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Guo S, Zheng Y, Meng D, Zhao X, Sang Z, Tan J, Deng Z, Lang Z, Zhang B, Wang Q, Bouzayen M, Zuo J. DNA and coding/non-coding RNA methylation analysis provide insights into tomato fruit ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:399-413. [PMID: 36004545 DOI: 10.1111/tpj.15951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/03/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Ripening is the last, irreversible developmental stage during which fruit become palatable, thus promoting seed dispersal by frugivory. In Alisa Craig fruit, mRNAs with increasing m5C levels, such as STPK and WRKY 40, were identified as being involved in response to biotic and abiotic stresses. Furthermore, two mRNAs involved in cell wall metabolism, PG and EXP-B1, also presented increased m5C levels. In the Nr mutant, several m5C-modified mRNAs involved in fruit ripening, including those encoding WRKY and MADS-box proteins, were found. Targets of long non-coding RNAs and circular RNAs with different m5C sites were also found; these targets included 2-alkenal reductase, soluble starch synthase 1, WRKY, MADS-box, and F-box/ketch-repeat protein SKIP11. A combined analysis of changes in 5mC methylation and mRNA revealed many differentially expressed genes with differentially methylated regions encoding transcription factors and key enzymes related to ethylene biosynthesis and signal transduction; these included ERF084, EIN3, AP2/ERF, ACO5, ACS7, EIN3/4, EBF1, MADS-box, AP2/ERF, and ETR1. Taken together, our findings contribute to the global understanding of the mechanisms underlying fruit ripening, thereby providing new information for both fruit and post-harvest behavior.
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Affiliation(s)
- Susu Guo
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yanyan Zheng
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Zhaoze Sang
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Jinjuan Tan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bo Zhang
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Qing Wang
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Mondher Bouzayen
- Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Castanet-Tolosan, France
| | - Jinhua Zuo
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
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