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Nat Ecol Evol. 2019 Apr;3(4):679-690. doi: 10.1038/s41559-019-0822-5. Epub 2019 Mar 11.

Rapid evolution of protein diversity by de novo origination in Oryza.

Author information

1
Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA.
2
BGI-Shenzhen, Shenzhen, China.
3
National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
4
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.
5
Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
6
Key Laboratory of Zoological Systematics and Evolution & State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
7
Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA. rwing@mail.arizona.edu.
8
BGI-Shenzhen, Shenzhen, China. siqiliu@genomics.cn.
9
Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA. mlong@uchicago.edu.

Abstract

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.

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PMID:
30858588
DOI:
10.1038/s41559-019-0822-5
[Indexed for MEDLINE]

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