Towards an integrated phylogenetic classification of theTremellomycetes

Abstract

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 taxa. Circumscriptions of the taxonomic units at the order, family and genus levels recognised were quantitatively assessed using the phylogenetic rank boundary optimisation (PRBO) and modified general mixed Yule coalescent (GMYC) tests. In addition, a comprehensive phylogenetic analysis on an expanded LSU rRNA (D1/D2 domains) gene sequence dataset covering as many as available teleomorphic and filamentous taxa within Tremellomycetes was performed to investigate the relationships between yeasts and filamentous taxa and to examine the stability of undersampled clades. Based on the results inferred from molecular data and morphological and physiochemical features, we propose an updated classification for the Tremellomycetes. We accept five orders, 17 families and 54 genera, including seven new families and 18 new genera. In addition, seven families and 17 genera are emended and one new species name and 185 new combinations are proposed. We propose to use the term pro tempore or pro tem. in abbreviation to indicate the species names that are temporarily maintained.

ANaganishiain high places: functioning populations or dormant cells from the atmosphere?

“…N. antarcticus, N. consortionis , and N. vishniacii ) and Himalayan ( N. bhutanensis ) cryptococci grouped in a clade with N. albidus (Takashima and Nakase 1999). This grouping has been confirmed by numerous other studies including the recent work of Liu et al (2015a, 2015b) who showed that N. friedmannii, N. antarcticus, N. vishniacii and N. bhutanensis are in the albidus clade of the Filobasidiales based on a seven-gene (RPB1, RPB2, TEF1, CYTB, and 3 rDNA genes) phylogeny. Also relevant to the present study, Vimercati et al (2016) showed that the isolate from Volcán Llullaillaco (discussed below) forms a monophyletic clade with N. friedmannii based on long-read 18S environmental sequences (1739 bp, JX099190) from Llullaillaco (Lynch et al 2012).…”

Yeast diversity and species recovery rates from beech forest soils

“…Two novel species represented by strains TSN-538 and TSN-649 (forest soils, Hainich National Park) were placed in the genus Piskurozyma in the phylogenetic analysis performed by Liu et al (2015) and in the present study (Fig. 5).…”

“…Following the "one fungus = one name" principle, systematics of basidiomycetous yeasts was recently revised and unified with the classification of filamentous (often sexual) fungi (Liu et al 2015;Wang et al 2015). Also, the polyphyletic genera Cryptococcus and Rhodotorula were restricted to the lineages, where the type species belong.…”

“…Recent phylogenetic analysis performed by Liu et al (2015) demonstrated that it represents a hitherto undescribed species in the newly introduced genus Vishniacozyma. Again, a formal description needs additional data, which would go beyond the scope of this study.…”

Evaluating and Improving Vitek MS for Identification of Clinically Relevant Species of Trichosporon and the Closely Related Genera Cutaneotrichosporon and Apiotrichum

“…Among these pathogenic species, T. asahii, T. asteroides, T. faecale, T. inkin, T. coremiiforme, T. dermatis, and T. mycotoxinivorans are the main species associated with deep-seated infections (2,4). Recently, based on multiple-gene sequence analysis, Trichosporon taxonomy has been reassessed, and new genera have been proposed for the monophyletic clades, which include Trichosporon, Cutaneotrichosporon, and Apiotrichum for pathogenic species (5). These genera are intrinsically resistant to echinocandins, and resistance to other antifungal classes has been described (2,4).…”