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Rapid evolution of protein diversity by de novo origination in Oryza

Nature Ecology & Evolution volume 3, pages 679–690 (2019)Cite this article

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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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Fig. 1: Identification of de novo genes that originated recently during Oryza diversification.
Fig. 2: Stepwise origination processes for the de novo gene Osjap05g30030.
Fig. 3: Stepwise origination process for the de novo gene Osjap06g21910.
Fig. 4: Patterns of de novo origination in evolution, expression and gene structures.
Fig. 5: Example of the verification of protein products translated from a candidate de novo gene, Osjap05g20760.
Fig. 6: Summary of the protein products translated from candidate de novo genes in O. sativa subspecies japonica, as detected by experimental proteomics and ribosomal profiling analyses.

Data availability

The data that support the findings of this study are available in Supplementary Files 1 and 2, Supplementary Figs. 4 and 5, and Supplementary Tables 11 and 14.

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Acknowledgements

We appreciate valuable discussions with N. Jiang at MSU, the group of M. L. at Chicago, Y. Liao and M. Chen at the Institute of Genetics and Development in Beijing, and J. P. Staley at Chicago. We are thankful for the editing done by E. Mortola. This work was supported by the USA National Science Foundation (NSF) under Plant Genome Research Program numbers 0321678, 0638541 and 0822284, the Bud Antle Endowed Chair of Excellence in Agriculture and Life Sciences, and the AXA Chair for Evolutionary Genomics and Genome Biology (to R.A.W.), NSF MCB number 1026200 (to M.L. and R.A.W.), NSF MCB 1051826 and NIH R01 GM 100768 (to M.L.), the National Key R&D Program of China 2017YFC0908400 (to S.L.) and the National Program for Support of Top-notch Young Professionals of China (to Y.O.).

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  1. These authors contributed equally: Li Zhang, Yan Ren.

Authors and Affiliations

  1. Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA

    Li Zhang, Jianhai Chen, Andrea R. Gschwend, Chengjun Zhang & Manyuan Long

  2. BGI-Shenzhen, Shenzhen, China

    Yan Ren, Jin Zi, Ruo Zhou, Bo Wen, Zhiyu Peng & Siqi Liu

  3. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China

    Tao Yang, Guangwei Li, Guixue Hou & Yidan Ouyang

  4. Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA

    Yeisoo Yu, Jianwei Zhang, Kapeel Chougule, Muhua Wang, Dario Copetti & Rod A. Wing

  5. Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China

    Chengjun Zhang

  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

    Yong Zhang

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Contributions

L.Z., R.A.W., S.L. and M.L. conceived and designed the project. L.Z., Y.R., R.A.W., S.L. and M.L. wrote the manuscript, with significant contributions from C.Z., A.R.G., J.C. and Y.Z. L.Z. conducted the computational genomic analysis, with significant contributions from A.R.G., K.C., J.Z. and Y.Z. C.Z., Y.Y., J.Z., K.C., M.W., D.C. and R.A.W. generated and annotated the genome sequences. Y.R., G.H., J.Z., L.Z. and S.L. designed and conducted the proteomics experiments to detect proteins translated from de novo genes. R.Z., B.W., L.Z. and Z.P. conducted the analysis of public proteomics databases. Y.R., L.Z., J.C., M.L. and S.L. performed further evolutionary and proteomics analyses. T.Y., G.L. and Y.O. grew rice strains in Sanya (China) and dissected rice tissues. J.C., L.Z., C.Z. and M.L. conducted the evolutionary substitution analyses of de novo genes.

Corresponding authors

Correspondence to Rod A. Wing, Siqi Liu or Manyuan Long.

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Competing interests

The authors declare no competing interests.

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Supplementary information

Supplementary Figures

Supplementary Figures 1–6

Reporting Summary

Supplementary File 1

Sequence alignments of 929 orphan genes exported from the MASCE program. Alignments were manually annotated at a later stage and can be found online

Supplementary File 2

Ribosome profiling evidence for candidate de novo genes

Supplementary Table 1

ORF status of de novo gene candidates in each species

Supplementary Table 2

Transcription status of de novo gene candidates in each species

Supplementary Table 3

Candidate de novo genes with matches in the Genbank’s nr database

Supplementary Table 4

Statistics of mutations that are crucial for the transformation of noncoding to coding sequences

Supplementary Table 5

Population genomics of indels and SNP in O. sativa japonica and O. barthii.

Supplementary Table 6

Expression level and tissue specificity of candidate de novo genes and old singleton 76 genes derived from OGE datasets including leaf, root, and panicle.

Supplementary Table 7

Gene structures with relevant statistics

Supplementary Table 8

Intron phase distributions for different gene categories

Supplementary Table 9

Candidate de novo genes with signals of natural selection resulting from the branch model analyses in PAML

Supplementary Table 10

. Candidate de novo genes that have been identified with peptide supports by the MRM method.

Supplementary Table 11

The eight datasets used for proteomics analysis of candidate de novo genes

Supplementary Table 12

Candidate de novo genes that have been identified with peptide supports.

Supplementary Table 13

Candidate de novo genes with ribosomal profiling evidence supports.

Supplementary Table 14

tRNA adaptive indexes (tAIs) in 175 de novo genes (plus 7 isoforms) and 4,965 single-copy genes (plus 2,079 isoforms).

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Zhang, L., Ren, Y., Yang, T. et al. Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol 3, 679–690 (2019). https://doi.org/10.1038/s41559-019-0822-5

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