The molecular systematics of 337 strains of basidiomycetous yeasts and yeast-like fungi, representing 230 species in 18 anamorphic and 24 teleomorphic genera, was determined by sequence analysis of the D1/D2 region of the large-subunit rDNA. The data were compared with published sequences of other basidiomycetous fungi. The results demonstrated that the yeast species and genera are phylogenetically distributed among the Microbotryum, Sporidiobolus, Agaricostilbum and Erythrobasidium clades of the Urediniomycetes; the Tremellales, Trichosporonales ord. nov., Filobasidiales and Cystofilobasidiales clades of the Hymenomycetes; and the Ustilaginales, Microstromatales and Malasseziales clades of the Ustilaginomycetes. Genera such as Bensingtonia, Cryptococcus, Rhodotorula and Sporobolomyces are polyphyletic, i.e. they occur in two or more clades. In contrast, other genera, e.g. Bullera, Cystofilobasidium, Fellomyces, Filobasidiella, Filobasidium, Kondoa, Kurtzmanomyces, Leucosporidium, Rhodosporidium, Sporidiobolus and Udeniomyces, are monophyletic. The majority of the species can be identified using D1/D2 analyses, although the internal transcribed spacer region is required to distinguish closely related species. The intergenic spacer region is recommended for additional differentiation of species and strains.

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Biodiversity and systematics of basidiomycetous yeasts as determined by large-subunit rDNA D1/D2 domain sequence analysis.

Notes on 113 fungal taxa are compiled in this paper, including 11 new genera, 89 new species, one new subspecies, three new combinations and seven reference specimens. A wide geographic and taxonomic range of fungal taxa are detailed. In the Ascomycota the new genera Angustospora (Testudinaceae), Camporesia (Xylariaceae), Clematidis, Crassiparies (Pleosporales genera incertae sedis), Farasanispora, Longiostiolum (Pleosporales genera incertae sedis), Multilocularia (Parabambusicolaceae), Neophaeocryptopus (Dothideaceae), Parameliola (Pleosporales genera incertae sedis), and Towyspora (Lentitheciaceae) are introduced. Newly introduced species are Angustospora nilensis, Aniptodera aquibella, Annulohypoxylon albidiscum, Astrocystis thailandica, Camporesia sambuci, Clematidis italica, Colletotrichum menispermi, C. quinquefoliae, Comoclathris pimpinellae, Crassiparies quadrisporus, Cytospora salicicola, Diatrype thailandica, Dothiorella rhamni, Durotheca macrostroma, Farasanispora avicenniae, Halorosellinia rhizophorae, Humicola koreana, Hypoxylon lilloi, Kirschsteiniothelia tectonae, Lindgomyces okinawaensis, Longiostiolum tectonae, Lophiostoma pseudoarmatisporum, Moelleriella phukhiaoensis, M. pongdueatensis, Mucoharknessia anthoxanthi, Multilocularia bambusae, Multiseptospora thysanolaenae, Neophaeocryptopus cytisi, Ocellularia arachchigei, O. ratnapurensis, Ochronectria thailandica, Ophiocordyceps karstii, Parameliola acaciae, P. dimocarpi, Parastagonospora cumpignensis, Pseudodidymosphaeria phlei, Polyplosphaeria thailandica, Pseudolachnella brevifusiformis, Psiloglonium macrosporum, Rhabdodiscus albodenticulatus, Rosellinia chiangmaiensis, Saccothecium rubi, Seimatosporium pseudocornii, S. pseudorosae, Sigarispora ononidis and Towyspora aestuari. New combinations are provided for Eutiarosporella dactylidis (sexual morph described and illustrated) and Pseudocamarosporium pini. Descriptions, illustrations and / or reference specimens are designated for Aposphaeria corallinolutea, Cryptovalsa ampelina, Dothiorella vidmadera, Ophiocordyceps formosana, Petrakia echinata, Phragmoporthe conformis and Pseudocamarosporium pini. The new species of Basidiomycota are Agaricus coccyginus, A. luteofibrillosus, Amanita atrobrunnea, A. digitosa, A. gleocystidiosa, A. pyriformis, A. strobilipes, Bondarzewia tibetica, Cortinarius albosericeus, C. badioflavidus, C. dentigratus, C. duboisensis, C. fragrantissimus, C. roseobasilis, C. vinaceobrunneus, C. vinaceogrisescens, C. wahkiacus, Cyanoboletus hymenoglutinosus, Fomitiporia atlantica, F. subtilissima, Ganoderma wuzhishanensis, Inonotus shoreicola, Lactifluus armeniacus, L. ramipilosus, Leccinum indoaurantiacum, Musumecia alpina, M. sardoa, Russula amethystina subp. tengii and R. wangii are introduced. Descriptions, illustrations, notes and / or reference specimens are designated for Clarkeinda trachodes, Dentocorticium ussuricum, Galzinia longibasidia, Lentinus stuppeus and Leptocorticium tenellum. The other new genera, species new combinations are Anaeromyces robustus, Neocallimastix californiae and Piromyces finnis from Neocallimastigomycota, Phytophthora estuarina, P. rhizophorae, Salispina, S. intermedia, S. lobata and S. spinosa from Oomycota, and Absidia stercoraria, Gongronella orasabula, Mortierella calciphila, Mucor caatinguensis, M. koreanus, M. merdicola and Rhizopus koreanus in Zygomycota.

Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa

Basidiomycetous yeasts in the Urediniomycetes and Hymenomycetes were examined by sequence analysis in two ribosomal DNA regions: the D1/D2 variable domains at the 5' end of the large subunit rRNA gene (D1/D2) and the internal transcribed spacers (ITS) 1 and 2. Four major lineages were recognized in each class: Microbotryum, Sporidiobolus, Erythrobasidium and Agaricostilbum in the Urediniomycetes; Tremellales, Trichosporonales, Filobasidiales and Cystofilobasidiales in the Hymenomycetes. Bootstrap support for many of the clades within those lineages is weak; however, phylogenetic analysis provides a focal point for in-depth study of biological relationships. Combined sequence analysis of the D1/D2 and ITS regions is recommended for species identification, while species definition requires classical biological information such as life cycles and phenotypic characterization.

Systematics of basidiomycetous yeasts: a comparison of large subunit D1/D2 and internal transcribed spacer rDNA regions

The primary taxa of eukaryote classification should be monophyletic and based on fundamental cell structure rather than nutritional adaptive zones. The classical two kingdom classification into "plants" and "animals" and the newer four kingdom classifications into "protis", "fungi" "animals" and "plants" are therefore both unsatisfactory. Eukaryotes can be classified into nine kingdoms each defined in terms of a unique constellation of cell structures. Five kingdoms have plate-like mitochondrial cristae: (1) Eufungi (the non-ciliated fungi, which unlike the other eight kingdoms have unstacked Golgi cisternae), (2) Ciliofungi (the posteriorly ciliated fungi), (3) Animalia (Animals, sponges, mesozoa, and choanociliates; phagotrophs with basically posterior ciliation), (4) Biliphyta (Non-phagotrophic, phycobilisome-containing, algae; i.e. theGlaucophyceae and Rhodophyceae), (5) Viridiplantae (Non-phagotrophic green plants, with starch-containing plastids). Kingdom (6), the Euglenozoa, has disc-shaped cristae and an intraciliary dense rod and may be phagotrophic and/or phototrophic with plastids with three-membraned envelopes. Kingdom (7), the cryptophyta, has flattened tubular cristae, tubular mastigonemes on both cilia,m and starch in thecompartment between the plastid endoplasmic reticulum and the plastid envelope; their plastids, if present, have phycobilins inside the paired thylakoids and chlorophyll c2. Kingdom (8), the Chromophyta, has tubular cristae, together with tubular mastigonemes on one anterior cilum and/or a plastid endoplasmic reticulum and chlorophyll c1 + c2. Members of the ninth kingdom, the Protozoa, are mainly phagotrophic, and have tubular or vesicular cristae (or lack mitochondria altogether), and lack tubular mastigonemes on their (primitively anterior) cilia; plastids if present have three-envelop membranes, chlorophyll c2, and no internal starch, and a plastid endoplasmic reticulum is absent. Kingdoms 4-9 are primitively anteriorly biciliate. Detailed definitions of the new kingdoms and lists of the phyla comprising them are given. Advantages of the new system and its main phylogenetic implications are discussed. A simpler system of five kingdoms suitable for very elementary teaching is possible by grouping the photosynthetic and fungal kindoms in pairs. Various compromises are possible between the nine and five kingdoms systems; it is suggested that the best one for general scientific use is a system of seven kingdoms in which the Eufungi and Ciliofungi become subkingdoms of the Kingdom Fungi, and the Cryptophyta andChromophyta subkingdoms of th Kingdom Chromista; the Fungi, Viridiplantae, Biliphyta, and Chromista can be subject to the Botanical Code of Nomenclature, while the Zoological Code can govern the Kingdoms Animalia, Protozoa and Euglenozoa...

Eukaryote kingdoms: Seven or nine?

Phylogenetic relationships of resupinate Homobasidiomycetes (Corticiaceae s. lat. and others) were studied using ribosomal DNA (rDNA) sequences from a broad sample of resupinate and nonresupinate taxa. Two datasets were analysed using parsimony, a 'core' dataset of 142 species, each of which is represented by four rDNA regions (mitochondrial and nuclear large and small subunits), and a 'full' dataset of 656 species, most of which were represented only by nuclear large subunit rDNA sequences. Both datasets were analysed using traditional heuristic methods with bootstrapping, and the full dataset was also analysed with the Parsimony Ratchet, using equal character weights and six-parameter weighted parsimony. Analyses of both datasets supported monophyly of the eight major clades of Homobasidiomycetes recognised by Hibbett and Thorn, as well as independent lineages corresponding to the Gloeophyllum clade, corticioid clade and Jaapia argillacea. Analyses of the full dataset resolved two additional groups, the athelioid clade and trechisporoid clade (the latter may be nested in the polyporoid clade). Thus, there are at least 12 independent clades of Homobasidiomycetes. Higher- level relationships among the major clades are not resolved with confidence. Nevertheless, the euagarics clade, bolete clade, athelioid clade and Jaapia argillacea are consistently resolved as a monophyletic group, whereas the cantharelloid clade, gomphoid-phalloid clade and hymenochaetoid clade are placed at the base of the Homobasidiomycetes, which is consistent with the preponderance of imperforate parenthesomes in those groups. Resupinate forms occur in each of the

