National Research Council of Italy

Institute of Biosciences and BioResources

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IBBR publication #1433

Coding and non-coding RNAs in a long shelf-life tomato variety

Conicella C, Cammareri M, Consiglio FM, Grandillo S, Palombieri S, Termolino P, D’Esposito M, Matarazzo M, Della Ragione F, other co-authors participating to Consortium EPITOM

In: “Joint Congress SIBV-SIGA ’Feeding the planet: plant science and breeding for the future of agriculture’”. Milano, 8-11/9/2015. [ISBN: 978-88-904570-5-0] (2015)

Epigenetics has been proven to be involved in the regulation of tomato fruit ripening, but a comprehensive investigation on post-harvest related processes is still lacking. By applying next generation sequencing technologies, the EPITOM Consortium is performing integrative analyses including coding and non-coding RNAs, DNA methylation, and histone post-translational modifications in long shelf-life traditional variety Lucariello, recognized as ’Pomodorino del Piennolo del Vesuvio PDOP’. Fruit pericarps have been sampled at the red ripe stage and at two and five months in post-harvest. Currently, the data of high throughput sequencing of mRNA, small RNAs (sRNA), and long non-coding RNAs (lncRNA) are available. RNA-sequencing (RNA-Seq) analysis allowed the identification of several new genes in comparison to the current tomato genome annotation (ITAG2.4, SL2.50). In addition, a large number of alternative transcript variants were identified at the post-harvest stages compared to the red ripe one. Gene ontology (GO) enrichment analysis of all differentially expressed genes highlighted nine over-represented GO terms involved in epigenetic mechanisms, thereby suggesting a pivotal role of the epigenome during tomato post-harvest. Putative miRNAs were also predicted to target differentially expressed mRNAs involved in fruit ripening-related processes. In addition, a number of miRNA precursors showed upstream binding sites for stress related transcription factors. LncRNAs, isolated from RNA-seq experiment selecting ORFs longer than 200 nt are under evaluation to identify novel lncRNAs and to investigate their role in the regulatory mechanisms of tomato fruit ripening during post-harvest. All the data are being reconciled in a web-based platform to allow multilevel integrated analyses of the available collections.

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