Giant transposons promote strain heterogeneity in a major fungal pathogen

Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity. However, the genetic mechanisms driving pathogen variation remain poorly understood. Here, we determined the extent to which -giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the human pathogen . We analyzed 519 diverse strains, including 12 newly sequenced with long-read technology, to reveal 20 distinct that are generating genomic heterogeneity over timescales potentially relevant for experimental reproducibility. -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 evolution wherein help generate variation in gene content and expression among fungal strains. Together, our results demonstrate that are a previously hidden mechanism generating genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.