The Chinese ginseng Panax notoginseng is a domesticated herb with significant medicinal and economic value. Here we report a chromosome-level P. notoginseng genome assembly with a high (∼79%) repetitive sequence content. The juxtaposition with the widely distributed, closely related Korean ginseng (Panax ginseng) genome revealed contraction of plant defense genes (in particular R-genes) in the P. notoginseng genome. We also investigated the reasons for the larger genome size of Panax species, revealing contributions from two Panax-specific whole-genome duplication events and transposable element expansion. Transcriptome data and comparative genome analysis revealed the candidate genes involved in the ginsenoside synthesis pathway. We also performed a genome-wide association study on 240 cultivated P. notoginseng individuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). The P. notoginseng genome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.

人参Panax notoginseng是一种具有重要药用和经济价值的驯化草药。在这里，我们报告了染色体水平三七基因组组装，具有高（~79%）重复序列含量。与广泛分布的、密切相关的高丽人参（Panax ginseng ）基因组的并置揭示了三七基因组中植物防御基因（特别是R基因）的收缩。我们还研究了人参物种基因组较大的原因，揭示了两个人参特异性全基因组复制事件和转座元件扩展的贡献。转录组数据和比较基因组分析揭示了参与人参皂苷合成途径的候选基因。我们还对 240 个栽培三七个体进行了全基因组关联研究，并鉴定了与干根重量（63 个基因）和茎厚度（168 个基因）相关的基因。三七基因组代表了充分利用这种经济上重要且神秘的植物潜力的关键一步。