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From comparisons of ITS1-5.8S-ITS2 and gene sequences for nuclear D1/D2 LSU rRNA, nuclear SSU (18S) rRNA, translation elongation factor 1-α (EF1-α) and RNA polymerase II subunit 2 (RPB2), the following four new ascosporogenous yeast species were resolved and are described as Metschnikowia anglica (NRRL Y-7298 T [type strain], CBS 15342, MycoBank MB 823167), Metschnikowia leonuri (NRRL Y-6546 T , CBS 15341, MB 823166), Metschnikowia peoriensis (NRRL Y-5942 T , CBS 15345, MB 823164) and Metschnikowia rubicola (NRRL Y-6064 T , CBS 15344, MB 823165). The following six species of Candida are members of the Metschnikowia clade and are proposed for transfer to Metschnikowia as new combinations: Candida chrysomelidarum (NRRL Y-27749 T , CBS 9904, MB 823223), Candida gelsemii (NRRL Y-48212 T , CBS 10509, MB 823192), Candida kofuensis (NRRL Y-27226 T , CBS 8058, MB 823195), Candida picachoensis (NRRL Y-27607 T , CBS 9804, MB 823197), Candida pimensis (NRRL Y-27619 T , CBS 9805, MB 823205) and Candida rancensis (NRRL Y-48702 T , CBS 8174, MB 823224). Candida fructus (NRRL Y-17072 T , CBS 6380, MB 823206) is transferred to Clavispora as a new combination, and Candida musae is shown to be a synonym of C. fructus. Apparent multiple alleles for ITS, D1/D2, EF1-α and RPB2 were detected in strains of some species.

DNA sequence analysis has shown that species of the Candida kruisii clade and species of the C. tanzawaensis clade represent phylogenetically circumscribed genera, which are described as Teunomyces gen. nov., type species T kruisii, and Suhomyces gen. nov., type species S tanzawaensis Many of the species are distributed worldwide and they are often isolated from fungus-feeding insects and their habitats. Included is the description of S. kilbournensis (type strain NRRL Y-17864, CBS 14276), a species found almost exclusively on maize kernels (Zea mays) in IL, USA., (Published by Oxford University Press on behalf of FEMS 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

During a study of microorganisms associated with maize (Zea mays) cultivation, yeasts were isolated from overwintered stalks, cobs and surrounding soil, which were collected from an agricultural field in south-central Illinois, USA. Predominant among isolates were two species of Cryptococcus (Cr. flavescens, Cr. magnus) and a red yeast that D1/D2 LSU rRNA gene sequences revealed to be a new species of the basidiomycete yeast genus Occultifur. The species, which was not detected in the same field during the growing season, is described here as Occultifur kilbournensis (MycoBank number MB 811259; type strain NRRL Y-63695, CBS 13982, GenBank numbers, D1/D2 LSU rRNA gene, KP413160, ITS, KP413162; allotype strain NRRL Y-63699, CBS 13983). Mixture of the type and allotype strains resulted in formation of hyphae with clamp connections and a small number of apparent basidia following incubation on 5% malt extract agar at 15 °C for 2 months. In view of the uncertainty of the life cycle, the new species is being designated as forma asexualis. From analysis of D1/D2 and ITS nucleotide sequences, the new species is most closely related to Occultifur externus.

The new anamorphic yeast Kuraishia piskuri, f.a., sp. nov. is described for three strains that were isolated from insect frass from trees growing in Florida, USA (type strain, NRRL YB-2544, CBS 13714). Species placement was based on phylogenetic analysis of nuclear gene sequences for the D1/D2 domains of large subunit rRNA, small subunit rRNA, translation elongation factor-1α, and subunits B1 and B2 of RNA polymerase II B. From this analysis, the anamorphic species Candida borneana, Candida cidri, Candida floccosa, Candida hungarica, and Candida ogatae were transferred to the genus Kuraishia as new combinations and Candida anatomiae, Candida ernobii, Candida ishiwadae, Candida laoshanensis, Candida molendini-olei, Candida peltata, Candida pomicola, Candida populi, Candida wickerhamii, and Candida wyomingensis were transferred to the genus Nakazawaea., (Published 2014. This article is a U.S. Government work and is in the public domain in the USA.)

