De novo transcriptome assembly and conserved microRNAs identification of medicinal plant, Kelussia odoratissima Mozaff.

Kelus (Kelussia odoratissima Mozaff.), a medicinal plant rich in active pharmaceutical ingredients with therapeutic effects, is found only in central Zagros Mountains, west of IRAN. Despite being in danger of extinction, there are no genetic evidences regarding kelus Omics as well as valuable compounds biosynthesis pathways. MicroRNAs (miRNAs) play an important role in different processes such as growth and development, cell proliferation, response to stresses and biosynthesis metabolite. As far as the bioinformatic data are concern, the genome/transcriptome of kelus has not been sequenced. The present study was performed to identify the conserved miRNAs and their target genes in the kelus leaf transcriptome. After pair-end sequencing with the Illumina HiSeq 2500 platform, clean reads were assembled. In total, 4658 unigenes were found to contain potential miRNAs sequences. Following strict filtering criteria, five miRNAs belonging to five conserved miRNA families (miR156-3P, miR408, miR169, miR171 and miR398) were identified among candidate sequences. Results of this study revealed that the target genes of the identified miRNAs were involved in various metabolic pathways, including butanoate metabolism, glyoxylate and dicarboxylate metabolism, starch and sucrose metabolism, carbon fixation in photosynthetic organisms, peroxisome degradation, and fatty acid degradation. By affecting genes associated with six metabolic pathways, miR408 was identified as the most influential conserved microRNA in the kelus leaf transcriptome. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of kelus, these miRNAs can be used as candidate genes for breeding kelus quantitative and qualitative traits.