Relationships between genome methylation, levels of non-coding RNAs, mRNAs and metabolites in ripening tomato fruit
文献类型： 外文期刊
作者： Zuo, Jinhua 1 ; Grierson, Donald 4 ; Courtney, Lance T. 2 ; Wang, Yunxiang 5 ; Gao, Lipu 1 ; Zhao, Xiaoyan 1 ; Zhu, Be 1 ;
作者机构： 1.Beijing Acad Agr & Forestry Sci, Key Lab Vegetable Postharvest Proc,Beijing Vegeta, Minist Agr & Rural Affairs,Beijing Key Lab Fruits, Minist Agr,Key Lab Urban Agr North,Key Lab Biol &, Beijing, Peoples R China
2.USDA ARS, Cornell Univ Campus, Ithaca, NY 14853 USA
3.Boyce Thompson Inst Plant Res, Cornell Univ Campus, Ithaca, NY 14853 USA
4.Univ Nottingham, Sch Biosci, Sutton Bonington Campus, Loughborough LE12 5RD, Leics, England
5.Beijing Acad Agr & Forestry Sci, Beijing Acad Forestry & Pomol Sci, Beijing 100093, Peoples R China
6.China Agr Univ, Coll Food Sci & Nutr Engn, Dept Food Biotechnol, Lab Postharvest Mol Biol Fruits & Vegetables, Beijing 100083, Peoples R China
关键词： ethylene response; carotenoid pathway; non-coding RNAs; genome methylation; tomato fruit
期刊名称：PLANT JOURNAL （ 影响因子：6.417； 五年影响因子：7.627 ）
ISSN： 0960-7412
年卷期： 2020 年 103 卷 3 期
页码：
收录情况： SCI
摘要： Ripening of tomato fruit is a complex tightly orchestrated developmental process that involves multiple physiological and metabolic changes that render fruit attractive, palatable and nutritious. Ripening requires initiation, activation and coordination of key pathways at the transcriptional and post-transcriptional levels that lead to ethylene synthesis and downstream ripening events determining quality. We studied wild-type, Gr and r mutant fruits at the coding and non-coding transcriptomic, metabolomic and genome methylation levels. Numerous differentially expressed non-coding RNAs were identified and quantified and potential competing endogenous RNA regulation models were constructed. Multiple changes in gene methylation were linked to the ethylene pathway and ripening processes. A combined analysis of changes in genome methylation, long non-coding RNAs, circular RNAs, micro-RNAs and fruit metabolites revealed many differentially expressed genes (DEGs) with differentially methylated regions encoding transcription factors and key enzymes related to ethylene or carotenoid pathways potentially targeted by differentially expressed non-coding RNAs. These included ACO2 (targeted by MSTRG.59396.1 and miR396b), CTR1 (targeted by MSTRG.43594.1 and miR171b), ERF2 (targeted by MSTRG.183681.1), ERF5 (targeted by miR9470-3p), PSY1 (targeted by MSTRG.95226.7), ZISO (targeted by 12:66127788|66128276) and NCED (targeted by MSTRG.181568.2). Understanding the functioning of this intricate genetic regulatory network provides new insights into the underlying integration and relationships between the multiple events that collectively determine the ripe phenotype.
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