Abstract
Rhodotorula toruloides is a basidiomycete yeast known for accumulating lipids within its cells. Owing to its oil-producing potential, many strains of this species have been isolated and studied. However, substantial genetic diversity has been reported within this species, making the true taxonomic boundaries of R. toruloides ambiguous. In this study, we sequenced the whole genomes of multiple strains of R. toruloides and related species, generated complete chromosome-level assemblies, and conducted comparative analyses. We found that the genomes of Rhodotorula and Rhodosporidiobolus generally comprise 17 chromosomes with conserved chromosomal synteny. However, some strains of R. toruloides exhibited chromosomal shuffling. Notably, several of these rearrangements were observed among strains that had diverged under laboratory conditions, suggesting that irregular structural mutations occurred in artificial culture environments. Our findings revealed such abnormal chromosomal evolution under artificial conditions and underscore the potential for cryptic mutations, which are undetectable by phenotype or gene sequence comparisons, to arise in laboratory strains. We also found that the genome of the haploid strain NP11, which is a descendant of the type strain of R. toruloides, comprises only one parental genome.