A Chromosome-Level Genome Assembly Reveals triterpenoid biosynthesis in Clinopodium chinense

Background Clinopodium chinense is an important medicinal plant belonging to the Lamiaceae. The desiccated roots of C. chinense exhibit a variety of pharmacological properties and are utilized in traditional Chinese medicine. Results We present the first chromosome-level genome assembly of C. chinense , comprising 20 pseudochromosomes with an aggregate size of 0.61 Gb and 45,466 protein-coding genes. The analysis of genome evolution indicated that two recent bursts of long terminal repeats (LTRs) significantly increased the size of the C. chinense genome. Additionally, numerous large-scale chromosomal rearrangements have been identified between the genomes of C. chinense and Thymus quinquecostatu genomes. Through comparative genomics studies, it was found that a recent whole-genome duplication event unique to Labiatae plants has resulted in a notable expansion of gene families related to the biosynthesis of triterpenoids and flavonoids in C. chinense . Subsequently, we identified several putative key genes responsible for triterpenoid biosynthesis. The results of our study offer new perspectives on the biosynthesis of triterpenoids and flavonoids, potentially advancing future investigations into the genetic and medicinal properties of C. chinense . Conclusions Our research outcomes offer new perspectives on the biosynthesis of triterpenoids and flavonoids, and may aid subsequent studies on the genetic properties and medicinal uses of C. chinense.