Identification and characterization of miRNAs in various Thymus species

Today, medicinal plants are used in the treatment of many diseases because of their secondary metabolites. Thyme as one of these plants contains a wide range of secondary metabolites such as terpenes. Various methods have been developed to increase these materials. In classical methods, environmental factors are changed to produce the most effective substance in medicinal plants, but in newer approaches that are based on plant genetics, higher yields are observed. One of these approaches is the use of miRNAs. These miRNAs control gene expression after transcription by mRNA analysis or inhibition of their translation, and play different roles in biological and metabolic processes in plants and animals. One of the simplest and least expensive methods for identifying miRNAs is the use of bioinformatics tools and methods. To identify distinct miRNA in different species of thyme, a study based on homology search was conducted using transcriptomic data of thyme. First, this information was refined and then aligament performed against all known miRNAs in the miRBase database. After screening of results based on factors such as length and e-value level, the secondary structure of miRNAs was analyzed with UNAfold tool. Target genes were identified using psRNATARGET tool and phylogenetic relationships were investigated using maximum likelihood method and RaxML tool. In total 64 distinct candidate’s miRNAs were identified in different species of thymus and 14 miRNAs included miR172 and miR396 played an important role in terpenes synthesis and it has been proven in previous studies. The phylogenetic tree was able to show the relationship between miRNAs in different species.