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  • 1
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    Redefining Microascus, Scopulariopsis and allied genera (2016)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (1878-9080) vol.36 (2016) p.1
    Details
    Publication Date: 2016-06-07
    Description: The genera Microascus and Scopulariopsis comprise species commonly isolated from soil, decaying plant material and indoor environments. A few species are also recognised as opportunistic pathogens of insects and animals, including humans. In the past, the taxonomy of these fungi has been based on morphology only. With the aim to clarify the taxonomy and phylogeny of these fungi, we studied a large set of clinical and environmental isolates, including the available ex-type strains of numerous species, by means of morphological, physiological and molecular analyses. Species delineation was assessed under the Genealogical Phylogenetic Species Recognition (GCPSR) criterion using DNA sequence data of four loci (ITS region, and fragments of rDNA LSU, translation elongation factor 1-α and β-tubulin). The genera Microascus and Scopulariopsis were found to be separated in two distinct lineages. The genus Pithoascus is reinstated and the new genus Pseudoscopulariopsis is erected, typified by P. schumacheri. Seven new species of Microascus and one of Scopulariopsis are described, namely M. alveolaris, M. brunneosporus, M. campaniformis, M. expansus, M. intricatus, M. restrictus, M. verrucosus and Scopulariopsis cordiae. Microascus trigonosporus var. macrosporus is accepted as a species distinct from M. trigonosporus. Nine new combinations are introduced. Microascus cinereus, M. longirostris, P. schumacheri and S. flava are neotypified. A table summarising the morphological features of the species treated and identification keys for each genus are provided.
    Keywords: Ascomycota ; Microascaceae ; Microascales ; multigene phylogeny ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 2
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    Phylogeography and evolutionary patterns in Sporothrix spanning more than 14 000 human and animal case reports (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-5850) vol.35 (2015) p.1
    Details
    Publication Date: 2016-01-07
    Description: Pathology to vertebrate hosts has emerged repeatedly in the order Ophiostomatales. Occasional infections have been observed in Sporothrix mexicana at a low level of virulence, while the main pathogenic species cluster in a derived clade around S. schenckii s.str. In this paper, phylogeny and epidemiology of the members of this clade were investigated for 99 clinical and 36 environmental strains using four genetic loci, viz. rDNA ITS and partial CAL, TEF1, and TEF3; data are compared with amplified fragment length polymorphism (AFLP) genotyping. The four main species of the pathogenic clade were recognised. The species proved to show high degrees of endemicity, which enabled interpretation of literature data where live material or genetic information is lacking. The clade of four species comprised nine subclusters, which often had limited geographic distribution and were separate from each other in all partitions, suggesting low degrees of interbreeding between populations. In contrast, S. globosa exhibited consistent global distribution of identical AFLP types, suggesting another type of dispersal. Sporothrix brasiliensis is known to be involved in an expanding zoonosis and transmitted by cats, whereas S. globosa infections originated from putrid plant material, causing a sapronosis. Sporothrix schenckii s.str., the most variable species within the clade, also had a plant origin, with ecological similarities to that of S. globosa. A hypothesis was put forward that highly specific conditions in the plant material are required to promote the growth of Sporothrix. Fermented, self-heated plant debris may stimulate the thermodependent yeast-like invasive form of the fungus, which facilitates repeated infection of mammals.
    Keywords: epidemiology ; historical biogeography ; phylogeny ; sapronosis ; Sporothrix ; sporotrichosis ; transmission routes ; yeast conversion ; zoonosis
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 3
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    Phylogeny of Sarocladium (Hypocreales) (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.34 (2015) nr.1 p.10
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    Publication Date: 2015-07-02
    Description: The circumscription of the genus Acremonium (Hypocreales) was recently reviewed on the basis of a DNA phylogenetic study. Several species were subsequently transferred to Sarocladium, but the relationships between both genera remained unresolved. Based on multilocus phylogenetic inferences combined with phenotypic data, we have revised the species concepts within Sarocladium and some genetically related species of Acremonium. As a result of these studies, six species are described as new, viz. S. bifurcatum, S. gamsii, S. hominis, S. pseudostrictum, S. subulatum and S. summerbellii. In addition, the new combinations S. implicatum and S. terricola are proposed for A. implicatum and A. terricola, respectively. Sarocladium attenuatum is confirmed as synonym of the type species of the genus, S. oryzae. An epitype and neotype are also introduced for S. oryzae and S. implicatum, respectively. Although Sarocladium species have traditionally been considered as important phytopathogens, the genus also contains opportunistic human pathogens. This study extends the spectrum of clinical species that could be diagnosed as causal agents of human infections.
