Identification of miRNAs and target genes in Satureja khuzistanica Jamzad

MicroRNAs (miRNAs) are one of the small and non-coding regulatory molecules, which regulate gene expression by transcriptional cleavage or translational suppression. miRNAs are involved in regulating a wide range of metabolic and physiological processes in plants.The mint family plants, especially Satureja khuzistanica, are well known herbs for its flavor, fragrance and medicinal properties. To date, no miRNAs have been identified in Satureja species. In present study, a computational approach based on homology search was used to identify miRNAs and their targets of Satureja khuzistanica. Non-coding unigenes were identified and considered for candidates of miRNAs precursor. After evaluating the general parameters such as GC percentage, minimum folding free energy (MFE), minimum free energy index (MFEI) and secondary structure, 58 miRNAs were identified, which among them, by applying plant specific parameters and filtring the miRNAs from several transcripts, overall ten miRNAs were identified. Then, 930 target transcripts were predicted using psRNATarget website and the annotation of them was performed by using BLASTx tools of NCBI Blast+ software (v2.6.0). Examination of target genes showed that auxin-responsive genes, GRAS, AGO2 and LAC family genes are the main targets of the identified miRNAs in S. khuzistanica. Pathway enrichment analysis of the target genes revealed that the secondary metabolic pathway is significantly among the targets of the identified miRNAs. This is the first study describing miRNAs and their role in the regulation of target genes in S. khuzistanica.