Giant transposons promote strain heterogeneity in a major fungal pathogen.

Fungal infections are difficult to prevent and treat in large part due to heterogeneity in clinically relevant phenotypes. However, the genetic mechanisms driving pathogen variation remain poorly understood. Here, we determined the extent to which Starships -giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the human pathogen Aspergillus fumigatus . We analyzed 519 diverse strains, including 12 newly sequenced with long-read technology, to reveal 20 distinct Starships that generate genomic heterogeneity over timescales impacting experimental reproducibility. Starship -mobilized genes encode diverse functions, including biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal pathogenesis wherein Starships mediate variation in virulence-related gene content and expression. Together, our results demonstrate that Starships are a foundational mechanism generating disease-relevant genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.