Whole-Genome Sequencing and Analysis of the Chinese Herbal Plant Panax notoginseng

Abstract

Panax notoginseng (Burk.) F.H. Chen (2n = 2x = 24, common name sanqi or tianqi), belonging to the Araliaceae family, is a slow-growing plant species documented in the ancient Chinese medical literatures for its ability to ameliorate hemostasis and improve blood circulation (Wang et al., 2016). After decades of pharmacological research, a variety of P. notoginseng-specific secondary metabolites (notably ginsenosides, notoginsenosides and gypenosides) were isolated, identified, and implicated in conferring medicinal properties (Wang et al., 2016). These discoveries allowed the design and production of numerous modern oral and topical drugs to treat cardiovascular diseases, contusions, and soft tissue pain (Wang et al., 2016). To help identify novel bioactive compounds in P. notoginseng and delineate their biosynthetic pathways, we propose the construction of a reference P. notoginseng genome. This information will be an important addition to the existing expressed sequence tag (Luo et al., 2011) and RNA-seq data (Liu et al., 2015) for P. notoginseng genetics. J.Z. is an employee and shareholder of NOWBIO Technology Co. Ltd. Y.L. is an employee and shareholder of Longjing Pharmaceutical Co. Ltd. L.Z. is an employee and shareholder of Farlong Pharmaceutical. This work is not financially supported by the abovementioned companies. The three companies took no roles in acquiring or interpreting the results of this manuscript. No conflict of interest declared.

The unprecedented diversity of UGT94-family UDP-glycosyltransferases in Panax plants and their contribution to ginsenoside biosynthesis

“…ginseng and P . notoginseng has revealed few subfamily UGTs to support such a proposal; for example, only five and four (identity > 50%; coverage > 50%) of UGT94 homolog sequences were assembled, respectively 4 – 7 . The unprecedented diversity of UGT94s was revealed through cloning of P .…”

“…ginseng and P . notoginseng 4 – 7 . More than 150 structurally diverse ginsenosides have been isolated from Panax species; they are conjoined with one to six sugar units, and up to three at the C3 and C20 sites of PPD-type ginsenosides or the C6 and C20 sites of PPT-type ginsenosides 8 .…”

Sequencing of Panax notoginseng genome reveals genes involved in disease resistance and ginsenoside biosynthesis

“…Because P. notoginseng is an important Chinese traditional medicine, two draft genomes of P. notoginseng were published in 2017. Chen etc.’s genome assembly was about 2.39 Gb with a contig N50 of 16 kb and scaffold N50 of 96 kb and Zhang etc.’s was a ~1.85 Gb assembly with scaffold N50 of 158 kb and contig N50 of 13.2 kb 2,3 . There was a notable difference of genome assembly size (~540 Mb) between two genomes.…”

“…There was a notable difference of genome assembly size (~540 Mb) between two genomes. In general, the estimation of genome size using flow cytometry analysis is considered as a golden standard approach and the estimated result of diploid P. notoginseng was about 2.31 Gb 3 . Besides, these two papers also annotated the repetitive sequences and protein-coding genes.…”

HMOD: An Omics Database for Herbal Medicine Plants

“…To provide the latest advances and more analysis tools for herbal medicine plants, HMOD will be updated when new data are available (ftp://202.203.187.112:2222/). HMOD collects 23 published genomes of medicinal herbs including Panax notoginseng and other important species ( Figure 1B and Supplemental Table 1) (Chen et al, 2017;Zhang et al, 2017). The data for every species consist of an introduction, resequencing information, downloadable information, the Gbrowse internet browser, and BLAST.…”