A structurally unique effector shared between vascular wilt fungi drives cotton and olive defoliation.

Defoliating (D) strains of the vascular wilt fungus Verticillium dahliae cause severe yield losses in cotton and olive, but the genetic basis of this pathotype remained unknown. Using comparative genomics, functional genetics, structural analysis, and phylogenomics, we identify a D-pathotype-specific genomic region encoding two duplicated secreted effector genes. Simultaneous deletion of both copies abolishes pathogenicity and defoliation in cotton and olive, and affects virulence in Nicotiana benthamiana and Arabidopsis thaliana. Expression of the effector in non-defoliating strains induces cotton defoliation, and purified protein causes wilting and leaf drop. Structural analyses reveal a previously uncharacterized protein fold conserved across Verticillium and Fusarium species, with evidence of functional diversification and host specificity. Phylogenomic and genomic context analyses indicate repeated horizontal transfer mediated by giant transposable elements known as Starships. Together, these findings identify the D effector as a central determinant of defoliation and virulence and show how Starship-mediated gene transfer drives emergence of an agriculturally important fungal trait.