Computational screening of miRNAs and their targets in leaves of Hypericum spp. by transcriptome-mining: a pilot study

Abstract

Main conclusion: Our work provides a survey of mature miRNAs, their target genes and primary precursors identified by in-silico approach in leaf transcriptomes of five selected Hypericum species. Abstract: MiRNAs are small non-coding RNA molecules found in animals, terrestrial plants, several algae and molds. As their role lies in the post-transcriptional gene silencing, these tiny molecules regulate many biological processes. Phyto-miRNAs are considered the important regulators of secondary metabolism in medicinal plants. The genus Hypericum comprises many producers of bioactive compounds, mainly unique naphtodianthrones with a great therapeutic potential. The main goal of our work was to identify genetically conserved miRNAs, characterize their primary precursors and target sequences in the leaf transcriptomes of five Hypericum species using in-silico approach. We found 20 sequences of potential Hypericum pri-miRNAs, and predicted and computationally validated their secondary structures. The mature miRNAs were identified by target genes screening analysis. Whereas predicted miRNA profiles differed in less genetically conserved families, the highly conserved miRNAs were found in almost all studied species. Moreover, we detected several novel highly likely miRNA–mRNA interactions, such as mir1171 with predicted regulatory role in the biosynthesis of melatonin in plants. Our work contributes to the knowledge of Hypericum miRNAome and miRNA–mRNA interactions.