Three new non-ascosporic, ascomycetous yeast genera are proposed based on their isolation from currently described species and genera. Phylogenetic placement of the genera was determined from analysis of nuclear gene sequences for D1/D2 large subunit rRNA, small subunit rRNA, translation elongation factor-1α and RNA polymerase II, subunits B1 and B2. The new taxa are: Deakozyma gen. nov., type species Deakozyma indianensis sp. nov. (type strain NRRL YB-1937, CBS 12903); Danielozyma gen. nov., type species Danielozyma ontarioensis comb. nov. (type strain NRRL YB-1246, CBS 8502); D. litseae comb. nov. (type strain NRRL YB-3246, CBS 8799); Middelhovenomyces gen. nov., type species Middelhovenomyces tepae comb. nov. (type strain NRRL Y-17670, CBS 5115) and M. petrohuensis comb. nov. (type strain NRRL Y-17663, CBS 8173).

Ambrosiozyma oregonensis sp. nov. is described from two strains, one isolated from a mountain stream in Oregon, USA (NRRL Y-6106(T) = CBS 5560(T)), and a second (NRRL YB-4169) from an unknown substrate from Marion, Illinois, USA. The species forms four hat-shaped ascospores in each deliquescent ascus and appears to be homothallic. Abundant true hyphae are produced with some having apparent dolipore-like septa. Analyses of nuclear gene sequences for the D1/D2 domains of large-subunit rRNA, small-subunit rRNA, translation elongation factor-1α, and subunits B1 and B2 of RNA polymerase II show the proposed novel species to be distinct from other species of the Ambrosiozyma clade. Because of their placement in the Ambrosiozyma clade, Candida kashinagacola, Candida llanquihuensis, Candida maleeae, Candida pseudovanderkliftii and Candida vanderkliftii are reassigned to the genus Ambrosiozyma as new combinations, and the description of the genus Ambrosiozyma is emended to reflect the resulting changes in phenotypic characters.

Phylogenetic analysis of concatenated nuclear gene sequences for large and small subunit rRNAs, translation elongation factor 1-α, and the two large subunits of RNA polymerase II (RPB1, RPB2) demonstrated that species assigned to the yeast genus Ascoidea represent two separate and distantly related clades, that is, Ascoidea (A. asiatica, NRRL Y-17632, CBS 377.68; A. rubescens, NRRL Y-17699, CBS 116.35, type species; A. tarda sp. nov., NRRL Y-2393, CBS 12609, type strain), which is near the genus Saccharomycopsis, and Alloascoidea gen. nov. (Al. africana comb. nov., NRRL Y-6762-3, CBS 12606, Al. hylecoeti comb. nov., NRRL Y-17634, CBS 355.80, type species), which is near Nadsonia and related genera. From these analyses and from comparison of herbarium specimens, it appears that type strains of A. asiatica and Al. africana had been reversed. Sequence analysis further showed that Schizoblastosporion starkeyi-henricii is a sister species of Nadsonia fulvescens and it is proposed for transfer to Nadsonia., (© 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.)

Relationships among ascomycetous yeast genera (subphylum Saccharomycotina, phylum Ascomycota) have been uncertain. In the present study, type species of 70 currently recognized genera are compared from divergence in the nearly entire nuclear gene sequences for large subunit rRNA, small subunit (SSU) rRNA, translation elongation factor-1α, and RNA polymerase II, subunits 1 (RPB1) and 2 (RPB2). The analysis substantiates earlier proposals that all known ascomycetous yeast genera now assigned to the Saccharomycotina represent a single clade. Maximum likelihood analysis resolved the taxa into eight large multigenus clades and four-one- and two-genus clades. Maximum parsimony and neighbor-joining analyses gave similar results. Genera of the family Saccharomycetaceae remain as one large clade as previously demonstrated, to which the genus Cyniclomyces is now assigned. Pichia, Saturnispora, Kregervanrija, Dekkera, Ogataea and Ambrosiozyma are members of a single large clade, which is separate from the clade that includes Barnettozyma, Cyberlindnera, Phaffomyces, Starmera and Wickerhamomyces. Other clades include Kodamaea, Metschnikowia, Debaryomyces, Cephaloascus and related genera, which are separate from the clade that includes Zygoascus, Trichomonascus, Yarrowia and others. This study once again demonstrates that there is limited congruence between a system of classification based on phenotype and a system determined from DNA sequences., (Published 2012. This article is a U.S. Government work and is in the public domain in the USA.)

Saitoella coloradoensis sp. nov. (NRRL YB-2330, CBS 12360, type strain, MycoBank accession number 563858) is described. This new member of the phylum Ascomycota, subphylum Taphrinomycotina was isolated from insect frass occurring in an Engelmann spruce (Picea engelmannii) that was growing in Colorado, USA. Multigene sequence analysis showed that S. coloradoensis is distinct from Saitoella complicata, the only other known species of Saitoella. The two species may be separated phenotypically from growth reactions on D: -xylose, ribitol and methyl-α-D: -glucoside. Asexual reproduction is by budding and both species produce thick-walled, spherical cells that appear morphologically similar to the ascogenous cells formed in plant host tissue by species of Protomyces and some species of Taphrina. The thick-walled cells did not form ascospores but did produce buds when placed on fresh growth media.

