Sanchi ginseng (Panax notoginseng (Burkill) F. H. Chen) has been cultivated in China for more than 400 years, whose root is an important traditional Chinese medicine mainly used to stanch blood, to disperse gore and to reduce pain caused by injury due to falls. The cultivated populations of this crop are distributed in Wenshan mountain area of Yunnan with a narrow habitat, whose location is around N 23.5°, E 104°and altitude ranges from 1,200 to 2,000 m. Although its wild species has not been found, current cultivated populations show rich morphological variations in stem, leaf, root, flower and fruit. Recent studies exhibit that Sanchi root has more active compounds than the roots of P. ginseng and P. quinquefolius. Therefore, this crop needs further utilization.

Triterpenoid saponins are one of the key active components of many medicinal plants. The biosynthetic pathway of triterpenoid saponins in higher plants and a lot of experimental results both indicated that the key enzymes involved in triterpenoid saponin synthesis are squalene synthase (SS), squalene epoxidase (SE), lupeol synthase (LS), dammarenediol synthase (DS), β-amyrin synthase (β-AS), cytochrome P 450-dependent monooxygenase (PDMO), and glycosyltransferase (GT). The activities and coding genes of the key enzymes could be induced by a range of factors in various plant species. However, the effects of the factors on the content and composition of the triterpenoid saponins in specific plants are not certainly coincident, and different factors appear to induce the gene expressions of the key enzymes by different signal pathways and at different levels. This paper could provide a reference for strengthening the triterpenoid saponin-synthesizing capability of specific medicinal plants at enzyme and/or gene expression levels in order to improve the plants' commercial values.

Background: Panax notoginseng (Burkill) F. H. Chen is a Chinese medicinal plant of the Araliaceae family commonly used in the treatment of cardiovascular and cerebrovascular diseases in Asia and elsewhere. To meet an increase in Chinese herbal medicine market demand, most P. notoginseng is planted artificially, and is vulnerable to various plant diseases. Root rot disease, in particular, causes substantial P. notoginseng yield reduction and economic losses. High-depth next-generation sequencing technology was used to analyze the rhizosphere and root endophyte microbial communities of P. notoginseng to compare the characteristics of these two communities between healthy and root rot diseased P. notoginseng plants, and to clarify the relationship between these microbial communities and root rot disease.Results: The P. notoginseng rhizosphere microbial community was more diverse than the root endophyte community, and the difference in functional pathways between healthy and diseased P. notoginseng plants was greater in the root endophyte than in the rhizosphere communities. Multi-database annotation results showed that the highest number of endophytic bacteria occurred in the roots of diseased plants. The number of carbohydrate-active enzymes database families was also higher in diseased roots. The RND antibiotic efflux function was higher in the healthy samples. A high abundance of Variovorax paradoxus and Pseudomonas fluorescens occurred in the healthy and diseased root endophyte communities, respectively. Ilyonectria mors-panacis and Pseudopyrenochaeta lycopersici were most abundant in the diseased samples. In addition, the complete genome of two unknown Flavobacteriaceae species and one unknown Bacteroides species were obtained based on binning analysis.Conclusions: The rhizosphere and root endophyte microbial communities of healthy and root rot diseased P. notoginseng showed marked differences in diversity and functional pathways. The higher mapping values obtained for the diseased samples reflected the occurrence of root rot disease at the molecular level. Variovorax paradoxus and Pseudomonas fluorescens may be antagonistic bacteria of root rot in P. notoginseng, whereas Ilyonectria mors-panacis and Pseudopyrenochaeta lycopersici appear to be P. notoginseng root rot pathogens. Our study provides a theoretical basis for understanding the occurrence of root rot in P. notoginseng and for further research on potential biological control agents.