A chromosome-level genome assembly reveals triterpenoid biosynthesis in Clinopodium chinense.

BACKGROUND: Clinopodium chinense is an important medicinal plant in the family Lamiaceae. The desiccated roots of C. chinense possess various pharmacological activities and are widely used in traditional Chinese medicine. RESULTS: Here we present the first chromosome-level genome assembly of C. chinense, comprising 20 pseudochromosomes with a total size of 0.61 Gb and containing 45,466 predicted protein-coding genes. Genome evolution analyses indicated that two recent bursts of long terminal repeats (LTRs) significantly contribute to genome expansion in C. chinense. Additionally, numerous large-scale chromosomal rearrangements have been identified between the genomes of C. chinense and Thymus quinquecostatus. Comparative genomics analyses further indicated that tandem duplication may be one of the potential factors affecting the amplification of genes related to the synthesis pathway of and triterpenoid (including key metabolic nodes CYP and UGT genes). Subsequently, we identified several putative key genes involved in triterpenoid biosynthesis. CONCLUSIONS: Overall, this study gives new perspectives on the biosynthesis pathway of triterpenoids and lays a foundation for investigations into the genetic mechanism and medicinal properties of C. chinense.