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Rapid evolution of protein diversity by de novo origination in Oryza

Zhang, Li, Ren, Yan, Yang, Tao, Li, Guangwei, Chen, Jianhai, Gschwend, Andrea R., Yu, Yeisoo, Hou, Guixue, Zi, Jin, Zhou, Ruo, Wen, Bo, Zhang, Jianwei, Chougule, Kapeel, Wang, Muhua, Copetti, Dario, Peng, Zhiyu, Zhang, Chengjun, Zhang, Yong, Ouyang, Yidan, Wing, Rod A., Liu, Siqi, Long, Manyuan·2019·Nature Ecology & Evolution
DOI 10.1038/s41559-019-0822-5
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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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  • Most of the ab initio potential lineage-specific genes are artifacts, as the number of singletons is too high considering estimates of the rate of emergence of new genes.

    “It appears that most of the ab initio potential lineage-specific genes are artifacts, as the number of singletons is too high considering estimates of the rate of emergence of new genes (Casola 2018, Zhang et al. 2019, Zile et al. 2020, Vakirlis et al. 2024).”

    From Annotation matters: the effect of structural gene annotation on orthology inference (2025) · cites this paper as Zhang et al. 2019

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Metadata

Authors
Zhang, L., Ren, Y., Yang, T., Li, G., Chen, J., Gschwend, A. R., Yu, Y., Hou, G., Zi, J., Zhou, R., Wen, B., Zhang, J., Chougule, K., Wang, M., Copetti, D., Peng, Z., Zhang, C., Zhang, Y., Ouyang, Y., Wing, R. A., Liu, S., & Long, M.
ORCID
Venue
Nature Ecology & Evolution
Publisher
Springer Science and Business Media LLC
Published
2019-03-11
Volume
3
Issue
4
Pages
679-690
ISSN
2397-334X
DOI
10.1038/s41559-019-0822-5
Cited by
197
References
9
Language
en
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