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Families and genera assigned to Tremellomycetes have been mainly circumscribed by morphology and for the yeasts also by biochemical and physiological characteristics. This phenotype-based classification is largely in conflict with molecular phylogenetic analyses. Here a phylogenetic classification framework for the Tremellomycetes is proposed based...

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... total of 294 tremellomycetous yeast strains, including the type strains of 286 currently recognised species and varieties as listed in Table 1 of Liu et al. (2015), were employed in this study. In addition, 47 tremellomycetous yeast species which were pub- lished too late to be included in the study of Liu et al. (2015) and 47 more fruiting body forming species from the genera Tremella, Syzygospora, Rhynchogastrema, Tetragoniomyces and Trimor- phomyces were employed in this study (Table 1). ...
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... total of 294 tremellomycetous yeast strains, including the type strains of 286 currently recognised species and varieties as listed in Table 1 of Liu et al. (2015), were employed in this study. In addition, 47 tremellomycetous yeast species which were pub- lished too late to be included in the study of Liu et al. (2015) and 47 more fruiting body forming species from the genera Tremella, Syzygospora, Rhynchogastrema, Tetragoniomyces and Trimor- phomyces were employed in this study (Table 1). Additionally, 23 novel but undescribed species retrieved from the public dataset were also included. ...
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... 23 novel but undescribed species retrieved from the public dataset were also included. Five Cryptococcus species recently described by Hagen et al. (2015) were listed in Table 1 of accepted species names but not included in the phylogenetic analyses. Large ribosomal subunit (LSU) rRNA gene sequences were additionally sampled specifically from related and fila- mentous taxa in Tremellomycetes, for which no culture material or other nucleotide data are available. ...
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... boundary optimisation is done using the rpart package ( Therneau et al. 2015) with the MaSH values of each clade as dependent and the rank as independent variable. One hundred bootstrap replicates were applied to obtain 95 % Table 1. List of accepted tremellomycetous yeast and dimorphic taxa. ...
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... at present we prefer to assign this species to the emended genus Kock- ovaella. The new genus Vishniacozyma is proposed for the strongly supported dimennae clade (Table 1, Fig. 1) (i.e. vic- toriae clade in Fonseca et al. ...
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... arun- dinariae, Cryptococcus arrabidensis, C. mujuensis, Filobasidium capsuligenum, and Tremella giraffa (Fig. 2). In addition, a few new clades were identified (Fig. 2, Table 1). The addition of the recently described species Cryptococcus tahquamenonensis ( Sylvester et al. 2015) to the monotypic huempii clade recog- nised in the seven-genes dataset in the Cystofilobasidiales supports the proposal of a new genus (Krasilnikovozyma gen. ...
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... on 1) the multigene phylogenetic framework presented by in Liu et al. (2015), 2) the quantitative assessment of taxonomic units using the PRBO approach as well as the iterative modified GMYC tests, 3) a further phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset containing as many as available teleomorphic and filamentous taxa within Tremellomycetes, and finally 4) phenotypical criteria, we propose to update the taxonomic system for tremellomycetous yeasts and related filamentous taxa ( Table 1). The phylogenetic classifica- tion includes five orders, 17 families and 54 genera. ...
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... phylogenetic classifica- tion includes five orders, 17 families and 54 genera. Among the genera accepted here, 18 are newly described and 18 are emended ( Table 1, Figs 1 and 2). Seven of the families are newly proposed and seven are emended from existing ones. ...
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... affinity of Mrakiella cryoconiti, which was not included in the seven-genes phylogeny, to Mrakia is shown in the trees obtained from the LSU rRNA gene sequences in this study (Fig. 3) as well as in Boekhout et al. (2011a) and Weiss et al. (2014). The emended genus Mrakia currently contains eight species (Table 1) ...
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... the species in Krasilnikovo- zyma can grow at 25 °C and thus differ from the species of the genus Mrakia emend., which are psychrophilic with a maximum growth temperature below 20 °C (Fell 2011). Krasilnikovozyma currently contains two species (Table 1) and two additional se- quences representing potential new species were obtained from public databases (Fig. 3). ...
