Relationships between genome methylation, levels of noncoding RNAs, mRNAs and metabolites in ripening tomato fruit.

Tomato fruit ripening is a complex tightly orchestrated developmental process that involves multiple physiological and metabolic changes rendering 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 noncoding transcriptomic, metabolomic, and genome methylation levels. Numerous differentially expressed noncoding RNAs were identified and quantified and potential ceRNAs regulation models were constructed. Multiple gene methylation changes were linked to the ethylene pathway and ripening processes. A combined analysis of genome methylation changes, lncRNAs, circRNAs, miRNAs and fruit metabolites revealed many differentially expressed (DE) genes with differentially methylated regions (DMRs) encoding transcription factors and key enzymes related to ethylene or carotenoid pathways potentially targeted by DE noncoding 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.