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 thousands of years because of its extensive pharmacological effects. Here, we report a high-quality reference genome of P. notoginseng , with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb, produced with third-generation PacBio sequencing technology. This is the first chromosome-level genome assembly for the genus Panax . Through genome evolution analysis, we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis. We performed a detailed transcriptional analysis of P. notoginseng and explored gene-level mechanisms that regulate the formation of characteristic tubercles. Next, we studied the biosynthesis and regulation of saponins at temporal and spatial levels. We combined multi-omics data to identify genes that encode key enzymes in the P. notoginseng terpenoid biosynthetic pathway. Finally, we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P. notoginseng . The genetic information obtained in this study provides a resource for further exploration of the growth characteristics, cultivation, breeding, and saponin biosynthesis of P. notoginseng .

The chromosome‐scale high‐quality genome assembly of Panax notoginseng provides insight into dencichine biosynthesis

“…Four versions of P. notoginseng genome assembly have been reported (Chen et al, 2017; Fan et al, 2020; Jiang et al, 2020; Zhang et al, 2017). The first two assemblies are highly fragmented, which limits genomic studies of P. notoginseng .…”

Dynamic evolution of Panax species

“…Jiang et al reported a significantly improved chromosome-level assembly of P. notoginseng . The 2.66 Gb reference genome has a scaffold N50 of 216.47 Mb with 37,606 genes annotated (Jiang et al 2020 ). The assembly statistics of the P. ginseng and P. notoginseng genome are provided in Table 1 .…”

“…In 2017, Zhang et al completed a 1.85 Gb whole genome with a scaffold N50 of 157.81 kb and annotated 34,369 genes (Zhang et al 2017). In the same year, Chen et al reported a 2.39 Gb whole genome sequence with a scaffold N50 of 96 kb, annotating 36,790 genes (Chen et al 2017 (Jiang et al 2020). The assembly statistics of the P. ginseng and P. notoginseng genome are provided in Table 1.…”

Ginsenosides in Panax genus and their biosynthesis

“…3 ). Four to twelve SE isoforms were predicted in P. ginseng 98 , 99 and five isoforms were in P. notoginseng 100 . PnSE1 and PnSE2, belonging to two separate large groups, were similar to PgSE1 and PgSE2, respectively 95 .…”