Transcriptomic profile analysis of non-coding RNAs involved in Capsicum chinense Jacq. fruit ripening

•Herein, we identify ncRNAs involved in fruit ripening of Capsicum chinense Jacq.•142 novel miRNAs, 9928 circRNAs and 20563 lncRNAs were identified.•In this, 4627 mRNA, 5918 lncRNA and 85 circRNA were upregulated as 3046 mRNA, 5908 lncRNA and 86 circRNA were downregulated.•Two miRNA’s (Capana10g000965 and Capana12g001292) involved in carotenoid synthesis were identified.•One circRNA that targets alanine-glyoxylate aminotransferase 2 and is involved in pepper aroma formation was identified. Capsicum species are highly diverse plants, with over 200 species. Their fruits are important, both nutritionally and economically. Plant non-coding RNAs (ncRNAs) and microRNAs (miRNAs) significantly influence several plant biological processes, including regulating their gene expression. Specifically, in pepper plants, in excess of 300 conserved and novel miRNAs have previously been described. However, the functional role and influence of ncRNAs in pepper fruit ripening processes have not been sufficiently addressed. Herein, we used high-throughput sequencing to identify ncRNAs in Capsicum chinense Jacq. at three distinct fruit ripening stages (green ripening stage, the colour transition stage and the red ripening stage). 142 novel miRNAs, 9928 circRNAs and 20,563 lncRNAs were identified. DE analysis revealed that 4627 mRNA, 5918 lncRNA and 85circRNA were upregulated. Two miRNAs were associated with pigment biosynthetic process hence are linked to carotenoid synthesis in pepper fruits. Similarly, two known miRNAs; miR157d-3p and miR396h, that target beta-glucosidase – a vital enzyme in the fruit ripening process were identified. Further, circRNA that targets alanine-glyoxylate aminotransferase 2 (Capana00g005022); which contributes to pepper aroma formation was identified. In conclusion, CircRNAs, lncRNAs and mRNAs can perform as ceRNAs in gene regulation in plants. Overall, the findings from this study provide knowledge on ncRNAs functional and regulation dynamism during Capsicum chinense Jacq. pepper fruit ripening process.