Phylogenomic insights into Taphrinomycotina and genomic features of <i>Saitoella coloradoensis</i> based on whole-genome sequencing at the chromosome level, with a proposal of the new class Saitoellomycetes

Taphrinomycotina, a subphylum of the phylum Ascomycota, comprises fungi with diverse morphologies and ecologies. <i>Saitoella</i> and <i>Savitreella</i> are genera of red-colored yeasts within Taphrinomycotina, but their precise phylogenetic positions have remained controversial. In this study, we sequenced the whole genomes of <i>Saitoella coloradoensis</i> and <i>Savitreella phatthalungensis</i> in order to elucidate their phylogenetic relationships using a phylogenomic approach based on chromosome-level genome assemblies generated by long-read sequencing technologies. Our phylogenetic analyses suggest that <i>Saitoella</i> is distinct from all currently described classes within Taphrinomycotina, whereas <i>Savitreella</i> seems to belong to the class Taphrinomycetes. Furthermore, <i>Saitoella</i> shares high average amino acid identity with all other classes in Taphrinomycotina, suggesting that it retains ancient gene sequences. Our findings enable us to propose a new class, order, and family-namely, Saitoellomycetes, Saitoellales, and Saitoellaceae-automatically typified by the genus <i>Saitoella</i>. Our chromosome-level assembly reveals that <i>Saitoella coloradoensis</i> possesses 38 chromosomes, the highest number of chromosomes among fungi reported to date. We also identify structural differences between two <i>Saitoella</i> species and a chromosome structure lacking the canonical palindromic centromeric repeat sequence.