Identification of circular RNAs and their targets during tomato fruit ripening

Circular RNAs (circRNAs) have been found to be highly abundant and evolutionarily conserved in both animals and plants. Tomato is a widely characterized model plant, but very little information is available about the feature and functions of circRNAs in this species. In the present study, to invest whether circRNAs are involved in fruit ripening process, we used deep sequencing to monitor the changes in circRNAs between mature green tomato fruit and red ripening ones. A total of 705 circRNAs were detected in these two samples, of which 340 were differentially regulated. CircRNAs were reported to function as cis-regulator and miRNA sponge to regulate physiological and biochemical metabolism in animals. In this study, 19 differentially expressed circRNAs were found to function as putative miRNA sponges to regulate the expression of 94 target mRNAs. Furthermore, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation of both parent genes and target mRNAs were performed to reveal the functions of differentially expressed circRNAs during ripening. The results revealed that circRNAs may be involved in regulating fruit ripening by mediating metabolism adaptation, hormone balance, and photosynthesis related pathways. Besides, circRNAs were predicted to be involved in transcription regulation through targeting transcription factors such as ethylene-responsive transcription factor (ERF), squamosa promoter binding-like protein (SBP) and myeloblastosis (MYB) proto-oncogene protein. These results shed light on the role of circRNAs in fruit ripening and help to identify novel circRNAs in tomato.