Assessment of characteristic orthologs in Ascomycota and Basidiomycota and their implications for fungal taxonomy

Fungal populations and species can be characterised using DNA sequences from specific genomic regions or entire genomes. However, recognising taxa above the species level still relies primarily on phenotypic characters, particularly morphology, which are often limited in many fungal groups. We examined whether gene presence/absence information could be used for taxonomic characterisation. Using 259 genomes, including 71 newly sequenced ones, we generated a presence/absence matrix of orthologous groups (OGs). Cluster analysis using the Yule coefficient revealed that, in Ascomycota, the presence/absence patterns of OGs were likely associated with evolutionary processes down to the subphylum level. Conversely, in Basidiomycota, these patterns did not necessarily correspond to subphylum classifications, although the reason for this discrepancy remains unclear. Principal component analysis showed that each subphylum could be distinguished by its axes in both Ascomycota and Basidiomycota. We then identified characteristically present and absent OGs (98 for Ascomycota, 108 for Basidiomycota, and 321 across both subphyla). Gene Ontology analysis revealed statistically significant functional differences between Ascomycota and Basidiomycota: genes related to RNA polymerase II, nucleosome assembly (including the Rpd3L complex), and fungal-type cell wall organisation were enriched in Ascomycota, whereas the membrane and ubiquitin ligase complex were enriched in Basidiomycota. At the subphylum level, several OGs were identified as potential taxonomic markers, such as those associated with methylation (Pezizomycotina), mitochondria (Saccharomycotina), signal transduction (Agaricomycotina), and cell wall synthesis (Pucciniomycotina). Overall, presence/absence ortholog analysis provides a promising approach for characterising taxa based on genomic traits and may contribute to advancing fungal taxonomy above the species level.