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The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes)

The question of special features in fungal mitochondria which may have phylogenetic significance has been raised several times in recent literature. A representative survey of the micromorphology of over fifty genera of Eumycota shows a variability of mitochondrial structure similar to that of algae, higher plants, and metazoa. It is concluded from these observations that there is apparently nothing structurally characteristic of fungal mitochondria. Also pointed out is the similarity between a netlike endomembrane configuration in the cells of an Ascomycete containing as well typical mitochondria and the mitochondrial equivalents proposed in bacteria; the consequent caution is made that the identification of these structures with mitochondria should await substantiating biochemical evidence.

Fine Structure of Mycota

SUMMARYMost basidiomycetes are characterized by dolipores that at some time form a granule in each opening and by parenthesomes that are either multiperforate (homobasidiomycetes) or imperforate or pauciperforate (jelly fungi). Electron micrographs of Tremella brasiliensis and T. mesenterica dikaryons, however, show vesiculate parenthesomes and dolipore septa with banded material in the orifices, similar to the septa of the Filobasidiaceae. Because of this exceptional character and because these taxa also share the unusual condition of unicellular Cryptococcus like monokaryons, they are segregated in a new Suborder Tremellineae. The remainder of the Tremellales are preserved in the additional new taxa Exidiaceae and Exidiineae. Also presented is a taxonomic outline of the fungi treated as a kingdom and based on an expanded hierarchy using superranks.

Taxonomic Significance of Septal Ultrastructure With Particular Reference to the Jelly Fungi

Electron microscope observations of fungal hyphae and yeast-like cells, using conventional fixation methods and freeze-etching, demonstrate that plasmalemmasomes are not fixation artifacts. The small invaginations of the plasmalemma observed in aldehyde-fixed preparations are also present in frozen-etched samples. The morphology of plasmalemmasomes in the species examined is variable and ranges from vesicles or tubules within the plasmalemma invagination to parallel arrays of membrane lamellae. Plasmalemmasomes thus appear to be primarily excess plasma membrane that has accumulated, perforce, endocellularly. Lomasomes, in contrast, appear to be accumulations of ejected material between the plasmalemma and cell wall that have become sequestered by the deposition of wall material.

Lomasomes and plasmalemmasomes in fungi

Though the dictyosome of the Golgi apparatus appears to be generally distributed in plant and animal cells, it is here described for the first time in the fungi. The present report illustrates, in electron micrographs of thin sections, the characteristic structure of the Golgi dictyosome in a special cell type of a supporting pseudo-tissue (the inner ectal excipulum) of a highly evolved Ascomycete, Neobulgaria pura (Fr.) Petrak, a monotypic discomycete. This organelle may secrete the gelatinous matrix filling the cup formed by the inner ectal excipulum. All the other cells in this species appear more typical of fungal cells; i.e., they have no dictyosome and, unlike the cup-forming cells, they show characteristic continuities of the plasma membrane with the perinuclear cisternae. The dictyosome, in those cells in which it appears in this fungus, is formed by a series of vesiculations of the outer component of the nuclear envelope that align to form a stack of sacs. The sacs near the nucleus are flattened (by what appears to be an intermembrane cement) while those near the plasma membrane are more distended. These observations suggest three possibilities: first, fungi may be more closely related to other eukaryotic cells than previously suspected from electron microscopic studies; second, the outer nuclear membrane may have been the primitive precursor of the dictyosome; and third, the inverse relationship of the occurrence of the nuclear membrane plasma membrane continuities and the dictyosome suggests that the latter may have evolved as a means of removing from the cell the products of reactions occurring on a discontinuous membrane system.

https://rupress.org/jcb/article-pdf/16/1/131/1318947/131.pdf

FINE STRUCTURE OF MYCOTA: 4. The Occurrence of the Golgi Dictyosome in the Fungus Neobulgaria pura (Fr.) Petrak

Electron microscopy of the two species of Filobasidium show representative basidiomycete dolipores, but in which the pore-occluding material, instead of being a homogenous, electropaque, dome-shape...

Royall T. Moore

Papers

Fine Structure of Mycota

Taxonomic Significance of Septal Ultrastructure With Particular Reference to the Jelly Fungi

Lomasomes and plasmalemmasomes in fungi

FINE STRUCTURE OF MYCOTA: 4. The Occurrence of the Golgi Dictyosome in the Fungus Neobulgaria pura (Fr.) Petrak

Ultrastructure of Filobasidium Olive.