The Virulence Gene ToxB Is Both Amplified and Disrupted by Transposons in the Wheat Pathogen Pyrenophora tritici-repentis

Summary Mechanisms that drive virulence gene duplication in plant pathogenic fungi remain poorly understood. In Pyrenophora tritici-repentis ( Ptr ), responsible for tan spot of wheat, ToxB is a multicopy virulence gene encoding a proteinaceous necrotrophic effector. ToxB exhibits a virulence dosage effect, where higher copy numbers are associated with increased disease severity. In this work, we sought to resolve a 25-year old question as to what drove the proliferation of ToxB within Ptr . To investigate this, 23 long-read assemblies were generated and analyzed from a collection of globally distributed isolates with various ToxB copy numbers, with a specific focus on regions containing ToxB . Extensive comparative alignments identified a Helitron-like element, ToxB-HLE , that appears to be driving the duplication of ToxB in an accessory region of chromosome 4. This region is entirely absent in isolates lacking ToxB or its nonfunctional homolog toxb . In addition to gene amplification by transposons, multiple independent transposon insertion events were identified in several isolates that disrupted the ToxB open reading frame creating inactive toxb haplotypes. This study provides strong evidence supporting the hypothesis that transposons play dual roles in the rapid evolution of fungal pathogenicity by both amplifying and disrupting a key virulence gene in a globally distributed plant pathogen.