Salvia sclarea genome assembly and annotation

Plant specialized metabolites play essential ecological roles, yet the mechanisms underlying their diversification remain poorly understood. We investigated the biosynthesis of sclareol, a potent antifungal diterpene produced by Salvia sclarea (clary sage). A complete telomere-to-telomere genome assembly of clary sage, compared with genomes of related Lamiaceae species that do not produce sclareol, revealed a recent tandem duplication of a class II diterpene synthase gene (SsLPPS). This duplicated enzyme has acquired a novel function, synthesizing labda-13-en-8-ol diphosphate (LPP), the direct precursor of sclareol. Structural modeling and site-directed mutagenesis identified key amino acid substitutions responsible for this neofunctionalization. Integrative genome, chromatin, and transcriptome analyses showed that SsLPPS and additional diterpenoid biosynthetic genes are organized in a trichome-specific, co-regulated gene cluster. Together, our findings illustrate how enzyme innovation and regulatory rewiring can give rise to new metabolic pathways and may inform future strategies for engineering valuable plant terpenoids.