Regulation of the alkaloid biosynthesis by miRNA in opium poppy

Summary Opium poppy ( P apaver somniferum ) is an important medicinal plant producing benzylisoquinoline alkaloids ( BIA ). Micro RNA s (mi RNA s) are endogenous small RNA s ( sRNA s) of approximately 21 nucleotides. They are noncoding, but regulate gene expression in eukaryotes. Although many studies have been conducted on the identification and functions of plant mi RNA , scarce researches on mi RNA regulation of alkaloid biosynthesis have been reported. In this study, a total of 316 conserved and 11 novel mi RNA s were identified in opium poppy using second‐generation sequencing and direct cloning. Tissue‐specific regulation of mi RNA expression was comparatively analysed by mi RNA microarray assays. A total of 232 mi RNA s were found to be differentially expressed among four tissues. Likewise, 1469 target transcripts were detected using in silico and experimental approaches. The Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that mi RNA putatively regulates carbohydrate metabolism and genetic‐information processing. Additionally, mi RNA target transcripts were mostly involved in response to stress against various factors and secondary‐metabolite biosynthesis processes. Target transcript identification analyses revealed that some of the mi RNA s might be involved in BIA biosynthesis, such as pso‐miR13, pso‐miR2161 and pso‐miR408. Additionally, three putatively mature mi RNA sequences were predicted to be targeting BIA ‐biosynthesis genes.