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... has been suggested to consider sexual and asexual strains in a single species with four genetic lineages, and we adopt this proposal in the present study. The genus currently contains one species (Table 1) and the discovery of two more potential novel species was recently reported by David-Palma et al. (2014 absent. Low-weight aromatic compounds not uti- lised. ...
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... perplexans and U. pannonicus are phenotypically similar by forming grayish to yellowish colonies, whereas the other Udeniomyces species form pinkish-white to orange-white colonies. The emended genus Itersonilia currently contains two species (Table 1) and an additional sequence representing a potential new species was obtained from public databases (Fig. 3). Liu et al. 2015). ...
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... two species are phenotypically similar in producing arthroconidia. The genus currently contains two species (Table 1) and an additional sequence representing a potential new species was obtained from public databases (Fig. 3). Genus accepted: Cystofilobasidium. ...
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... they were not resolved as separate groups in the previous and present mo- lecular phylogenetic analyses. Therefore, the families and genera within this order are recircumscribed in this study based on the phylogenetic analyses of the seven-genes (Fig. 1) and the LSU rRNA datasets (Figs 2 and 4), resulting in the recognition of two families and seven genera (Table 1) Notes: The family Filobasidiaceae was proposed by Olive (1968) to accommodate the species Filobasidium floriforme. Three tel- eomorphic genera, namely Filobasidium, Filobasidiella and Cystofilobasidium, were then included in this family (KwonChung 1987). ...
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... these two Cryptococcus species are transferred to the genus Naganishia together with the Crypto- coccus species included in the albidus clade in the seven-genes dataset ( Liu et al. 2015). Fifteen species are presently accepted in the genus Naganishia (Table 1) Etymology: The genus is named in honour of the yeast biologist and geneticist Andr e Goffeau, who was the initiator and coor- dinator of the genome sequence project of Saccharomyces cerevisiae. ...
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... PRBO test indicated that the six species of the gastricus clade did not show significant deviation compared to the species in the reference clades (Table 2). Thus they are assigned to a single genus at present which currently contains six species (Table 1). ...
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... type species of Syzygospora, S. alba, is located in a separate clade (Fig. 4). The emended genus Heterocephalacria currently contains four described species (Table 1) and four additional sequences representing potential new species were obtained from public databases (Fig. 4). This genus is restricted to include the species in the clade rep- resented by Syzygospora alba, the type species of the genus, as recognised in the tree drawn from the LSU D1/D2 dataset (Fig. 4). ...
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... species form zygoconidia and are mycoparasitic on the hymenial surface of Corticiaceae (aphyllophoralean fungi) differing from the hosts of other Syzy- gospora species (Ginns 1986). Thus, the genus Syzygospora currently includes only S. alba and S. pallida (Table 1). ...
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... This genus currently contains seven described species (Table 1) and two additional sequences representing potential new species were obtained from public databases (Fig. 4). ...
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... have a pronounced ability to assimilate aldaric acids and low- weight aromatic compounds, such as L-malic, L-tartaric, sac- charic, mucic, caffeic, gentisic, p-coumaric, protocatechuic and hydroxybenzoic acids ( Fonseca et al. 2011). This genus currently contains six described species (Table 1) This order was proposed by Wuczkowski et al. (2011) to include the monotypic teleomorphic genus Holtermannia and the anamorphic genus Holtermanniella. The latter was proposed to accommodate four Cryptococcus species and a new anamorphic species closely related to Holtermannia corniformis ( Wuczkowski et al. 2011). ...
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... five anamorphic Holtermanniella species clustered together in a robust clade separate from the teleomorphic spe- cies Holtermannia corniformis (Figs 1 and 2). Therefore, the two genera Holtermannia with one species and Holtermanniella with five species are accepted here (Table 1). ...
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... re- circumscribed the families and genera in Tremellales based on the multigene phylogeny ( Liu et al. 2015) and the PRBO test performed in this study. A total of 11 families and 28 genera are accepted in Tremellales here (Table 1, Figs 1, 2 and 5). ...
