The chromosome-scale assembly of the Salvia rosmarinus genome provides insight into carnosic acid biosynthesis.

Salvia rosmarinus is considered a sacred plant because of its special fragrance and is commonly used in cooking and traditional medicine. Here, we report a high-quality chromosome-level assembly of the S. rosmarinus genome of 1.11 G in size; the genome has a scaffold N50 value of 95.5 Mb and contains 40,701 protein-coding genes. In contrast to other diploid Labiatae, an independent whole genome duplication (WGD) event was shown by S. rosmarinus at approximately 15 MYA. Transcriptomic comparison of two S. rosmarinus cultivars with contrasting carnosic acid (CA) content identified 842 genes significantly positively associated with carnosic acid biosynthesis in S. rosmarinus. Many of these genes have been reported to be involved in CA-biosynthesis previously, such as several MVA/MEP pathways and CYP71-coding genes. Based on the genomes and these genes, we propose a model of CA biosynthesis in S. rosmarinus. Further, comparative genome analysis of the congeneric species revealed the species-specific evolution of CA biosynthetic genes. The genes encoding diterpene synthase and the cytochromes P450 (CYPs) family of CA synthesis-associated genes form a biosynthetic gene cluster (CPSs-KSLs-CYP76AHs) responsible for the synthesis of leaf and root diterpenoids, which are located on S. rosmarinus chromosome 1 and 2, respectively. Such clustering is also observed in other sage plants, thus suggesting that genes involved in diterpenoid synthesis are conserved in the Labiataceae family. These findings provide new insights into the synthesis of aromatic terpenoids and their regulation.