Significance: This paper constructs an error-correcting code for the { A , C , G , T } alphabet of DNA. By contrast with previous work, the code corrects insertions and deletions directly, in a single strand of DNA, without the need for multiple alignment of strands. This code, when coupled to a standard outer code, can achieve error-free storage of petabyte-scale data even when ∼ 10% of all nucleotides are erroneous.

Candida species exhibit a variety of ploidy states and modes of sexual reproduction. Most species possess the requisite genes for sexual reproduction, recombination, and meiosis, yet only a few have been reported to undergo a complete sexual cycle including mating and sporulation. Candida albicans , the most studied Candida species and a prevalent human fungal pathogen, completes its sexual cycle via a parasexual process of concerted chromosome loss rather than a conventional meiosis. In this study, we examine ploidy changes in Candida tropicalis , a closely related species to C. albicans that was recently revealed to undergo sexual mating. C. tropicalis diploid cells mate to form tetraploid cells, and we show that these can be induced to undergo chromosome loss to regenerate diploid forms by growth on sorbose medium. The diploid products are themselves mating competent, thereby establishing a parasexual cycle in this species for the first time. Extended incubation (>120 generations) of C. tropicalis tetraploid cells under rich culture conditions also resulted in instability of the tetraploid form and a gradual reduction in ploidy back to the diploid state. The fitness levels of C. tropicalis diploid and tetraploid cells were compared, and diploid cells exhibited increased fitness relative to tetraploid cells in vitro , despite diploid and tetraploid cells having similar doubling times. Collectively, these experiments demonstrate distinct pathways by which a parasexual cycle can occur in C. tropicalis and indicate that nonmeiotic mechanisms drive ploidy changes in this prevalent human pathogen.

Phenotypic switching allows for rapid transitions between alternative cell states and is important in pathogenic fungi for colonization and infection of different host niches. In Candida albicans, the white-opaque phenotypic switch plays a central role in regulating the program of sexual mating as well as interactions with the mammalian host. White-opaque switching is controlled by genes encoded at the MTL (mating-type-like) locus that ensures that only a or α cells can switch from the white state to the mating-competent opaque state, while a/α cells are refractory to switching. Here, we show that the related pathogen C. tropicalis undergoes white-opaque switching in all three cell types (a, α, and a/α), and thus switching is independent of MTL control. We also demonstrate that C. tropicalis white cells are themselves mating-competent, albeit at a lower efficiency than opaque cells. Transcriptional profiling of C. tropicalis white and opaque cells reveals significant overlap between switch-regulated genes in MTL homozygous and MTL heterozygous cells, although twice as many genes are white-opaque regulated in a/α cells as in a cells. In C. albicans, the transcription factor Wor1 is the master regulator of the white-opaque switch, and we show that Wor1 also regulates switching in C. tropicalis; deletion of WOR1 locks a, α, and a/α cells in the white state, while WOR1 overexpression induces these cells to adopt the opaque state. Furthermore, we show that WOR1 overexpression promotes both filamentous growth and biofilm formation in C. tropicalis, independent of the white-opaque switch. These results demonstrate an expanded role for C. tropicalis Wor1, including the regulation of processes necessary for infection of the mammalian host. We discuss these findings in light of the ancestral role of Wor1 as a transcriptional regulator of the transition between yeast form and filamentous growth. The white-opaque phenotypic switch has been extensively characterized in the human fungal pathogen Candida albicans, where it plays a central role in regulating entry into sexual reproduction. This epigenetic switch is strictly regulated by the MTL locus so that only a or α cell types can switch to the opaque state, whereas a/α cells are locked in the white state. In contrast, we show that in the related pathogen C. tropicalis white cells are capable of sexual mating and that the white-opaque switch is independent of MTL control. Thus, MTLa, α, and a/α cells all undergo reversible switching between white and opaque states. Despite these differences, switching in both C. tropicalis and C. albicans is dependent on the expression of the Wor1 transcription factor. This factor is conserved amongst fungal ascomycetes and, in several species, acts as a master regulator of the yeast-to-filament transition. We show that, in addition to regulating the white-opaque switch in C. tropicalis, Wor1 expression also promotes filamentation and biofilm formation in this species. We therefore propose that C. tropicalis Wor1 has retained the ancestral role of this family of transcription factors while also gaining control over the more recently evolved white-opaque phenotypic switch.