| Rapid evolution of protein diversity by de novo origination in Oryza | |
Zhang, Li1; Ren, Yan2; Yang, Tao3,4 ; Li, Guangwei3,4; Chen, Jianhai1; Gschwend, Andrea R.1; Yu, Yeisoo5; Hou, Guixue3,4; Zi, Jin2; Zhou, Ruo2; Wen, Bo2; Zhang, Jianwei5; Chougule, Kapeel5; Wang, Muhua5; Copetti, Dario5; Peng, Zhiyu2; Zhang, Chengjun1,6; Zhang, Yong7,8; Ouyang, Yidan3,4; Wing, Rod A.5; Liu, Siqi2; Long, Manyuan1
| |
| 通讯作者 | Wing, Rod A.(rwing@mail.arizona.edu) ; Liu, Siqi(siqiliu@genomics.cn) ; Long, Manyuan(mlong@uchicago.edu) |
| 2019-04-01 | |
| 发表期刊 | NATURE ECOLOGY & EVOLUTION
 |
| ISSN | 2397-334X |
| 卷号 | 3期号:4页码:679-690 |
| 摘要 | New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection. |
| DOI | 10.1038/s41559-019-0822-5 |
| 收录类别 | SCI |
| 语种 | 英语 |
| WOS记录号 | WOS:000462542100031 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.kib.ac.cn/handle/151853/67723 |
| 专题 | 中国西南野生生物种质资源库 |
| 通讯作者 | Wing, Rod A.; Liu, Siqi; Long, Manyuan |
| 作者单位 | 1.Univ Chicago, Dept Ecol & Evolut, 940 E 57Th St, Chicago, IL 60637 USA 2.BGI Shenzhen, Shenzhen, Peoples R China 3.Huazhong Agr Univ, Natl Key Lab Crop Genet Improvement, Wuhan, Hubei, Peoples R China 4.Huazhong Agr Univ, Natl Ctr Plant Gene Res Wuhan, Wuhan, Hubei, Peoples R China 5.Univ Arizona, Sch Plant Sci, Arizona Genom Inst, Tucson, AZ 85721 USA 6.Chinese Acad Sci, Kunming Inst Bot, Kunming, Yunnan, Peoples R China 7.Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China 8.Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects, Beijing, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhang, Li,Ren, Yan,Yang, Tao,et al. Rapid evolution of protein diversity by de novo origination in Oryza[J]. NATURE ECOLOGY & EVOLUTION,2019,3(4):679-690. |
| APA | Zhang, Li.,Ren, Yan.,Yang, Tao.,Li, Guangwei.,Chen, Jianhai.,...&Long, Manyuan.(2019).Rapid evolution of protein diversity by de novo origination in Oryza.NATURE ECOLOGY & EVOLUTION,3(4),679-690. |
| MLA | Zhang, Li,et al."Rapid evolution of protein diversity by de novo origination in Oryza".NATURE ECOLOGY & EVOLUTION 3.4(2019):679-690. |
| 条目包含的文件 | 下载所有文件 | |||||
| 文件名称/大小 | 文献类型 | 版本类型 | 开放类型 | 使用许可 | ||
| Zhang-2019-Rapid evo（1636KB） | 期刊论文 | 出版稿 | 开放获取 | CC BY-NC-SA | 浏览 下载 | |
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。
修改评论