The Chromosome-level Reference genome Assembly for Panax notoginseng and Insights into Ginsenoside Biosynthesis

ABSTRACT Panax notoginseng, a perennial herb of the genus Panax in the family Araliaceae, has played an important role in clinical treatment in China for nearly thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng, whose genome size up to 2.66 Gb with a contig N50 of 1.12 Mb using third-generation PacBio sequencing technology, and which is the first chromosome-level genome of genus Panax. Through genome evolution analysis, we explored the phylogenetic and whole genome duplication (WGD) events, and also their impact on the biosynthesis of saponins. We further performed detailed transcriptional analysis of P. notoginseng and explored the gene-level regulatory mechanism of the formation of characteristic phenotype-tubercles. Then we studied the biosynthesis and regulation of saponins in temporal and spatial level, respectively. Combining multi-omics data, we identified key enzyme genes involved in the terpenoid biosynthetic pathway of P. notoginseng. Finally, we identified 5 glycosyltransferase genes that could catalyze the formation of different ginsenosides in P. notoginseng. The genetic information obtained in this study provides a resource for further exploring the growth characteristics, cultivation, breeding and biosynthesis of saponins in P. notoginseng.