Comparative genomics reveals that metabolism underlies evolution of entomopathogenicity in bee-loving Ascosphaera spp. fungi

Ascosphaera (Eurotiomycetes: Onygenales) is a diverse genus of fungi that is exclusively found in association with bee nests and comprises both saprophytic and entomopathogenic species. To date, most genomic analyses have been focused on the honeybee pathogen A. apis, and we lack a genomic understanding of how pathogenesis evolved more broadly in the genus. To address this gap we sequenced the genomes of the leaf-cutting bee pathogen A. aggregata as well as three commensal species: A. pollenicola, A. atra and A. acerosa. De novo annotation and comparison of the assembled genomes was carried out, including the previously published genome of A. apis. To identify candidate virulence genes in the pathogenic species, we performed secondary metabolite-oriented analyses and clustering of biosynthetic gene clusters (BGCs). Additionally, we captured single copy orthologs to infer their phylogeny and created codon-aware alignments to determine orthologs under selective pressure in our pathogenic species. Our results show several shared BGCs between A. apis, A. aggregata and A. pollenicola, with antifungal resistance related genes present in the bee pathogens and commensals. Genes involved in metabolism and protein processing exhibit signatures of enrichment and positive selection under a fitted branch-site model. Additional known virulence genes in A. pollenicola, A. acerosa and A. atra are identified, supporting previous hypotheses that these commensals may be opportunistic pathogens. Finally, we discuss the importance of such genes in other fungal pathogens, suggesting a common route to evolution of pathogenicity in Ascosphaera.