Authors: Riccardo Aiese Cigliano, Riccardo Aversano, Antonio Di Matteo, Samuela Palombieri, Pasquale Termolino, Claudia Angelini, Hamed Bostan, Maria Cammareri, Federica Maria Consiglio, Floriana Della Ragione, Rosa Paparo, Vladimir Totev Valkov, Antonella Vitiello, Domenico Carputo, Maria Luisa Chiusano, Maurizio D’Esposito, Silvana Grandillo, Maria Rosaria Matarazzo, Luigi Frusciante, Nunzio D’Agostino, Clara Conicella


  • Sequentia Biotech SL, Carrer de Valencia, 08009, Barcelona, Spain
  • Department of Agricultural Sciences, University of Naples Federico II, Via Universita’ 100, 80055 Portici, Italy
  • Institute of Biosciences and Bioresources, National Research Council of Italy, Via Universita` 133, 80055 Portici, Italy
  • Institute for Applied Calculus, National Research Council of Italy, Via P. Castellino 111, 80131, Napoli
  • Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, National Research Council of
    Italy, Via P. Castellino 111, 80131, Napoli

Publication: Horticulture Research

Date: January 2022

Full paper: 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 ~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.