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... species usually form yellowish to brownish colonies ( Nakase et al. 2004), being distinct from those of Dioszegia species that usually are orange-coloured ( Wang & Bai 2008). This genus currently contains two described species (Table 1 , Fig. 5E). Etymology: The genus is named in honour of the American microbiologist Helen S. Vishniac for her contributions to the study of microbial diversity and yeast ecology, especially of cold- adapted yeasts. ...
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... possible myco- parasitic nature has been suggested for these yeasts, which may have sexual trimorphomyces-like morphs . This genus currently contains eleven described species (Table 1) and four additional sequences representing potential new species were obtained from public databases (Fig. 5D). ...
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... genus Bullera emend. currently includes four species (Table 1, Fig. 5B), which were located into two closely related clades in the tree obtained from the seven-genes dataset ( Liu et al. 2015). Though these species show a significant deviation from the reference threshold (Table 2), they are kept in the genus Bullera at present to accommodate their phenotypic similarity and close phyloge- netic relationship and to minimise name changes. ...
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... the tree obtained from the expanded LSU rRNA gene dataset, Cr. mujuensis, Cr. tronadorensis and K. betulae formed a strongly supported clade, which was only distantly related to the Kwoniella and the S. intermedium clades (Fig. 5C). Thus, the new genus Fonsecazyma is proposed to accommodate these three species (Table 1). Other sequences obtained from public databases belong to a mislabelled K. heveanensis (GenBank AF406890) and three undescribed Cryptococcus species (Fig. 5C). ...
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... we propose the new genus Pseudotremella to accommodate this clade. Four species are currently accepted in this genus (Table 1, Fig. 5B). ...
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... we keep this species unassigned to any lineage as Tremella indecorata pro tem. (Table 1). ...
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... accepted: Fellomyces, Kockovaella and Ster- igmatosporidium (Table 1, Fig. 1). ...
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... Four species are currently accepted in this new genus (Table 1) and an additional sequence representing a potential new species was obtained from public databases (Fig. 5E). ...
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... further studies are needed to fully under- stand the taxonomic relationship between these two species. Ten species are currently accepted in this genus (Table 1). ...
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... containing C. mujuensis and C. tronadorensis (Fig. 5C). Eleven species are accepted in Kwoniella emend. in this study (Table 1) and three sequences representing potential new species were ob- tained from public databases (Fig. 5C). Kwoniella species are usually saprobic and differ from the closely aligned pathogenic yeasts in the genus Cryptococcus emend. ...
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... combinations for Kwoniella above, the foliacea clade was consistently resolved as a well supported clade in different studies using various datasets, though its phylogenetic position varied (Chen 1998, Millanes et al. 2011, this study Fig. 1). Seven species, including two Crypto- coccus and five Tremella species were included in this clade with 100 % bootstrap support ( Fig. 1) and therefore are transferred to Phaeotremella (Table 1). ...
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... we propose to erect a new genus for this single-species lineage. The genus Gelidatrema currently con- tains one species (Table 1), but a few additional sequences representing potential new species (ITS: GenBank KC455886, DQ242634) were found in public databases. ...
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... Tetragoniomycetaceae emend. and ten genera, including one emended and four new genera are accepted in this order (Table 1). This family is emended to accommodate the monophyletic lineage comprising the brassicae/gracile, cutaneum, haglerorum, porosum, Trichosporon and Vanrija clades, and four single-species lineages comprising three Cryptocococcus and one Trichosporon species as recognised in multigene phy- logenies ( Liu et al. 2015). ...
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... belonging to this newly circumscribed genus Trichosporon have serotype II. Twelve species are accepted in this genus (Table 1, Fig. 6). ...
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... reasons of conservatism we combine the three clades into a single genus Apiotrichum. The genus currently contains 20 species (Table 1). ...
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... the genus contains one species (Table 1). ...
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... close phylogenetic relationship between Cryptotrichosporon and Tetragoniomyces was supported in . The genus Tetragoniomyces remains monotypic and the genera Cryptotrichosporon ( Okoli et al. 2007) and Taka- shimella ( ) contain two and four species, respectively (Table 1). Cryptococcus marinus was branching more early than this family in the Bayesian and ML trees derived from the seven-genes dataset, but its position was not resolved in the seven-genes NJ tree and the combined rRNA genes tree ( Liu et al. 2015). ...

