Towards an integrated phylogenetic classification of the Tremellomycetes

@article{Liu2015TowardsAI,
  title={Towards an integrated phylogenetic classification of the Tremellomycetes},
  author={X. Liu and Q.-M. Wang and M. G{\"o}ker and M. Groenewald and A. V. Kachalkin and H. Lumbsch and A. Millanes and M. Wedin and Andrey M. Yurkov and T. Boekhout and F. Bai},
  journal={Studies in Mycology},
  year={2015},
  volume={81},
  pages={85 - 147}
}
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 on the results of phylogenetic analyses from a seven-genes dataset covering the majority of tremellomycetous yeasts and closely related filamentous… Expand
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References

SHOWING 1-10 OF 265 REFERENCES
Phylogeny of tremellomycetous yeasts and related dimorphic and filamentous basidiomycetes reconstructed from multiple gene sequence analyses
TLDR
The phylogeny of the majority of described anamorphic and teleomorphic tremellomycetous yeasts is reconstructed using Bayesian inference, maximum likelihood, and neighbour-joining analyses based on the sequences of seven genes to form a phylogenetic framework that will be the basis for the proposal of an updated taxonomic system of tremellomers accommodating the ‘one fungus, one name’ principle. Expand
12 Tremellomycetes and Related Groups
TLDR
The state of knowledge of the morphology, ultrastructure, and ecology of Tremellomycetes are reviewed and their phylogenetic relationships are discussed, complemented by a comprehensive molecular phylogenetic analysis, including most of the species for which sequence data are available. Expand
Selection of Orthologous Genes for Construction of a Highly Resolved Phylogenetic Tree and Clarification of the Phylogeny of Trichosporonales Species
TLDR
This study proposes a set of genes suitable for constructing a phylogenetic tree with high resolution to examine evolutionary diversification in Trichosporonales and finds that several genes, such as phosphatidylinositol 3-kinase TOR1 and glutamate synthase (NADH), had good resolution in this group. Expand
Phylogeny and Phenotypic Characterization of Pathogenic Cryptococcus Species and Closely Related Saprobic Taxa in the Tremellales
TLDR
This study establishes a foundation for future comparative genomic approaches that will provide insight into the structure, function, and evolution of the mating type locus, the transitions in modes of sexual reproduction, and the emergence of human pathogenic species from related or ancestral saprobic species. Expand
Phylloplane yeasts from Portugal: seven novel anamorphic species in the Tremellales lineage of the Hymenomycetes (Basidiomycota) producing orange-coloured colonies.
A survey of epiphytic yeasts on leaves of selected Mediterranean plant species collected at the 'Arrábida Natural Park' (Portugal) yielded about 850 isolates, mostly of basidiomycetous affinity.Expand
Proposal of Mingxiaea gen. nov. for the anamorphic basidiomycetous yeast species in the Bulleribasidium clade (Tremellales) based on molecular phylogenetic analysis, with six new combinations and four novel species.
TLDR
Six new combinations are proposed for the described species of this clade which were formerly assigned to the genus Bullera and four novel species in the new genus were identified among 16 ballistoconidium-forming yeast strains isolated from plant leaves collected in Hainan province, southern China, by D1/D2 and ITS sequence analyses. Expand
Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora
TLDR
A clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence. Expand
Species Delimitation in Taxonomically Difficult Fungi: The Case of Hymenogaster
TLDR
This study reconsidered the species delimitations in Hymenogaster based on a comprehensive collection of Central European taxa comprising more than 140 fruiting bodies from 20 years of field work, and results indicate a highly variable morphology of H. citrinus and H. griseus. Expand
Molecular phylogeny of basidiomycetous yeasts in the Cryptococcus luteolus lineage (Tremellales) based on nuclear rRNA and mitochondrial cytochrome b gene sequence analyses: proposal of Derxomyces gen. nov. and Hannaella gen. nov., and description of eight novel Derxomyces species.
TLDR
The Dioszegia clade, two clades represented by Bullera mrakii and Bullera sinensis, respectively, were revealed to be well-separated monophyletic groups in the lineage. Expand
Molecular Phylogenetic Analysis of Ballistoconidium-Forming Yeasts in Trichosporonales (Tremellomycetes): A Proposal for Takashimella gen. nov. and Cryptotrichosporon tibetense sp. nov.
TLDR
In the present study, the three Bullera species, namely Bullera formosensis, Bullera koratensis and Bullera lagerstroemiae, and Cryptococcus tepidarius belonging to the Trichosporonales are transferred into a new genus Takashimella gen. nov. Expand
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