Chromosome-level genome assembly of Bupleuri radix provides insights into the evolution of its genome and saikosaponin biosynthesis. Bupleurum chinense

Abstract: Bupleuri radix (Chaihu) is a well-known traditional Chinese medicinal herb that has been used more than 2000 years. In the Chinese Pharmacopoeia, Chaihu is recorded as the dried roots of Bupleurum chinense DC and B. scorzonerifolium Wild. Bupleurum species are officially listed in the Chinese and Japanese Pharmacopoeias and on the WHO monographs of commonly used medicinal plants in China and Korea. Due to their important medicinal role, the biosynthesis of saikosaponins from Bupleurum L. plants has been more intensively studied than any of their other metabolic processes or bioactive constituents. However, at present, a high-quality genomic sequence has not yet been produced for any Bupleurum species. To circumvent this and address current limitations in understanding the molecular evolution of this genus, we have reported a high-quality chromosome-level genome assembly of B. chinense DC. Our approach allowed us to obtain a final assembly comprising 945Mb of sequence and an N50 scaffold of 160 Mb. A total of 46,423 protein-coding genes were predicted in the B. chinense DC genome. Enrichment analyses suggested that the gene families that expanded during the evolution of B. chinense DC are involved in the biosynthesis of anthocyanins, sesquiterpenoids, and triterpenoids. Furthermore, we identified and analyzed the genes involved in the biosynthesis of saikosaponins and estimated the divergence time between the euasterid I and II clades. The newly generated genomic data provides a valuable resource for future investigations of the molecular mechanisms, biological functions, and evolutionary adaptations of B. chinense DC.

摘要：柴胡（Bupleuri radix）是一种拥有2000余年应用历史的知名传统中药材。《中国药典》明确记载，柴胡为柴胡（Bupleurum chinense DC.）和狭叶柴胡（Bupleurum scorzonerifolium Willd.）的干燥根。柴胡属植物同时被收录于中国、日本药典，以及世界卫生组织（World Health Organization, WHO）收录的中、韩常用药用植物专论中。鉴于其重要的药用价值，柴胡属植物中柴胡皂苷（saikosaponins）的生物合成途径，是其所有代谢过程与生物活性成分中研究最为深入的方向。然而截至目前，尚无任何一种柴胡属植物获得高质量基因组序列。为突破这一瓶颈，解析该属植物的分子演化机制，本研究报道了柴胡（Bupleurum chinense DC.）的高质量染色体级别基因组组装结果。本次组装最终序列总长945 Mb，scaffold N50达160 Mb，共预测得到46423个蛋白质编码基因。富集分析结果显示，柴胡演化过程中扩张的基因家族，主要参与花青素（anthocyanins）、倍半萜类（sesquiterpenoids）以及三萜类（triterpenoids）化合物的生物合成。此外，本研究还鉴定并分析了柴胡皂苷（saikosaponins）生物合成相关基因，并估算了真菊I类与II类演化支的分化时间。本研究新生成的基因组数据，将为后续解析柴胡的分子调控机制、生物学功能以及演化适应性提供宝贵的研究资源。