Mining Ferula gummosa transcriptome to identify miRNAs involved in the regulation and biosynthesis of terpenes

Ferula gummosa is a well-known medicinal and industrial plant for its oleo-gum-resin named galbanum. So far, there is no information about the role of miRNAs on the production of terpenes as the major secondary metabolite of galbanum. In the present study, RNA-seq data on the root and flower of the plant were used to predict miRNAs and their targets using computational approaches. Additionally, biological network analyses were used to unravel the direct or indirect regulatory effects of miRNAs on the targets involved in terpene biosynthesis. For the first time, 220 miRNAs from 94 families have been reported in F. gummosa. miR5658, miR1533, miR5021, miR414, and miR1436 are the top five miRNAs with high abundance. Gene ontology (GO) analysis of the identified targets showed that in the biological process category, the miRNA-regulated genes were highly involved in transcription. According to the KEGG and PlantCyc results, six miRNAs from five miRNA families including miR2919, miR5251, miR838, miR5021, and miR5658 were found to be related to the pathway of terpene biosynthesis. Moreover, network analysis showed that three terpene-regulating TFs namely SPL7, SPL11, and ATHB13 are putatively regulated by three miRNAs including miR1533, miR5021, and miR5658 respectively. Differential gene expression results showed that the expression levels of these miRNAs are negatively correlated to the expression levels of both TFs and their co-expressed terpene biosynthesis genes.