Abstract
New gene origination is a major source of genomic innovations that confer phenotypic changes and biological diversity. Generation of new mitochondrial genes in plants may cause cytoplasmic male sterility (CMS), which can promote outcrossing and increase fitness. However, how mitochondrial genes originate and evolve in structure and function remains unclear. The rice Wild Abortive type of CMS is conferred by the mitochondrial gene WA352c (previously named WA352) and has been widely exploited in hybrid rice breeding. Here, we reconstruct the evolutionary trajectory of WA352c by the identification and analyses of 11 mitochondrial genomic recombinant structures related to WA352c in wild and cultivated rice. We deduce that these structures arose through multiple rearrangements among conserved mitochondrial sequences in the mitochondrial genome of the wild rice Oryza rufipogon, coupled with substoichiometric shifting and sequence variation. We identify two expressed but nonfunctional protogenes among these structures, and show that they could evolve into functional CMS genes via sequence variations that could relieve the self-inhibitory potential of the proteins. These sequence changes would endow the proteins the ability to interact with the nucleus-encoded mitochondrial protein COX11, resulting in premature programmed cell death in the anther tapetum and male sterility. Furthermore, we show that the sequences that encode the COX11-interaction domains in these WA352c-related genes have experienced purifying selection during evolution. We propose a model for the formation and evolution of new CMS genes via a “multi-recombination/protogene formation/functionalization” mechanism involving gradual variations in the structure, sequence, copy number, and function.
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Acknowledgements
We thank X Liu for providing some of the wild and cultivated rice materials preserved in South China Agricultural University, and H Yu for assistance in the sequence analysis with the CODEML program. We also thank H Wang, D Charlesworth, W Wang, C-I Wu, X-L He, H Ma, Q Zhang, Y Ouyang, and K Tsunewaki for comments on this study and/or the manuscript. This work was supported by grants from the National Nature Science Foundation of China (31230052), the Ministry of Science and Technology of China (2013CBA01401 and 2013CB126904), the Nature Science Foundation of Guangdong Province, China (2014A030310399), and the Postdoctoral Science Foundation of China (2015M570717).
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Supplementary information
Supplementary information, Table S2
Specific primers used for hiTAIL-PCR (Figure 1). (PDF 29 kb)
Supplementary information, Table S3
Primers used for preparation of the plant transformation vector constructs (Figure 2A). (PDF 25 kb)
Supplementary information, Table S5
Primers used for quantitative PCR (Figure 5B). (PDF 25 kb)
Supplementary information, Table S6
Primers used for qRT-PCR (Figure 3). (PDF 25 kb)
Supplementary information, Table S7
Primers used for construction of yeast two-hybrid vectors (Figure 6A, C, D and Figure S7). (PDF 29 kb)
Supplementary information, Figure S1
Male sterility and fertility and the co-segregation with the transgenes in the rice and Arabidopsis transgenic plants. (PDF 205 kb)
Supplementary information, Figure S2
Fertility phenotypes of Arabidopsis T1 plants with MTS-WA314. (PDF 295 kb)
Supplementary information, Figure S3
Male phenotype of the backcrossed rice lines. (PDF 197 kb)
Supplementary information, Figure S4
Detection of therpl5/cox1/orf284 configuration in Oryza species. (PDF 117 kb)
Supplementary information, Figure S5
Comparison among the conserved sequences of the recombinant structures and those from other plant species as references. (PDF 200 kb)
Supplementary information, Figure S6
The repeat sites for recombination events among the donor (source) sequences to generate the new structures. (PDF 417 kb)
Supplementary information, Figure S7
Coexistence of S314a, S276 and S310 and their substoichiometric shifting. (PDF 111 kb)
Supplementary information, Figure S8
Alignment of the protein sequences of the CMS genes and CMS-related ORFs. (PDF 82 kb)
Supplementary information, Figure S9
Yeast two-hybrid assay of the COX11-interaction of the cs1-encoded polypeptides of the CMS genes and the related ORFs. (PDF 147 kb)
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Tang, H., Zheng, X., Li, C. et al. Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes. Cell Res 27, 130–146 (2017). https://doi.org/10.1038/cr.2016.115
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DOI: https://doi.org/10.1038/cr.2016.115
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