Decoding the Genetic Basis of Aromatic Terpene Metabolism in Rosemary: Ancient Whole-Genome Duplications and Ancestral Karyotypes Shed Light on Evolutionary Signatures

Salvia rosmarinus , a commonly known aromatic plant belonging to the Salvia genus, is valued for its medicinal properties, derived primarily from the terpenoids present in its leaves. We have successfully created a chromosome-level genome assembly of S. rosmarinus , covering 1.24 Gb, with a scaffold N50 value of 107.45 Mb and 61,717 annotated protein-coding genes. Our analysis highlights a recent whole genome duplication (WGD) event as the primary driver of genomic rearrangement and fusion following speciation. As a result of the WGD, key genes involved in monoterpene biosynthesis, such as HMGR , 1,8-cineole synthase, and limonene synthase, underwent tandem duplication and double punctuation. Limonene synthase experienced a nonpolar mutation that favored structural diversity in monoterpene biosynthesis, while 1,8-cineole synthase underwent a polar mutation that favored 1,8-cineole(eucalyptol) accumulation. In addition, our analysis revealed differences in the mechanisms of diterpene biosynthesis between S. rosmarinus and S. miltiorrhiza , as evidenced by the tandem duplication, covariance, and high-level expression of genes essential for carnosol biosynthesis, specifically CYP76AK6–8 . These findings no punctuation for understanding the molecular-level diversity of terpenoids in S. rosmarinus and will facilitate molecular breeding and quality improvement efforts for this economically important plant.