De novo sequencing and functional annotation of the sage (Salvia officinalis L.) genome

Common sage (Salvia officinalis L.), a species within the Salvia genus, has been used throughout history and in modern times for various purposes, such as food, alternative medicine, cosmetics and hygiene, as a medicinal and aromatic plant. The medical use of the terpenoids in common sage essential oil has made these secondary metabolites a significant research subject. This thesis-based research, the common sage genome was de novo sequenced, assembled, its protein-coding gene content was annotated, and a variation detection analysis was performed using the existing reference genome. 75 terpene synthase genes and 67 terpenoid backbone biosynthesis pathway genes were predicted and mapped to assembly scaffolds. As a result of the variant analysis, 188 variable single nucleotide loci related to the predicted terpenoid biosynthesis genes were identified in the coding sequence regions of sage. In total, 24,570 single nucleotide polymorphisms were detected in the entire exome of common sage.