Relationships between genome methylation, levels of non‐coding RNAs, mRNAs and metabolites in ripening tomato fruit

SUMMARY 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. Significance Statement Understanding the functioning of the intricate genetic regulatory network behind tomato fruit ripening provides new insights into the underlying integration and relationships between the multiple events that collectively determine the ripe phenotype.