Four-species Aspergillus pan-GWAS reveals rare genome expansion in pathogenicity and contraction in domestication

A recent comprehensive analysis of the Aspergillus genus has uncovered intriguing insights into the genomic mechanisms underlying its diverse phenotypes. The study examined four species - A. fumigatus, A. flavus, A. oryzae, and A. niger - and their associated pathogenicity and domestication traits.

Initial genomic data for each species was curated, with 929 genomes filtered to 210 assemblies meeting stringent validation standards. These high-quality assemblies totaled 88 for A. fumigatus, 70 for A. flavus, 33 for A. oryzae, and 19 for A. niger. In addition, a genus-level pangenome encompassing 15,163 orthogroups was constructed to facilitate the pan-genome-wide association studies (pan-GWAS) analysis.

The pan-GWAS, which incorporated kinship corrections to account for shared ancestry across species, identified up to 117 significant orthogroup presence/absence associations per species-phenotype comparison. However, an intriguing convergence analysis revealed that while both A. fumigatus and A. flavus showed significant enrichment of pathogenicity-associated gene families, the two species seldom agreed on whether the association was due to the enrichment or depletion of specific gene families.

Simultaneously, the functional annotation convergence analysis yielded no significant results at a false discovery rate (FDR).

These findings suggest that despite the shared pathogenicity traits, the genomic mechanisms governing pathogenicity in A. fumigatus and A. flavus are not uniformly conserved. This pan-GWAS analysis thus underscores the complexity of genomic adaptations in the Aspergillus genus, highlighting the potential for unique evolutionary pathways even among closely related species.