Insights into the Life Cycle of Yeasts from the CTG Clade Revealed by the Analysis of the Millerozyma (Pichia) farinosa Species Complex

Abstract

Among ascomycetous yeasts, the CTG clade is so-called because its constituent species translate CTG as serine instead of leucine. Though the biology of certain pathogenic species such as Candida albicans has been much studied, little is known about the life cycles of non-pathogen species of the CTG clade. Taking advantage of the recently obtained sequence of the biotechnological Millerozyma (Pichiasorbitophila) farinosa strain CBS 7064, we used MLST to better define phylogenic relationships between most of the Millerozyma farinosa strains available in public collections. This led to the constitution of four phylogenetic clades diverging from 8% to 15% at the DNA level and possibly constituting a species complex (M. farinosa) and to the proposal of two new species:Millerozyma miso sp. nov. CBS 2004T ( = CLIB 1230T) and Candida pseudofarinosa sp. nov.NCYC 386T( = CLIB 1231T).Further analysis showed that M. farinosa isolates exist as haploid and inter-clade hybrids. Despite the sequence divergence between the clades, secondary contacts after reproductive isolation were evidenced, as revealed by both introgression and mitochondria transfer between clades. We also showed that the inter-clade hybrids do sporulate to generate mainly viable vegetative diploid spores that are not the result of meiosis, and very rarely aneuploid spores possibly through the loss of heterozygosity during sporulation. Taken together, these results show that in this part of the CTG clade, non-Mendelian genetic exchanges occur at high rates through hybridization between divergent strainsfrom distinct clades and subsequent massive loss of heterozygosity. This combination of mechanisms could constitute an alternative sexuality leading to an unsuspected biodiversity.

Unravelling genomic diversity ofZygosaccharomyces rouxiicomplex with a link to its life cycle

“…(). Similarly, M. farinosa allodiploid strains did not undergo meiosis, producing mainly diploid spores (Mallet et al ., ). The abundance of Z. sapae cells with conjugation tubes and without zygote supported the second rather than the first hypothesis: mating between diploid cells might occur without nuclear fusion and meiosis.…”

“…We hypothesize that the alternative mode of propagation to classical sexuality described in Saccharomyces species can account for this genome complexity and makes Z. rouxii complex prone to genome mosaicism and reticulate evolution. An increasing amount of evidence has shown that genome mosaicism is widespread in protoploid hemiascomycetes other than Z. rouxii complex, such as D. hansenii (Jacques et al ., ), P. sorbitophila (Louis et al ., ) and M. farinosa (Mallet et al ., ). Notably, all these yeasts are able to survive to harsh conditions, such as a high extracellular concentration of osmolytes, suggesting that this genome complexity may occur in response to environmental cues (Gompert et al ., ).…”

“…Recently, genome sequencing efforts have revealed an increasing number of yeast diploid mosaic species. In the GTG clade (so called because its constituent species translate CTG as serine instead of leucine), Candida albicans (Jones et al ., ), Debaryomyces hansenii (Jacques et al ., ), Pichia sorbitophila (Louis et al ., ) and Millerozyma ( Pichia ) farinosa (Mallet et al ., ) showed frequently complex diploid genomes, resulting from putative genetic exchanges between divergent strains and species at high frequency and thus referred to as ‘mosaic genomes’ (Zhaxybayeva et al ., ).…”

Candida utilis and Cyberlindnera (Pichia) jadinii: yeast relatives with expanding applications

“…Mukherjee et al (2014) recently described a negative correlation between C. albicans and several Pichia species in the oral mycobiome of HIV-infected patients suggesting antagonism between these fungi. The Pichia species involved were characterized as P. guillermondii, P. burtonii, and P. jadinii (renamed as C. jadinii, as described above); P. guillermondii is closely related to the better studied species Millerozyma (Pichia) farinosa (Mallet et al 2012). Spent medium of M. farinosa was able to block the growth, hyphal morphogenesis, and biofilm formation of C. albicans and improved oral candidiasis in an animal model of infection; some evidence suggested that the responsible inhibitory ingredient is a protein (Mukherjee et al 2014).…”

“…Thus, in spite of significant genomic similarities, C. utilis has lost this inhibitory action that is found in C. jadinii. On the other hand, C. jadinii and W. farinosa both act as antagonists for C. albicans, although unlike C. jadinii, W. farinosa is phylogenetically distant, as a member of the CTG-clade (Mallet et al 2012). It will be of great interest to explore the inhibitory mechanisms in both species, which may establish novel probiotic compounds and strategies to combat candidiasis.…”