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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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... deviating) when its MaSH was not even located within the outer confidence bounds. Ten genera (Table 2) of tremellomycetous yeasts and their parent taxa were chosen as references. These genera are considered as being well delimited phenotypically and phylogenetically because they were resolved as strongly supported monophyletic clades with stable positions in the trees derived from different datasets using different algo- rithms ( Liu et al. 2015) and the species in each genus exhibit similar morphological or physiological properties. ...
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... in ape (Paradis 2006). A Table 2. PRBO results showing the divergences, if any, of the proposed taxa (except for the families) from the optimal range of divergences for their rank as inferred from the selected reference taxa. ...
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... units assessed by PRBO and a modified GMYC approach A taxonomic framework was firstly proposed based on the seven-genes phylogeny ( Liu et al. 2015) as shown in Fig. 1, which was the basis for further taxonomic unit assessment and expanded LSU dataset analysis. Based on the PRBO analysis including 286 taxa represented by 294 strains of trem- ellomycetous yeasts, strong delimitation evidence was found for the orders Cystofilobasidiales, Holtermanniales and Tremellales, which showed no significant deviation from the range defined by the optimal boundaries calculated for their rank (Table 2). The demarcation of orders Filobasidiales and Trichosporonales showed a small negative, significant deviation (Sigdev = −0.1242 ...
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... genera or clades of tremellomycetous yeasts which were consistently resolved as monophyletic groups with strong sta- tistical support in the trees constructed using different datasets and algorithms ( Liu et al. 2015) were used as references in the PRBO test (Table 2). Six of these genera, Bulleribasidium emend., Derxomyces, Dioszegia, Fibulobasidium, Hannaella and Holtermanniella, have been accepted as well-established genera based on their distinct morphological characters and phyloge- netic positions ( Bandoni 1979, Wang & Bai 2008). ...
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... of these genera, Bulleribasidium emend., Derxomyces, Dioszegia, Fibulobasidium, Hannaella and Holtermanniella, have been accepted as well-established genera based on their distinct morphological characters and phyloge- netic positions ( Bandoni 1979, Wang & Bai 2008). Of the 44 monotypic genera or clades identified in this study based on the multigene phylogeny ( Liu et al. 2015), the majority (34 genera) was in agreement with the PRBO results (Table 2). Five genera showed significant deviation from the optimal range calculated for the genus rank, namely Bullera emend., Derxomyces, Kockovaella emend., Tremella sensu stricto and Vishniacozyma gen. ...
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... the species of the ARD ecoclade clustered together, they did not form a significantly supported clade in the seven-genes tree ( Liu et al. 2015) and in the LSU rRNA gene tree (Fig. 4). The 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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... we re-define the genus Tremella to include only the spe- cies in the Tremella sensu stricto clade as recognised in the tree derived from seven genes ( Liu et al. 2015). As discussed above, the Tremella sensu stricto clade showed a significant deviation from the reference thresholds in the PRBO analysis (Table 2) and two subclades, mesenterica and fuciformis, with distinguishable morphological characters could be identified within the clade as shown in Chen (1998) and Liu et al. (2015). These data imply that the Tremella sensu stricto clade probably can be reclassified into two genera in the future. ...
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... order to avoid creating genera for these small clades, we decided to combine them in a single genus. The PRBO test did not show significant deviation for the emended Papiliotrema generic concept (Table 2), sup- porting this taxonomic treatment. The genus Papiliotrema was proposed in 2002 ( Sampaio et al. 2002), thus having nomen- clature priority over Auriculibuller, which was proposed in 2004 ( Sampaio et al. 2004). ...
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... 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 basidiomycetous yeasts have also undergone substantial taxonomic change based on large-scale phylogenetic evidence [18,32]. The revision of the genus Cryptococcus coincided with the proposal to elevate the 7 lineages within the Cryptococcus neoformans and Cryptococcus gattii complexes to species [33], which, while now largely accepted, has not been without robust debate [34,35]. ...
... Invasive infections including fungemia [17] Candida pseudorugosa Diutina pseudorugosa Invasive infections including fungemia [14] Candida rugosa Diutina rugosa Invasive infections including fungemia [14] Cryptococcus albidus Naganishia albida Invasive infections including fungemia [18] Cryptococcus curvatus Cutaneotrichosporon curvatus Invasive infections [18] Cryptococcus cyanovorans Cutaneotrichosporon cyanovorans Respiratory infections, especially in cystic fibrosis [18] Cryptococcus laurentii Papiliotrema laurentii Invasive infections including fungemia [18] Pseudozyma antarctica Moesziomyces antarticus Fungemia [19] Pseudozyma aphidis Moesziomyces aphidis Fungemia [19] Pseudozyma churashimaensis Dirkmeia churashimaensis Fungemia [19] Pseudozyma crassa Triodiomyces crassus Fungemia [19] Pseudozyma parantarctica Moesziomyces parantarcticus Fungemia [19] Pseudozyma siamensis Ustilago siamensis Fungemia [19] Geotrichum capitatum Magnusiomyces capitatus Invasive infections including fungemia [20] Geotrichum clavatum, Saprochaete clavata ...