The relatedness among methanol-assimilating yeasts assigned to the genus Ogataea and neighboring taxa (Phylum Ascomycota, Subphylum Saccharomycotina, Class Saccharomycetes, Order Saccharomycetales) was determined from phylogenetic analyses of gene sequences for nuclear large and small subunit (SSU) rRNAs, translation elongation factor-1alpha and mitochondrial SSU rRNA. On the basis of the analyses, Williopsis salicorniae and seven species of Pichia are proposed for transfer to the genus Ogataea, which has been emended, and Pichia angophorae, a nonhyphal species, is proposed for transfer to the mycelium forming genus Ambrosiozyma. Pichia toletana and Pichia xylosa form an independent lineage and are assigned to the genus Peterozyma, which is newly proposed.

Relationships among species assigned to the yeast genera Pichia, Issatchenkia and Williopsis, which are characterized by the ubiquinone CoQ-7 and inability to utilize methanol, were phylogenetically analyzed from nucleotide sequence divergence in the genes coding for large and small subunit rRNAs and for translation elongation factor-1alpha. From this analysis, the species separated into five clades. Species of Issatchenkia are members of the Pichia membranifaciens clade and are proposed for transfer to Pichia. Pichia dryadoides and Pichia quercuum are basal members of the genus Starmera. Williopsis species are dispersed among hat-spored taxa in each of the remaining three clades, which are proposed as the new genera Barnettozyma, Lindnera and Wickerhamomyces. Lineages previously classified as varieties of Pichia kluyveri, 'Issatchenkia'scutulata, Starmera amethionina and 'Williopsis'saturnus are elevated to species rank based on sequence comparisons.

Relationships among species assigned to the ascosporic yeast genera Sporopachydermia, Stephanoascus, Trichomonascus, Wickerhamiella and Zygoascus, and to the associated anamorphic genera Arxula, Blastobotrys, Sympodiomyces and Trigonopsis, were determined from phylogenetic analyses of gene sequences from the nearly complete large-subunit rRNA gene, the mitochondrial small-subunit rRNA gene, and cytochrome oxidase II. The genus Stephanoascus is polyphyletic, resulting in reassignment of two species to the older genus Trichomonascus and the third to Sugiyamaella gen. nov. (type species Sugiyamaella smithiae). The genera Sporopachydermia, Wickerhamiella and Zygoascus appear to be monophyletic. The species Pichia ofunaensis and P. tannicola are proposed for transfer to Zygoascus. Arxula, Blastobotrys and Sympodiomyces are members of the Trichomonascus clade, with the genus Blastobotrys having taxonomic priority for anamorphic states. Trigonopsis variabilis and three species of Candida represent a distinct clade. From the foregoing gene sequence analyses, the new ascosporic genus Sugiyamaella is proposed, as are 14 new species combinations and the new family Trichomonascaceae.

A yeast causing widespread infection of laboratory mice was identified from 26S rRNA gene sequences as Candida pintolopesii. To determine the relationship of C. pintolopesii with other members of the Kazachstania (Arxiozyma) telluris species complex, nucleotide sequences from domains 1 and 2 of the 26S rRNA gene, the mitochondrial small-subunit rRNA gene, and the RNA polymerase II gene were phylogenetically analyzed. That analysis resolved the 48 strains examined into five closely related species: K. telluris, Candida bovina, C. pintolopesii, Candida slooffiae, and a previously unknown species. One or more strains of each of the last four species formed an ascosporic state much like that of K. telluris. To place these ascosporogenous strains taxonomically, it is proposed that they be assigned to the teleomorphic genus Kazachstania as K. bovina (type strain NRRL Y-7283, CBS 9732, from the nasal passage of a pigeon), K. heterogenica (type strain NRRL Y-27499, CBS 2675, from rodent feces), K. pintolopesii (type strain NRRL Y-27500, CBS 2985, from the peritoneal fluid of a dead guinea pig), and K. slooffiae (type strain NRRL YB-4349, CBS 9733, from the cecum of a horse). On the basis of multigene sequence analyses, K. heterogenica appears to be a hybrid of K. pintolopesii and a presently unknown species. With the exception of K. bovina, the phylogenetically defined species show a moderate degree of host specificity.

