Identification of conserved miRNAs and their putative target genes in Podophyllum hexandrum (Himalayan Mayapple)

• Identification of miRNAs in P.hexandrum — an endangered medicinal plant.
• Prediction of target genes of P.hexandrum miRNAs and their functional annotation.
• Validation of P.hexandrum miRNAs through stem-loop qRT-PCR.

MicroRNAs (miRNAs) are a class of naturally occurring, endogenous, small non-coding RNA molecules that play a crucial role in post-transcriptional gene regulation either by directing mRNAs for cleavage or translational repression. Plant miRNAs show near-perfect complementarity to their target mRNAs. Podophyllum hexandrum is an endangered medicinal plant. The rhizome and roots of P. hexandrum contain podophyllotoxin that possess antitumor activity. Several miRNAs have been identified in different plant species to date but, miRNAs and their target genes are still unknown in P. hexandrum. In the present study, a total of 60 mature miRNAs and 6 pre-miRNAs were identified in P. hexandrum by 454 pyrosequencing. Quantitative real-time PCR was used to validate the expression levels of some of the identified miRNAs. The P. hexandrum miRNAs targeted a variety of mRNAs. Gene ontology (GO) analysis of these target genes revealed 13 different biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the identified miRNAs regulate various metabolic pathways, especially biosynthesis of secondary metabolites. Our research work provides some elementary information about miRNA mediated regulation of secondary metabolite biosynthesis in P.hexandrum.