... Invasive infections including fungemia [17] Candida pseudorugosa Diutina pseudorugosa Invasive infections including fungemia [14] Candida rugosa Diutina rugosa Invasive infections including fungemia [14] Cryptococcus albidus Naganishia albida Invasive infections including fungemia [18] Cryptococcus curvatus Cutaneotrichosporon curvatus Invasive infections [18] Cryptococcus cyanovorans Cutaneotrichosporon cyanovorans Respiratory infections, especially in cystic fibrosis [18] Cryptococcus laurentii Papiliotrema laurentii Invasive infections including fungemia [18] Pseudozyma antarctica Moesziomyces antarticus Fungemia [19] Pseudozyma aphidis Moesziomyces aphidis Fungemia [19] Pseudozyma churashimaensis Dirkmeia churashimaensis Fungemia [19] Pseudozyma crassa Triodiomyces crassus Fungemia [19] Pseudozyma parantarctica Moesziomyces parantarcticus Fungemia [19] Pseudozyma siamensis Ustilago siamensis Fungemia [19] Geotrichum capitatum Magnusiomyces capitatus Invasive infections including fungemia [20] Geotrichum clavatum, Saprochaete clavata ...
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Fungal species have undergone and continue to undergo significant nomenclatural change, primarily due to the abandonment of dual species nomenclature in 2013 and the widespread application of molecular technologies in taxonomy allowing correction of past classification errors. These have effected numerous name changes concerning medically important species, but by far the group causing most concern are the Candida yeasts. Among common species, Candida krusei, Candida glabrata, Candida guilliermondii, Candida lusitaniae, and Candida rugosa have been changed to Pichia kudriavzevii, Nakaseomyces glabrata, Meyerozyma guilliermondii, Clavispora lusitaniae, and Diutina rugosa, respectively. There are currently no guidelines for microbiology laboratories on implementing changes, and there is ongoing concern that clinicians will dismiss or misinterpret laboratory reports using unfamiliar species names. Here, we have outlined the rationale for name changes across the major groups of clinically important fungi and have provided practical recommendations for managing change.
... Within the fungal groups including lichenicolous representatives, the Tremellomycetes (Agaricomycotina, Basidiomycota) are particularly interesting in terms of their varied ecology. They comprise species with a remarkably diverse range of lifestyles, including lichenicolous fungi, saprotrophs, parasites of non-lichenized fungi, and parasites of animals, including humans (Millanes et al., 2011;Liu et al., 2015). Lichenicolous Tremellomycetes have been comparatively less studied due to methodological constraints. ...
... We produced two phylogenies, one including Tremella caloplacae s. l. and the other including their lichenized fungal host in the Teloschistaceae. Outgroups chosen to root the trees were selected based on previous literature and preliminary trees (Millanes et al., 2011;Liu et al., 2015). For the phylogeny of the parasites, we chose Tremella candelariellae, while Megalospora tuberculosa was selected for the phylogeny of the hosts. ...
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... Tremellomycetes, belonging to Agaricomycotina, is a class of fungi with multiple morphological characteristics (Hibbett 2006;Liu et al. 2015a). To date, hundreds of Tremellomycetes species have been described, including yeasts, dimorphic taxa, and species that form hyphae and/or complex basidiocarps (Millanes et al. 2011;Yurkov and Kurtzman 2019). ...
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... [3][4][5] Trichosporon debeurmannianum was first isolated from bronchial aspirate, but it had not been determined whether it was pathogenic or not. 6 Recently, Liu et al. 7 reclassified Trichosporon into three genera: Apiotrichum, Cutaneotrichosporon, and Trichosporon. ...
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... al. 2019). Rhynchogastrema coronatum, also noted in the present study, acts as a hyperparasite of fungi (Liu et al. 2015). Solicoccozyma fuscescens, the most frequently identified yeast species in this study, had been previously detected in agricultural soil (Mašínová et al. 2017), but its ecosystem functions have not yet been fully elucidated. ...