Species of Saccharomyces, Arxiozyma, Eremothecium, Hanseniaspora (anamorph Kloeckera), Kazachstania, Kluyveromyces, Pachytichospora, Saccharomycodes, Tetrapisispora, Torulaspora, and Zygosaccharomyces, as well as three related anamorphic species assigned to Candida (C. castellii, C. glabrata, C. humilis), were phylogenetically analyzed from divergence in genes of the rDNA repeat (18S, 26S, ITS), single copy nuclear genes (translation elongation factor 1alpha, actin-1, RNA polymerase II) and mitochondrially encoded genes (small-subunit rDNA, cytochrome oxidase II). Single-gene phylogenies were congruent for well-supported terminal lineages but deeper branches were not well resolved. Analysis of combined gene sequences resolved the 75 species compared into 14 clades, many of which differ from currently circumscribed genera.

Three new anamorphic ascomycetous yeasts are described: Candida anglica (type strain NRRL Y-27079, CBS 4262), Candida cidri (type strain NRRL Y-27078, CBS 4241), and Candida pomicola (type strain NRRL Y-27083, CBS 4242). These three species were isolated from cider produced in the United Kingdom, and their identification was determined from unique nucleotide sequences in the species-specific D1/D2 domain of large subunit (26S) ribosomal DNA. Phylogenetic analysis of D1/D2 sequences placed C. anglica near Candida fragi, C. cidri near Pichia capsulata, and C. pomicola in the Pichia holstii clade.

Descriptions are given for the two new anamorphic ascomycetous yeasts Candida germanica (type strain NRRL Y-27064, CBS 4105) and Candida neerlandica (type strain NRRL Y-27057, CBS 434). The species were isolated, respectively, from the atmosphere over Germany and from pressed yeast cake in The Netherlands. Phylogenetic analysis of 26S domain D1/D2 ribosomal DNA sequences places C. germanica near Pichia philogaea, whereas C. neerlandica is a member of the Lodderomyces elongisporus/Candida albicans clade.

A new ascosporogenous yeast, Zygosaccharomyces kombuchaensis sp. n. (type strain NRRL YB-4811, CBS 8849), is described; it was isolated from Kombucha tea, a popular fermented tea-based beverage. The four known strains of the new species have identical nucleotide sequences in domain D1/D2 of 26S rDNA. Phylogenetic analysis of D1/D2 and 18S rDNA sequences places Z. kombuchaensis near Zygosaccharomyces lentus. The two species are indistinguishable on standard physiological tests used for yeast identification, but can be recognized from differences in restriction fragment length polymorphism patterns obtained by digestion of 18S-ITS1 amplicons with the restriction enzymes DdeI and MboI.

Three new species of Candida are described that were determined to be genetically isolated from all other currently accepted ascomycetous yeasts based on their sequence divergence in the species-variable D1/D2 domain of large subunit (26S) ribosomal DNA. One of the species was isolated from an ambrosia beetle, whereas the other two were from the frass of wood-boring beetle larvae. The new species and their type strains are the following: Candida ontarioensis NRRL YB-1246 (CBS 8502), Candida tammaniensis NRRL Y-8257 (CBS 8504), and Candida trypodendroni NRRL Y-6488 (CBS 8505).

Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.

Clinically important species of Candida and related organisms were compared for extent of nucleotide divergence in the 5' end of the large-subunit (26S) ribosomal DNA (rDNA) gene. This rDNA region is sufficiently variable to allow reliable separation of all known clinically significant yeast species. Of the 204 described species examined, 21 appeared to be synonyms of previously described organisms. Phylogenetic relationships among the species are presented.

Extent of divergence in partial nucleotide sequences from large and small subunit ribosomal RNAs was used to estimate the evolutionary relationship between the genera Wingea and Debaryomyces. These data showed the monotypic genus Wingea to be congeneric with Debaryomyces, and it is proposed to transfer W. robertsii to Debaryomyces.

Species of the genera Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces were compared from their extent of divergence in three regions from small (18S) and large (25S) subunit ribosomal RNAs comprising a total of 900 nucleotides. With the exception of the closely related Saccharomyces bayanus and S. pastorianus, which appear to have identical sequences, all other species could be distinguished by nucleotide differences in a variable region of the large subunit, and genus-specific nucleotides were discernible in all three regions. The taxon D. tamarii differed markedly from other species and is excluded from Debaryomyces. By contrast, Schwanniomyces occidentalis showed few nucleotide differences with Debaryomyces spp. and its transfer to Debaryomyces is proposed. Schizosaccharomyces proved to be somewhat more divergent than Saccharomyces and Debaryomyces, but species differences appear insufficient for dividing the genus. Some of the factors influencing estimates of phylogenetic distances from rRNA sequences are discussed.