Genomic and epigenomic analysis of tomato fruit senescence

Quantitative and qualitative post-harvest losses occur worldwide being estimated over 50% in some regions. It would be of great benefit to control fruit senescence thereby improving fruit quality and storability. Tomato (Solanum lycopersicum L.) is the best model for understanding the ripening process of climacteric fruit. However, it is still unclear whether fruit senescence is part of the ripening process or is a distinct downstream process. To accomplish a comprehensive investigation on the senescence-related processes, a multi-omics approach including coding and non-coding RNAs, DNA methylation, and histone post-translational modifications (H3K4me3, H3K27me3, H3K9K14ac) was performed in tomato by using the landrace Lucariello (LUC). LUC is recognized as 'Pomodorino del Piennolo del Vesuvio' and has a shelf-life up to 150 days. Fruit pericarps were sampled at the red ripe stage (RD0), and at 60 (RD60) and 150 (RD150) days after the harvest. Dry weight, soluble solids content and firmness decreased in LUC fruits at RD150by 13%, 10% and 67%, respectively, in comparison with the earliest RD0. Differentially expressed genes (DEGs=10285) from RNA-seq included many transcription factor genes involved in fruit ripening-related processes. Whole Genome Bisulfite Sequencing highlighted a genome-wide loss of methylation in CG and CHG residues at RD60 which is maintained to RD150. We focused on DEGs that were likely regulated by DNA methylation as well as by the abovementioned histone marks or miRNAs. In particular, more than 2000 putative miRNAs were associated with anti-correlated DEG targets in a predictive manner. Among the regions of significant H3K4me3, H3K27me3, H3K9K14ac ChIP enrichment, the peaks of read counts that were different between time points and located around the transcription start site were correlated with DEGs. Similarly, the regions that significantly gained/lost DNA methylation across time points (Differentially Methylated Regions) were analysed for the association with DEGs. Co-expression analysis is currently underway to find activator and/or repressor candidates in the regulatory pathways underlying tomato fruit senescence. All the genomic and epigenomic datasets are gathered into a dedicated and user-friendly web-based platform.