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Aims Saprotrophic soil fungi participate in biomass mineralization, inhibit pathogen development and promote plant growth. Pathogens accumulate in soil and decrease crop yields. The structure of fungal communities is determined mainly by the organic matter content and pH of soil. Little is known about the influence of crop rotation and long-term monoculture on saprotrophic fungi that decompose plant roots and crop residues as sources of soil biomass. Methods Fungal communities that promote plant growth (arbuscular mycorrhizal fungi (AMF), yeasts, Trichoderma spp.), cellulolytic fungi and pathogenic species were analyzed in a 6-year crop rotation system (maize – spring barley – peas – winter rapeseed – winter wheat – sugar beets) and in 50-year maize monoculture. Fungal DNA was extracted from the rhizosphere and plant roots, and the ITS2 region of fungal rDNA was analyzed by high-throughput sequencing. In both treatments, weeds were controlled chemically (terbuthylazine + mesotrione + s-metolachlor) or mechanically. Results A total of 311 fungal species were identified. The biodiversity of soil fungi, in particular AMF and yeasts, was higher in monoculture than in crop rotation. Maize pathogens were more frequently identified in monoculture, whereas species of the genus Trichoderma were more prevalent in crop rotation. Herbicides clearly increased the abundance of cellulolytic fungi of the phyla Mucoromycota and Mortierellomycota, Mortierella spp. and Minimedusa polyspora. The abiotic properties of soil were affected by the cropping sequence. The content of organic carbon (Corg) and the availability of P and Mg decreased in monoculture. Maize yields were bound by a strong positive correlation with the availability of macronutrients and Corg in soil, as well as a weak positive correlation with the abundance of Trichoderma spp., Mucoromycota and Mortierellomycota. Conclusions Fungi exert a complex and ambiguous effect on maize biomass yields, whereas a decrease in the macronutrient content of soil in monoculture strongly decreases maize yields. In the long term, the cropping sequence considerably influences the structure of the soil microbiome which can be a reservoir of unique species and species that minimize the negative effects of monoculture in agroecosystems. Graphical Abstract
... Although Basidiomycota contain a large diversity of macromycetes, micromycetes can be found in all its subphyla or are dominant in early diverging lineages (Cepero et al., 2012). Withinin Agaricomycotina, the microfungi recorded for Colombia belong mainly to yeast or yeast-like fungi (Liu et al., 2015) in the Tremellomycetes (45 species), including seven species of the genus Cryptococcus. Cryptococcus neoformans and C. gattii are responsible for cryptococcosis, often being isolated from soil and plant debris, respectively (Vélez & Escandón, 2020). ...
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Colombia is a Neotropical country with a highly diverse fauna, flora, and microbial biota. However, mycology is still a developing field, and currently, Colombia has reported only 5% of the fungal species known worldwide. The goal of this chapter is to revisit the current state of the knowledge on Colombian microfungi, according to species registered in the ColFungi database, excluding lichens. For this purpose, we categorised each taxon as macro-or micromycete according to the presence or absence of macroscopically visible structures. In our definition, a total of 2,498 (57%) out of the 4,406 non-lichenized species included in the database correspond to microfungi, most of them being members of the subkingdom Dikarya (92%). We found that early diverging fungal lineages are underrepresented and need to be prioritised in future diversity surveys. Although next-generation sequencing tools are being used worldwide to explore biodiversity, few studies to date have employed this approach to assess fungal diversity in Colombia. In general, the relevance of performing an assertive polyphasic identification to species level and the necessity to enrich our national culture collections are discussed. RESUMEN Colombia es considerado un país megadiverso en fauna, flora y microorganismos. En cuanto a los hongos, nuestro país ha reportado el 5% de las especies conocidas en el mundo. El objetivo de este capítulo fue estudiar el estado actual de la diversidad de microhongos en Colombia y resaltar los grupos taxonómicos que deben ser priorizados en futuros estudios de diversidad de hongos en el país. Para este fin, se utilizaron las especies registradas en la base de datos de ColFungi y se realizó una categorización adicional de las especies, asignándole a cada una la clasificación de macro-o micromicete, de acuerdo con la presencia o ausencia de estructuras macroscópicamente visibles. Los líquenes fueron excluidos. Del total de 4,406 especies pertenecientes al reino Fungi registradas en la base de datos de ColFungi, excluyendo los que son liquenizados, el 57% (2,498) corresponden a registros de microhongos, siendo la mayoría miembros del subreino Dikarya (92%). También encontramos que linajes basales de hongos, como por ejemplo los zigomicetes (filos Mucoromycota y Zoopagomycota), están subrepresentados y deben ser priorizados en futuros estudios de diversidad. En los últimos años, las herramientas de secuenciación de nueva generación han sido usadas para explorar la biodiversidad a nivel mundial. Aunque Colombia ha realizado esfuerzos para evaluar la diversidad fúngica en el país usando estas aproximaciones, aún siguen siendo pocos los estudios que emplean estas estrategias para estimar la diversidad fúngica. En este capítulo resaltamos la importancia de realizar estudios polifásicos dirigidos hasta el nivel de especie, con el fin de tener identificaciones rigurosas y una estimación más precisa de los grupos más representativos de comunidades fúngicas. Además, recalcamos la necesidad de enriquecer las colecciones nacionales de microhongos, para incentivar así las investigaciones en torno al aprovechamiento de la diversidad y bioeconomía.
... 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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