Multi-omics data integration provides insights into the post-harvest biology of a long shelf-life tomato landrace

In this study we investigated the transcriptome and epigenome dynamics of the tomato fruit during post-harvest in a landrace belonging to a group of tomatoes (Solanum lycopersicum L.) collectively known as Piennolo del Vesuvio, all characterized by a long shelf-life. Expression of protein-coding genes and microRNAs as well as DNA methylation patterns and histone modifications were analysed in distinct post-harvest phases. Multi-omics data integration contributed to the elucidation of the molecular mechanisms underlying processes leading to long shelf-life. We unveiled global changes in transcriptome and epigenome. DNA methylation increased and the repressive histone mark H3K27me3 was lost as the fruit progressed from red ripe to 150 days post-harvest. Thousands of genes were differentially expressed, about half of which were potentially epi-regulated as they were engaged in at least one epi-mark change in addition to being microRNA targets in similar to 5% of cases. Down-regulation of the ripening regulator MADS-RIN and of genes involved in ethylene response and cell wall degradation was consistent with the delayed fruit softening. Large-scale epigenome reprogramming that occurred in the fruit during post-harvest likely contributed to delayed fruit senescence.

Automated summary

In this study, we investigated the changes in the transcriptome and epigenome of a long shelf-life tomato landrace during post-harvest. We discovered global changes in the transcriptome and epigenome, with increased DNA methylation and loss of a repressive histone mark. Thousands of genes showed differential expression, with a significant portion potentially being regulated by epigenetic mechanisms. Down-regulation of genes related to fruit ripening and softening was consistent with the prolonged shelf-life. Large-scale epigenome reprogramming during post-harvest likely contributes to delayed fruit senescence.