In Silico Identification of key microRNAs in Cannabis sativa L.

Cannabis (Cannabis sativa L.) is an annual, herbaceous, and dicotyledonous plant of the Cannabinaceaefamily. Cannabis has not been considered as important food, medicinal and industrial source and littleresearch has been done on its agronomic, physiological, and biochemical properties. MiRNAs are small,non-coding RNAs that regulate gene expression in plants and animals. These small RNAs play animportant role in regulating post-transcriptional gene expression and act as negative regulators of geneexpression in eukaryotes. In recent years, the use of bioinformatics tools to identify miRNAs and theirtarget genes has been widely considered and used due to the availability of genomic sequences in databasesdue to their efficiency and low cost. The main purpose of this study was to identify conserved miRNAsin the genome of the Cannabis sativa L. through the computational genomics homology search approach.Therefore, to identify cannabis microRNAs, a homology-based search was performed between Cannabissativa L. genome data in the NCBI database and known microRNAs in the miRBase database, usingBLASTn, then to better identify the secondary structure, With the help of the BEDFile tool, ۲۰۰ nucleotideswere added to the beginning and end of each candidate target miRNA and in the next step, BLASTx wasperformed to remove the coding sequences of the proteins. The secondary structures of candidatemicroRNAs were predicted using MFOLD software. Finally, eight miRNAs were identified, whichbelonged to six different families. Csa-miR۱۶۹e ۵p and csa-miR۱۶۹k belonged to the miR۱۶۹ family andcsa-miR۳۱۹b along with csa-miR۳۱۹a۳p belonged to the miR۱۵۹ family. Other identified microRNAsinclude csa-miR۸۰۱۴ ۵p, csa-miR۸۰۰۵c, csa-miR۲۱۱۱b and csa-miR۱۵۳۳. The current results providemolecular evidence for understanding the possible involvement of miRNAs in the regulation of Growthand development by miR۱۵۹ family and Stresses response by miR۱۶۹ family in this plant species.