Similar mutation rates buthighlydiverse mutation spectra in ascomycete and basidiomycete yeasts

Abstract

Yeast species are extremely diverse and not monophyletic. Because the majority of yeast research focuses on ascomycetes, the mutational determinants of genetic diversity across yeast species are not well understood. By combining mutation-accumulation techniques withwhole-genome sequencing,weresolved the genomic mutation rate and spectrum of the oleaginous (oil-producing) 'red yeast' Rhodotorula toruloides, the first such study in the fungal phylum Basidiomycota.We find that the mutation spectrum is quite different from what has been observed in all other studied unicellular eukaryotes, but similar to that in most bacteria-a predominance of transitions relative to transversions. Rhodotorula toruloides has a significantly higher A:T!G:C transition rate- possibly elevated by the abundant flanking G/C nucleotides in the GC-rich genome, aswell as amuch lower G:C!T:A transversion rate. In spite of these striking differences, there are substantial consistencies between R. toruloides and the ascomycetemodel yeasts: a spontaneous base-substitutionmutation rate of 1.90-10-10 per site per cell division as well as an elevated mutation rate at nonmethylated 5'CpG3' sites. These results imply the evolution of variablemutation spectra in the face of similarmutation rates in yeasts.