Large Scale Identification of SSR Molecular Markers in Satureja khuzistanica Jamzad and Satureja rechingeri Jamzad

Satureja genus, from the Lamiaceae family, is a medicinal plant that is widely distributed in the southern regions of Iran. Different species of this plant have many medicinal properties such as antioxidant properties and medical applications. However, lack of molecular markers, especially microsatellite markers, has severely limited the development of Satureja genetic researches. Therefore, in this study, 271907 and 225534 transcripts were obtained with average lengths of 1079 and 1018 bp and N50 values equal to 1802 and 1740 for S. khuzistanica and S. rechengeri, respectively. The assembly process of short reads of transcriptome sequences of S. khuzistanica and S. rechengeri was used to identify microsatellite markers. In the present study, 44624 and 34546 SSR loci were identified in S. khuzistanica and S. rechengeri, respectively. Among these markers, dinucleotide repeat motifs were the most abundant, followed by mononucleotide and trinucleotide. In S. khuzistanica and S. rechengeri, the results of blast of transcripts containing SSR showed that 72.27% and 75.32% of the transcripts had at least one record in the non-redundant protein database, respectively. Functional annotation was performed through the search for homology and gene ontology (GO). In total, 14792 (33.4%) transcripts with SSR markers for S. khuzistanica and 12480 (36.12%) transcripts with SSR markers for S. rechengeri were classified into three groups of GO. Gene ontology analysis reported that most of the assembled transcripts are related to the Molecular Function (MF) group. 45% of the total transcripts containing microsatellites were allocated to 401 pathways, in which the biosynthesis of secondary metabolites was identified as the second pathway with the maximum number of members after the metabolic pathways. This is the first report about the identification of microsatellite markers from the transcriptome sequence of Satureja and this information could be an effective source for breeding programs of this medicinal plant.