Prospecting NGS-transcriptomes to assess regulation of miRNA-mediated secondary metabolites biosynthesis in Swertia chirayita, a medicinal herb of the North-Western Himalayas

Swertia chirayita is a high value medicinal herb that possesses diverse therapeutic traits. Molecular data related to the biosynthesis of major secondary metabolites exhibiting these pharmacological properties are limited. Growing demand and poor cultural procedures necessitate improved genetic intervention strategies, which can be implemented to positively influence the biosynthetic machinery and its regulatory network. miRNAs are indicated to play pivotal role in various biological processes, including growth and secondary metabolism. In an attempt to identify conserved miRNAs, computational methods were followed across two transciptomes of Swertia contrasting for metabolite levels and cultural conditions. A total of ten miRNAs were predicted followed by target prediction that resulted in the identification of eleven potential targets having roles in secondary metabolism. RT-qPCR analysis showed six miRNAs (miR-168, miR-11320, miR-166a, miR-11071, miR-156a and miR-166b), targeting Acetyl -CoA acetyltransferase (AACT), Aspar tate aminotransferase (PHAT), premnaspirodiene oxygenase (PSO), ribulose-phosphate 3-epimerase (RPE), phosphoglycerate mutase (PGM) and a gene encoding homeobox-leucine zipper protein (HD-ZIP) having negative correlations with their targets, thereby indicating their possible association in secondary metabolites biosynthesis. The study sheds light on miRNA mediated regulation of secondary metabolites biosynthesis in a lesser explored herbal plant Swertia chirayita. Besides, the putatively identified miRNAs can be targeted for genetic manipulation to enhance secondary metabolites biosynthesis in S. chirayita.