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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
Corresponding AuthorWing, Rod A.(rwing@mail.arizona.edu) ; Liu, Siqi(siqiliu@genomics.cn) ; Long, Manyuan(mlong@uchicago.edu)
2019-04-01
Source PublicationNATURE ECOLOGY & EVOLUTION
ISSN2397-334X
Volume3Issue:4Pages:679-690
AbstractNew 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.
DOI10.1038/s41559-019-0822-5
Indexed BySCI
Language英语
WOS Research AreaEnvironmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectEcology ; Evolutionary Biology
WOS IDWOS:000462542100031
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/67723
Collection中国西南野生生物种质资源库
Corresponding AuthorWing, Rod A.; Liu, Siqi; Long, Manyuan
Affiliation1.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
Recommended Citation
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.
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