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

Abstract

SUMMARY Rosemary (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 Gb 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 Labiataceae, an independent whole‐genome duplication event occurred in S. rosmarinus at approximately 15 million years ago. Transcriptomic comparison of two S. rosmarinus cultivars with contrasting carnosic acid (CA) content revealed 842 genes significantly positively associated with CA biosynthesis in S. rosmarinus. Many of these genes have been reported to be involved in CA biosynthesis previously, such as genes involved in the mevalonate/methylerythritol phosphate 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 biosynthesis genes. The genes encoding diterpene synthase and the cytochrome P450 (CYP450) 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 chromosomes 1 and 2, respectively. Such clustering is also observed in other sage (Salvia) 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.

Haplotype-resolved genomes and population genetics to analyze glandular secretory trichome formation mechanism in oregano

“…In this study, we report two high-quality haplotype-resolved reference genomes for Origanum which provide insight into the GSTs formation molecular mechanism. To date, a few of genomes of Lamiaceae have been reported, e.g., S. miltiorrhiza (Xu et al 2016), S. splendens (Dong et al 2018), S. baicalensis (Zhao et al 2019), Salvia rosmarinus (Han et al 2023), T. quinquecostatus (Sun et al 2022), L. angustifolia (Li et al 2021) , L. × intermedia, and L. latifolia (Li et al 2023). We now provide two oregano haplotype-resolved genomes sequence, those genomic data will provide a starting point for comparing the genomes of different Lamiaceae members.…”

“…At present, haplotype-resolved genomes sequencing can fully assemble and annotate the genomes of species with highly heterozygous, and mask allelic variation and functional differentiation of divergent alleles in heterozygous species (Hu et al 2022; Lin et al 2022; Han et al 2023). Finding divergent bialleles on homologous chromosomes is made possible by the high-quality, allele-defined reference genome, which is useful for investigating the differentiation and expression dominance of bialleles (Hu et al 2021).…”

Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia

“…Furthermore, the distinct transcription patterns of each CYP76AK clade represented another aspect of function evolution. Their organ-specific patterns are not independent, but are accompanied by other catalytic genes involved in carnosic acid derivatives and tanshinones biosynthesis as KSL s, CYP76AH s, and CYP71D s. In the meantime, such patterns are maintained in different Salvia lineages 30 , 53 , 75 , thus, raising the question about the origin of their organ-specific transcriptions as a further research topic. To summarize, ATD differentiation in Salvia provides a complete model involving multiple species, gene families, metabolic diversity, and ecological evolution, making it an ideal research object for the genetic mechanisms responsible for chemical diversity in plants.…”

A comparative analysis of morphology, microstructure, and volatile metabolomics of leaves at varied developmental stages in Ainaxiang (Blumea balsamifera (Linn.) DC.)

“…But peppermint’s critical aromatic metabolites are enriched only in rapidly expanding leaves ( Gershenzon et al., 2000 ). Young leaves in rosemary ( Salvia rosmarinus ) performed higher gene expression levels related to carnosic acid biosynthesis ( Han et al., 2023 ). In summary, metabolites exhibit different accumulation patterns in different plants and organs, and further research on metabolomics and flavor related to leaf maturity is necessary.…”