Lack of universal mutational biases in a fungal phylum

Mutations fuel the diversity of life forms on earth through changes of nucleotides in DNA sequence. Patterns of mutations are biased; for example, mutational biases toward adenine and thymine have been previously noted in bacteria and biases for transitions over transversions are observed in diverse groups of organisms. However, the mutational biases in fungi, whose genomes vary widely in their GC content, remain poorly understood. Here, we characterized patterns of single nucleotide polymorphisms among 537 strains from 30 species and four classes from Ascomycota, the most species-rich fungal phylum. We found that mutational biases vary across Ascomycota; for example, some species in the class Saccharomycetes, in particular the bipolar budding yeast Hanseniaspora uvarum and the emerging pathogen Candida auris, show strong mutational bias toward A|T substitutions whereas the black mold Stachybotrys chartarum in the class Sordariomycetes shows substantial mutational bias toward G|C substitutions. Examination of GC content and GC equilibrium content, a measure that represents the GC content under selective neutrality and accounts for rates of G|C > A|T and A|T > G|C substitutions, revealed that fungal species vary in how their genome nucleotide composition is affected by neutral processes, mutational biases, and external evolutionary forces, such as selection. Whereas genome nucleotide composition is consistent with neutral expectations and is mainly driven by mutational bias in some species (e.g., Zymoseptoria tritici), the composition of others is influenced by both mutational bias and selection (e.g., H. uvarum and S. chartarum). These results highlight the variation of patterns of mutations across a fungal phylum and suggest that both neutral and selective processes shape the nucleotide composition of fungal genomes.