Epimedium is commonly used to treat bone injury and kidney disease, with prenylated flavonol glycosides (PFGs) as its active ingredients. It has attracted much attention due to prominent healthcare and therapeutic effects, but faces problems of adulteration with closely related species and confusion about geographical origins. In this study, multiple technical approaches were employed to identify its genetic characteristics and metabolic differences. Based on DNA barcoding, 20 batches of samples were analyzed. The genetic distances of matK, ITS and psbA-trnH within species were all smaller than those between species, and psbA-trnH along with ITS + psbA-trnH proved most effective in distinguishing botanical sources. With Inter-simple sequence repeat (ISSR) technology, 12 highly polymorphic and reproducible primers were selected from 21, and 189 alleles were detected. Epimedium sagittatum showed distinct genetic diversity. Samples with similar genetic distance and geographical location also tended to cluster together. Eight index components were analyzed, and their contents showed significant differences. The total content ranged from 0.50% to 7.09%, and icariin and epimedin C were identified as potential biomarkers. Integrative analysis revealed that the differences in index components were jointly driven by genetic diversity and ecological factors. Additionally, “mean temperature of driest quarter”, “precipitation seasonality”, and “temperature annual range” were identified as key environmental factors. This study provides a reliable experimental basis for the authenticity and quality evaluation of Epimedium.

Keystone taxa are critical for microbial community homeostasis and ecological niche interactions. However, the functions and genomic traits of endophytic keystone fungi in plant tissues remain unclear. Via network analysis, this study identified keystone fungi Plectosphaerella (Plec) and Cladosporium (Clad) in roots/leaves of medicinal Panax plants (P. ginseng, P. quinquefolius, P. notoginseng). Both correlated strongly positively with ginsenoside Rd content in respective tissues (ρ > 0.6, p < 0.001). Co-cultivation confirmed their ability to convert ginsenoside Rb1 to Rd, linked to β-glucosidase activity. Whole-genome sequencing/assembly/evolutionary analysis of the two strains elucidated genomic features for their keystone roles and saponin biotransformation. Genome mining found multiple GH3 genes (potential saponin transformers) in both; 11 (Plec) and 5 (Clad) were upregulated by cellobiose. Gene family phylogenetic analysis showed expanded transmembrane transport and environmental response functions. Both also had abundant secondary metabolic gene clusters and secretome genes, linking biotic interaction functions to their keystone roles. In summary, this study shows Panax endophytic keystone fungi can participate in ginsenoside biotransformation and clarifies their genomic traits, offering insights for functional endophytic fungal resource development.