In silico identification, characterization and expression analysis of miRNAs in Cannabis sativa L.

•Homology based computational approach of miRNA identification was conducted in Transcript Sequence Assemblies (TSA) and ESTs of Cannabis sativa L.•Eighteen miRNAs belonging to 9 independent miRNA families were identified in C. sativa L. for the first time.•Expression of 6 predicted miRNAs was confirmed in young and mature leaf tissues of C. sativa seedlings using Real Time-PCR.•A total of 80 potential target genes were identified for the predicted miRNAs in Arabidopsis genome.

Cannabis sativa L. is an annual herb and economically important as a source of fiber, oil, food and for its medicinal and intoxicating properties. MicroRNAs are a class of short (~ 21 nt), non-coding regulatory RNAs that play a major role in post-transcriptional gene silencing. By in silico analysis of the publically available Transcript Sequence Assemblies (TSA) and Expressed Sequence Tags (ESTs) of C. sativa, a total of 18 conserved miRNAs belonging to 9 independent families were identified. To validate the predicted miRNAs, SYBR green based assay of qPCR was applied to detect the tissue-specific (young and mature leaf) expression of 6 putative miRNAs (csa-miR156, csa-miR159a, csa-miR171b, csa-miR172a, csa-miR5021a, csa-miR6034) in C. sativa. A total of 80 target genes were also recognized for the newly identified miRNAs, and subsequently assigned to three broad functional categories: biological processes, cellular components and molecular functions as defined for the Arabidopsis proteome. The potential target genes consist of transcription factors (33.75%), transporters (5%), kinase and other enzymes (20%) as well as signaling and other functional proteins (32.50%). The findings in this study on C. sativa miRNA precursors, mature miRNAs, and miRNA targets will be helpful for future research on miRNA-mediated gene regulation in this important plant species.