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... In more recent studies, however, the sequences of Sirobasidium spp., including those obtained in this study and already published, were added to the dataset of phylogenetic analyses, supporting their attribution to Tremellales (Liu et al. 2015;Kachalkin et al. 2019;Li et al. 2020). The sequence of Sirotrema obtained in this study has also been included in the above phylogenetic analyses, supporting the attribution to the genus Phaeotremella (Kachalkin et al. 2019;Li et al. 2020). ...
... 1). It should be noted that these sequences have already been publicly available for several years and have been added to the dataset of phylogenetic analyses in some studies (e.g., Liu et al. 2015;Kachalkin et al. 2019;Li et al. 2020). In our constrained ML analysis based on a concatenated (SSU-ITS-LSU D1/D2) dataset, Sirobasidium sp. ...
... magnum). Many studies have shown that Sb. intermedium was phylogenetically separated from the other Sirobasidium species (e.g., Boekhout et al. 2011;Millanes et al. 2011;Liu et al. 2015;Kachalkin et al. 2019;Li et al. 2020; this study), and thus the genus is polyphyletic. In a phylogenetic tree in Liu et al. (2015), Sb. intermedium CBS 7805 formed a clade with another Sirobasidium species named Sb. ...
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Species in the genera Sirobasidium and Sirotrema (Tremellales, Tremellomycetes, Agaricomycotina, Basidiomycota) have been described based solely on the morphology of teleomorph, and many of them lack both isolates of anamorphic yeast state and nucleotide sequence data. Strains of Sirotrema translucens and Sirobasidium japonicum were established for the first time from basidiocarps collected in Japan. Also, an undescribed species in the genus Sirobasidium was isolated. Sirobasidium sp. was characterized by its apiculate epibasidia and 2-celled basidia divided by a longitudinal septum, which is a unique combination of characteristics in the genus. Although the phylogenetic placement of Sb. japonicum within the Tremellales was not resolved in our analysis, Sirobasidium sp. formed a well-supported monophyletic clade with Sb. magnum and Fibulobasidium spp., and Sirotrema translucens was located in the genus Phaeotremella. Mating experiments using single-basidiospore strains showed that Sb. japonicum produced basidia, epibasidia, and basidiospores on a nutrient-poor medium, and the life cycle was successfully completed in controlled conditions. In conclusion, we propose Sirobasidium apiculatum sp. nov. and Phaeotremella translucens comb. nov.
... are scattered among 11 of 12 clades in Saccharomycotina, as stated by Kurtzman and Robnett 17) , and Cryptococcus spp. were found in 3 of the 5 orders of Agaricomycotina, namely Filobasidiales, Tremellales, and Trichosporonales 27) . Because fungi in the environment can be detected using their DNA sequences, the dual nomenclature system was inconvenient for their identification. ...
... While the reclassification of basidiomycetous yeast species at that time had been delayed, both teleomorphs and anamorphs were reclassified on the basis of phylogenetic relationships to accommodate the requirements of the Code. Three studies have reported such reclassifications for the subphyla Agaricomycotina 27) , Pucciniomycotina 23) , and Ustilaginomycotina 34) . However, some species names remain unrevised and are treated as pro tempore. ...
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This review describes the changes in yeast species names in the previous decade. Several yeast species have been reclassified to accommodate the “One fungus=One name” (1F=1N) principle of the Code. As the names of medically important yeasts have also been reviewed and revised, details of the genera Candida, Cryptococcus, Malassezia, and Trichosporon are described in Section 3, along with the history of name changes. Since the phylogenetic positions of Candida species in several clades have not been clarified, revision of this species has not been completed. Among the species that remain unrevised despite their importance in the medical field, we propose the transfer of six Candida species to be reclassified in the Nakaseomyces clade, including Nakaseomyces glabratus and Nakaseomyces nivalensis.
