Identification of conserved and novel microRNAs in Catharanthus roseus by deep sequencing and computational prediction of their potential targets

•Conserved and novel miRNAs were identified in C. roseus by deep sequencing.•Expression of selected cro-miRNAs was studied in vegetative tissues of C. roseus.•Targets were predicted for cro-miRNAs in C. roseus and other plant species.•This work enriches the existing information regarding miRNAs and their targets.

MicroRNAs are small endogenous non-coding RNAs of ~ 19–24 nucleotides and perform regulatory roles in many plant processes. To identify miRNAs involved in regulatory networks controlling diverse biological processes including secondary metabolism in Catharanthus roseus, an important medicinal plant, we employed deep sequencing of small RNA from leaf tissue. A total of 88 potential miRNAs comprising of 81 conserved miRNAs belonging to 35 families and seven novel miRNAs were identified. Precursors for 16 conserved and seven novel cro-miRNAs were identified, and their stem-loop hairpin structures were predicted. Selected cro-miRNAs were analyzed by stem-loop qRT-PCR and differential expression patterns were observed in different vegetative tissues of C. roseus. Targets were predicted for conserved and novel cro-miRNAs, which were found to be involved in diverse biological role(s) including secondary metabolism. Our study enriches available resources and information regarding miRNAs and their potential targets for better understanding of miRNA-mediated gene regulation in plants.