An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genus <i>Aspergillus</i>. Roughly 70% of infections are caused by <i>Aspergillus fumigatus</i>, with the rest stemming from approximately a dozen other <i>Aspergillus </i>species. Several of these pathogens are closely related to <i>A. fumigatus </i>and belong in the same taxonomic section, section <i>Fumigati</i>. Pathogenic species are frequently most closely related to non-pathogenic ones, suggesting <i>Aspergillus </i>pathogenicity evolved multiple times independently. To understand the repeated evolution of <i>Aspergillus </i>pathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in<i> </i>section <i>Fumigati</i>, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified over 1,700 genes whose evolutionary rate differed between pathogens and non-pathogens and dozens of genes whose rates differed between specific pathogens and the rest of the taxa. For example, we found 34 genes whose evolutionary rate was uniquely different in <i>A. fumigatus </i>and 85 genes whose rate was uniquely different in the pathogen <i>A. lentulus</i>. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity in <i>Aspergillus </i>involved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.<br>These files contain all of the supplementary information for the manuscript.<br>