Phylogenomic insights into Taphrinomycotina and genomic features of Saitoella coloradoensis 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. Saitoella and Savitreella 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 Saitoella coloradoensis and Savitreella phatthalungensis 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 Saitoella is distinct from all currently described classes within Taphrinomycotina, whereas Savitreella seems to belong to the class Taphrinomycetes. Furthermore, Saitoella 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 Saitoella. Our chromosome-level assembly reveals that Saitoella coloradoensis possesses 38 chromosomes, the highest number of chromosomes among fungi reported to date. We also identify structural differences between two Saitoella species and a chromosome structure lacking the canonical palindromic centromeric repeat sequence.