A Pangenome Framework Reveals Conserved Pathogenicity-Associated Biosynthetic Gene Clusters in Fusarium equiseti, a Root Rot Pathogen of Panax notoginseng.

Panax notoginseng (Chinese ginseng, sanqi) is an economically and medicinally important herb whose cultivation is increasingly threatened by destructive soilborne root rot. Although Fusarium species represent the dominant pathogens in this disease complex, the virulence determinants underlying Fusarium-P. notoginseng interactions remain largely unknown, particularly the contribution of secondary metabolite (SM) biosynthetic gene clusters (BGCs) in medicinal plants. Here, we present a pangenome-informed and experimentally validated framework linking Fusarium SM to disease development. By constructing a genus-scale BGC landscape from 54 Fusarium genomes, integrating it with infection-stage transcriptomics of Fusarium equiseti P26, and establishing an efficient CRISPR/Cas9-based genome-editing system, we functionally prioritized and interrogated conserved, infection-induced BGCs from dozens of predicted clusters. This integrative pipeline identified two broadly conserved and infection-essential BGCs that are indispensable for disease development, including an evolutionarily conserved ICS-NRPS hybrid cluster and a ferrichrome-type siderophore NRPS cluster widely distributed across Fusarium species. Notably, the pathogenic contribution of the ICS-NRPS pathway was independently corroborated in Fusarium oxysporum, supporting a conserved role for this BGC class across the genus. Together, our findings provide the first pangenome-guided gene-to-phenotype dissection of SM-associated virulence in P. notoginseng root rot, establishing conserved SM biosynthetic backbones as causal pathogenicity determinants and tractable targets for disrupting Fusarium disease development across BGC-rich fungal genomes.