Identification of conserved miRNAs of Hypericum perforatum using next-generation sequencing (NGS) data

miRNA genes consider as an important class of gene expression regulators that have diverse responses to environmental stresses and play a key role in regulating gene expression during post-transcriptional regulation. Hypericum perforatum, is well-known medicinal plant for its application in the treatment of depression due to the effects of its bioactive compounds named hypericin and hyperforin. The present study was performed to identify the conserved miRNAs and their target genes in the transcriptome of H. perforatum. First, RNA-seq data were obtained from the European Nucleotide Archive (ENA) of EMBL-EBI database and then the transcriptome (RNA) sequences were assembled. The non-coding transcripts were identified and considered as miRNA precursors candidate sequences. Finally, six miRNAs named Hp-miR395, Hp-miR845d, Hp-miR414, Hp-miR159, Hp-miR159e, and Hp-miR156c were identified from the candidate sequences using of C-mii software after applying strict filters.  Investigation of the protein-protein interaction network determined the relationships between the target genes and target proteins especially in transcription factors. In the next step, to confirm the target genes for the identified miRNAs, the foliar application of Methyl Jasmonate (MJ) with concentrations of 0 (control) and 200 μM was performed on H. perforatum plants and the expression pattern of two target genes was investigated. In the analysis of qRT-PCR expression changes at 12, 24, 48 and 72 hours after applying MJ, the relative expression level of Hyp-1 (DN121523_c1_g4_i2) and HD-Zip (DN121003_c0_g1_i1) transcripts increased after 72 hours of application of MJ. In general, regarding to the regulatory role of the identified miRNAs in the present study, these genes could be used to better and more accurately identify the biosynthetic pathway of hypercin and hyperforin.