A chromosomal-level Bupleuri Radix genome assembly provides new insights into saikosaponin biosynthesis and euasterids II genome evolution

Bupleuri radix (Chaihu) is one of the most famous Traditional Chinese Medicinal herbs, with a history of medical use for more than 2000 years. Bupleurum species are officially listed in the Chinese and Japanese Pharmacopoeias and the WHO monographs of the commonly used medicinal plants of China and Korea. The main active components of Radix Bupleuri are saikosaponins (SSs), in particular triterpene saponins. Due to their important medicinal role, the biosynthesis of saikosaponins from Bupleurum L. plants has been more intensively studied than any other bioactive constituents. However, no high-quality genome of Bupleurum has so far been published. In order to circumvent this and address current limitations on the molecular and population genetics knowledge of B. chinense DC, we report a high-quality chromosome-level genome assembly constructed using a combination of PacBio long reads, Illumina paired-end sequencing, and Hi-C reads. We constructed six scaffolds corresponding to 6 chromosomes from a total of 4354 contigs (contig N50=510 Kb), and obtained a final high-quality assembly comprising 945 Mb of sequence and a N50 scaffold of 160 Mb. This genome assembly represents 91.6% completeness after matching to 1440 Plantcore conserved genes (BUSCO). A total of 46,423 protein-coding genes were predicted in the B. chinense DC genome, of which 46,254 genes (99.64%) were functionally annotated. An enrichment analyses suggested that the gene families that expanded during the evolution of B. chinense DC are involved in the biosynthesis of anthocyanin, sesquiterpenoid and triterpenoid. Furthermore, in this study we identified and analyzed genes involved in Saikosaponin Biosynthesis, which gives important insights into this process. The genomic data generated in this work provide a valuable resource for investigating the molecular mechanisms, biological functions and evolutionary adaptations of B. chinense DC.