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

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

Impaired terpenoid backbone biosynthesis reduces saponin accumulation in Panax notoginseng under Cd stress

Panax notoginseng saponins (PNS) are major secondary metabolite of Panax notoginseng (Burk.) F.H. Chen. Previous studies identified that P. notoginseng planting soil usually with high content of Cd. However, the effects of Cd stress on the accumulation of PNS and the corresponding regulation mechanisms have yet to be reported. In the present study, the impact of Cd stress on the PNS accumulation of P. notoginseng was studied in pot culture experiments. The effect of Cd stress on antioxidant enzyme activity was studied using hydroponics. In addition, transcriptase sequencing analysis was used to study the effect of Cd stress on the expression of PNS metabolism transcripts in hydroponic experiments. Cd treatments significantly decreased the accumulation of PNS in the rhizome and main root. The sensitive concentration of antioxidant enzyme activity for both leaf and stem was 2.5μM, whereas the sensitive concentration for the root was 5.0μM. Transcriptome analysis showed that 5132 genes (2930 up- and 2202 downregulated) were regulated by 5.0μM Cd stress in the root of P. notoginseng. Among them, six upregulated differentially expressed genes (DEGs) were related to the methylerythritol 4-phosphate (MEP) pathway, whereas three of the downregulated DEGs were mevalonate kinase (MVK), phosphomevalonate kinase (PMK), and geranylgeranyl diphosphate synthase (type II, GGPS). Of the 15 transcripts selected for real-time quantitative-PCR, 13 were expressed in the same manner as identified using RNA-seq. In conclusion, Cd stress inhibited the accumulation of PNS in the root of P. notoginseng by reducing the expression of MVK, PMK, and GGPS in the terpenoid backbone biosynthesis pathway, and also caused by the removal of reactive oxygen species.