... Papiliotrema laurentii, previously known as Cryptococcus laurentii, is a non-conventional oleaginous yeast belonging to the Basidiomycota phylum, Tremellomycetes class, and Tremellales order (Liu et al. 2015b). It is a non-motile, encapsulated, and dimorphic yeast (Kurtzman 1973). ...
... Then, it was reclassified as Torulopsis laurentii by Diddens and Lodder (1934), and later as Cryptococcus laurentii by Skinner (1950). In 2015, an updated classification for the Tremellomycetes class was proposed by Liu et al. (2015b). They performed phylogenetic analyses using a dataset consisting of most species inside Tremellomycetes, with seven genes selected as molecular markers. ...
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Papiliotrema laurentii, previously classified as Cryptococcus laurentii, is an oleaginous yeast that has been isolated from soil, plants, and agricultural and industrial residues. This variety of habitats reflects the diversity of carbon sources that it can metabolize, including monosaccharides, oligosaccharides, glycerol, organic acids, and oils. Compared to other oleaginous yeasts, such as Yarrowia lipolytica and Rhodotorula toruloides, there is little information regarding its genetic and physiological characteristics. From a biotechnological point of view, P. laurentii can produce surfactants, enzymes, and high concentrations of lipids, which can be used as feedstock for fatty acid–derived products. Moreover, it can be applied for the biocontrol of phytopathogenic fungi, contributing to quality maintenance in post- and pre-harvest fruits. It can also improve mycorrhizal colonization, nitrogen nutrition, and plant growth. P. laurentii is also capable of degrading polyester and diesel derivatives and acting in the bioremediation of heavy metals. In this review, we present the current knowledge about the basic and applied aspects of P. laurentii, underscoring its biotechnological potential and future perspectives. Key points • The physiological characteristics of P. laurentii confer a wide range of biotechnological applications. • The regulation of the acetyl-CoA carboxylase in P. laurentii is different from most other oleaginous yeasts. • The GEM is a valuable tool to guide the construction of engineered P. laurentii strains with improved features for bio-based products.
... Similarly, Solicoccozyma and Apiotrichum species have also been identi ed as important organisms in forest soils(Buée et al., 2009;Mašínová et al., 2017), probably related to the presence of plant-derived labile carbon resources. Species within the genera Solicocozyma, Holtermanniella, and Naganishia have previously been identi ed as Crytococcus spp.(Liu et al., 2015), possibly suggesting that labile carbon inputs to soil may favour the growth of organisms that are closely related to those associated with mammalian disease. ...
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Inputs of carbon to soil may be used to stimulate microbial growth and immobilize excess nitrogen from sources such as livestock urine. However, the growth responses of microbial taxa to carbon inputs under conditions of excess soil nitrogen remain poorly understood. Using DNA metabarcoding and a field-based soil lysimeter experiment, we characterised the temporal responses (up to 112 days) of bacterial and fungal communities to a simulated bovine urine event plus inputs of labile carbon (sucrose) at two concentrations. Fungal communities were impacted more strongly than bacterial communities by carbon inputs under simulated urine patch conditions and had more variable responses among taxa. The richness of Chytridiomycota and Glomeromycota were most negatively affected, and Tremellomycetes most positively affected, by carbon inputs. A minority of fungal ASVs had greatly increased abundances in response to carbon, while fungal trophic composition became highly dominated by saprotrophs by the experiment end. Bacterial taxa showed consistent trends of declining (to about 14 days) and recovering (to 112 days) richness in response to urine and carbon inputs, but carbon-related evenness and abundance trends varied between taxa. Actinobacteria, Bacteroidetes, Betaproteobacteria, and Gammaproteobacteria each increased in abundance in response to carbon, whereas Acidobacteria, candidate division WPS-1, Planctomycetes, Deltaproteobacteria, and Verrucomicrobia each decreased in abundance. These results show that labile carbon inputs to limit nitrogenous leaching support the resilience of prokaryote communities to bovine urine events but may have long-term impacts on fungal community composition and function, with potential consequences for soil food webs, carbon sequestration, and agricultural productivity.