Phaffia is an orange-colored basidiomycetous yeast genus of the order Cystofilobasidiales that contains a single species, P. rhodozyma. This species is the only fungus known to produce the economically relevant carotenoid astaxanthin. Although Phaffia was originally found in the Northern hemisphere, its diversity in the southern part of the globe has been shown to be much greater. Here we analyze the genomes of two Australasian lineages that are markedly distinct from P. rhodozyma. The two divergent lineages were investigated within a comprehensive phylogenomic study of representatives of the Cystofilobasidiales that supported the recognition of two novel Phaffia species, for which we propose the names of P. australis sp. nov. and P. tasmanica sp. nov. Comparative genomics and other analyses confirmed that the two new species have the typical Phaffia hallmark—the six genes necessary for the biosynthesis of astaxanthin could be retrieved from the draft genome sequences, and this carotenoid was detected in culture extracts. In addition, the organization of the mating-type (MAT) loci is similar to that of P. rhodozyma, with synteny throughout most regions. Moreover, cases of trans-specific polymorphism involving pheromone receptor genes and pheromone precursor proteins in the three Phaffia species, together with their shared homothallism, provide additional support for their classification in a single genus.

During studies of yeasts associated with soil in a Cerrado–Atlantic Rain Forest ecotone site in Brazil, three orange-pigmented yeast strains were isolated from samples collected in Minas Gerais state, Brazil. Molecular analyses combining the 26S rRNA gene (D1/D2 domains) and the internal transcribed spacer (ITS) sequences as well as whole-genome sequence data showed that these strains could not be ascribed to any known species in the basidiomycetous genusPhaffia, and thus they are considered to represent a novel species for which the namePhaffia brasilianasp. nov. is proposed. The holotype is CBS 16121^Tand the MycoBank number is MB 839315. The occurrence ofP. brasilianain a tropical region is unique for the genus, since all other species occur in temperate regions. Two factors appear to contribute to the distribution of the novel taxon: first, the region where it was found has relatively moderate temperature ranges and, second, an adaptation to grow or withstand temperatures higher than those of the other species in the genus seems to be in place.

We showed previously that yeasts in Starmerella and Wickerhamiella genera (W/S clade) exhibit numbers of horizontal gene transfer (HGT) events much larger than found in any other yeast species, with bacteria and other fungi (Pezizomycotina) as donors. Here we shed light on HGT in the W/S clade by carrying out the characterization of xenologous genes present in three species harboring together close to 600 xenologous genes. Metabolic genes were strongly overrepresented and either introduced functions new to yeasts or restored functions that were likely absent in the W/S clade ancestor. RNA-sequencing revealed lower global levels of expression of xenologous vs native yeast genes in two species. This difference is associated with the preferential accumulation of xenologous genes in large, AT-enriched chromosome terminal regions, dubbed “End” domains, characterized by overall lower gene expression. In one species, “End” domains were shown to be more permissive for protein diversification, but only for xenologous genes. We posit that “End” domains may generate favorable conditions for the adaptation and retention of xenologous genes, helping explain the exceptional numbers of HGT events in the W/S clade.

We comprehensively surveyed the occurrence of hybridization events in three phylogenetically related yeast genera - Torulaspora, Zygotorulaspora and Zygosaccharomyces - using a dataset of 172 genomes, 123 of which were newly sequenced. We detected five new hybrids in Zygosaccharomyces, three in Torulaspora, and none in Zygotorulaspora. For most of the newly characterized hybrids we were able to identify their parental species. Moreover, we confirmed that Z. sapae is a triple hybrid that contains the contributions of Z. progenitor, Z. rouxii and Z. siamensis. One Torulaspora hybrid resulted from a hybridization event involving members of two very divergent populations of T. delbrueckii, which suggests that conventional mating is impaired and that one of the parental genomes might in fact represent a cryptic species. In general hybrid genomes had mitochondria from only one of the parental species and maintained the chromosomal architecture of their parental species. However, in Zygosaccharomyces the MAT regions tended to be dynamic and variable, a situation also seen, but to a lesser degree, in non-hybrid genomes. Our results suggest that hybridization in Zygosaccharomyces is linked to the colonization of anthropic environments, as all cases of hybridization in this genus are linked to man-made environments. However, this pattern is not evident in Torulaspora. This study and the resources it provides pave the way for a better understanding of the mechanisms underlying hybridization in yeasts.

A novel ascomycetous yeast species of the genus Zygosaccharomyces is proposed, based on isolates obtained in Japan, Portugal and the USA, and on a combination of conventional DNA barcode sequence analyses and whole-genome phylogenies. The new species is described as Zygosaccharomyces progenitor sp. nov. (PYCC 7198 ^T ) and was found in association with bees ( Apis mellifera and Bombus spp.) and their honey, besides being found in plants and soil. The novel species belongs to a Zygosaccharomyces subclade that also harbours Zygosaccharomyces rouxii . Although the two species can be differentiated at the sequence level, they cannot be distinguished at the phenotypic level. As is typical of the genus, Z. progenitor sp. nov. produces spherical ascospores after cell conjugation.