 100 mya remain affected by gene conversion at high frequency, with important implications for the divergence of rice subspecies. |
| 关键词 | Rice Polyploidization Whole-genome duplication Duplicated genes Ongoing gene conversion |
| 学科领域 | Biotechnology & Applied Microbiology ; Genetics & Heredity |
| DOI | 10.1186/s12864-021-07776-y |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS关键词 | PHYLOGENETIC ANALYSIS ; CONCERTED EVOLUTION ; BLAST RESISTANCE ; GENOME ; SEQUENCE ; RECOMBINATION ; MECHANISMS ; POLYPLOIDIZATION ; DIVERSIFICATION ; PROTEINS |
| WOS研究方向 | Science Citation Index Expanded (SCI-EXPANDED) |
| WOS记录号 | WOS:000664619500002 |
| 出版者 | BMC |
| 文献子类 | Article |
| 出版地 | LONDON |
| 资助机构 | Natural Science Foundation of Hebei Province [C20209064, C2015209069] ; National Science Foundation of China [3151333] ; National Natural Science Foundation of China [32000405] |
| 作者邮箱 | wlsh219@126.com ; wangjinpeng@ibcas.ac.cn |
| 作品OA属性 | Green Submitted, gold, Green Published |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.ibcas.ac.cn/handle/2S10CLM1/26563 |
| 专题 | 系统与进化植物学国家重点实验室 |
| 作者单位 | 1.North China Univ Sci & Technol, Sch Life Sci, Tangshan 063000, Hebei, Peoples R China 2.North China Univ Sci & Technol, Ctr Genom & Computat Biol, Tangshan 063000, Hebei, Peoples R China 3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 4.Chinese Acad Sci, State Key Lab Systemat & Evolutionary Bot, Inst Bot, Beijing 100093, Peoples R China |
| 推荐引用方式 GB/T 7714 | Wei, Chendan,Wang, Zhenyi,Wang, Jianyu,et al. Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence[J]. BMC GENOMICS,2021,22(1). |
| APA | Wei, Chendan.,Wang, Zhenyi.,Wang, Jianyu.,Teng, Jia.,Shen, Shaoqi.,...&Wang, Jinpeng.(2021).Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence.BMC GENOMICS,22(1). |
| MLA | Wei, Chendan,et al."Conversion between 100-million-year-old duplicated genes contributes to rice subspecies divergence".BMC GENOMICS 22.1(2021). |
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| Wei-2021-Conversion （3371KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 请求全文 | |
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