摘要：SummaryThe Chinese ginsengPanax notoginsengis a domesticated herb with significant medicinal and economic value. Here we report a chromosome-levelP. notoginsenggenome 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 particularR-genes) in theP. notoginsenggenome. We also investigated the reasons for the larger genome size ofPanaxspecies, revealing contributions from twoPanax-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 cultivatedP. notoginsengindividuals and identified the associated genes with dry root weight (63 genes) and stem thickness (168 genes). TheP. notoginsenggenome represents a critical step toward harnessing the full potential of an economically important and enigmatic plant.Graphical AbstractDisplay OmittedHighlights•A chromosome-levelP. notoginsenggenome assembly is provided•Panax-specific WGD events and TE expansion contribute to the larger genome size•Candidate genes involved in the ginsenoside synthesis pathway are revealed•The associated genes with agronomic traits were identified using GWAS dataBiological Sciences; Plant Biology; Genomics; Transcriptomics
