LAUSR

Significance Batrachochytrium salamandrivorans (Bsal) and its closest relative B. dendrobatidis (Bd) are fungal pathogens that threaten amphibians globally. Pathogenicity in vertebrates by species of Batrachochytrium is thought to have emerged from nonpathogenic and saprobic relatives over millions of years through gene expansions of secreted proteolytic enzymes families. Using deep nanopore sequencing and comparative genomics, we discover that Batrachochytrium genomes have undergone a repeat-driven expansion characterized by flanking repetitive elements enriched around pathogenicity genes, genes with signatures of positive selection, and genes upregulated during infection. These genomic features are the hallmarks of two-speed genomes that have to date only been described in plant pathogens. These discoveries shed new light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.