Keystone Fungal Endophytes of Panax Plants Drive the Conversion of Ginsenoside Rb1 to Rd

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.