    Keywords: Acremonium ; Hypocreales ; phylogeny ; Sarocladium ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 4
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    Taxonomy and epidemiology of Mucor irregularis, agent of chronic cutaneous mucormycosis (2013)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.30 (2013) nr.1 p.48
    Details
    Publication Date: 2015-04-20
    Description: Mucormycosis usually presents as a progressive infection with significant angio-invasion. Mucormycosis due to Mucor irregularis (formerly Rhizomucor variabilis var. variabilis), however, is exceptional in causing chronic cutaneous infection in immunocompetent humans, ultimately leading to severe morbidity if left untreated. More than 90 % of the cases known to date were reported from Asia, mainly from China. The nearest neighbour of M. irregularis is the saprobic species M. hiemalis. The aim of this study was to evaluate the taxonomic position, epidemiology, and intra- and inter-species diversity of M. irregularis based on 21 strains (clinical n = 17) by multilocus analysis using ITS, LSU, RPB1 and RPB2 genes, compared to results of cluster analysis with amplified fragment length polymorphism (AFLP) data. By combining MLST and AFLP analyses, M. irregularis was found to be monophyletic with high bootstrap support, and consisted of five subgroups, which were not concordant in all partitions. It was thus confirmed that M. irregularis is a single species at 96.1–100 % ITS similarity and low recombination rates between populations. Some geographic structuring was noted with some localised populations, which may be explained by limited air-dispersal. The natural habitat of the species is likely to be in soil and decomposing plant material.
    Keywords: Biodiversity ; chronic cutaneous infection ; epidemiology ; Mucor hiemalis ; Mucor irregularis ; Mucormycosis ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 5
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    The zygomycetes in a phylogenetic perspective (2013)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.30 (2013) nr.1 p.i
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    Publication Date: 2015-04-20
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 6
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    One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes (2015)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-5850) vol.35 (2015) p.242
    Details
    Publication Date: 2016-01-08
    Description: The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across 〉 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1–D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5–6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
    Keywords: DNA barcoding ; ITS supplement ; molecular taxonomy ; phylogeny ; species identification ; universal primers
    Repository Name: National Museum of Natural History, Netherlands
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  • 7
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    The hyphomycete genus Engyodontium a link between Verticillium and Aphanocladium (1984)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-5850) vol.12 (1984) nr.2 p.135
    Details
    Publication Date: 2015-04-20
    Description: Sporotrichum aranearum Cavara is redescribed from living cultures and found to have two kinds of conidiogenesis: phialidic and polyblastic. The latter type which is most conspicuous in this fungus, fits the genus Engyodontium de Hoog. This genus is considered to be a link between Verticillium and Aphanocladium and its generic diagnosis is extended to include both progressive and retrogressive formation of new conidiiferous pegs. Sporothrix (Tritirachium) rectidentatum (Matsushima) de Hoog and Cephalosporium aranearum Petch, in which some polyblastic conidiogenous cells with narrow denticles were also found, are transferred to Engyodontium. For the latter species the new name E. arachnophilum is proposed. The genus now comprises six species, including E. geniculatum, sp. nov. In addition, Acremonium obclavatum W. Gams is described as a new species for isolates that match the description formerly given by Gams for Verticillium tenuipes.
    Repository Name: National Museum of Natural History, Netherlands
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  • 8
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    Some notes on Torula (1975)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-5850) vol.8 (1975) nr.2 p.199
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    Publication Date: 2015-04-20
    Description: A new species of Torula Pers. per Fr., collected at Hyderabad, India, is described as T. rhombica Rao & de Hoog. It forms chains of reddish brown, regularly rhomboid conidia. A key to the accepted species of Torula is given. All CBS strains maintained under the name Torula are discussed; they can be assigned to six different genera. New combinations are proposed in Polypaecilum Smith and Moniliella Stolk & Dakin, and a new species of Scytalidium Pesante is described.
    Repository Name: National Museum of Natural History, Netherlands
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  • 9
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    Biodiversity and human-pathogenicity of Phialophora verrucosa and relatives in Chaetothyriales (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (1878-9080) vol.38 (2017) p.1
    Details
    Publication Date: 2016-08-25
    Description: Phialophora as defined by its type species P. verrucosa is a genus of Chaetothyriales, and a member of the group known as ‘black yeasts and relatives’. Phialophora verrucosa has been reported from mutilating human infections such as chromoblastomycosis, disseminated phaeohyphomycosis and mycetoma, while morphologically similar fungi are rather commonly isolated from the environment. Phenotypes are insufficient for correct species identification, and molecular data have revealed significant genetic variation within the complex of species currently identified as P. verrucosa or P. americana. Multilocus analysis of 118 strains revealed the existence of five reproductively isolated species apparently having different infectious potentials. Strains of the sexual morph Capronia semiimmersa cluster within P. americana. The newly defined taxa differ markedly in their predilection for the human host.
    Keywords: Chaetothyriales ; chromoblastomycosis ; phaeohyphomycosis ; Phialophora ; phylogeny ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
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  • 10
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    DNA barcoding in Mucorales: an inventory of biodiversity (2013)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (0031-05850) vol.30 (2013) nr.1 p.11
    Details
    Publication Date: 2015-04-20
    Description: The order Mucorales comprises predominantly fast-growing saprotrophic fungi, some of which are used for the fermentation of foodstuffs but it also includes species known to cause infections in patients with severe immune or metabolic impairments. To inventory biodiversity in Mucorales ITS barcodes of 668 strains in 203 taxa were generated covering more than two thirds of the recognised species. Using the ITS sequences, Molecular Operational Taxonomic Units were defined by a similarity threshold of 99 %. An LSU sequence was generated for each unit as well. Analysis of the LSU sequences revealed that conventional phenotypic classifications of the Mucoraceae are highly artificial. The LSU- and ITS-based trees suggest that characters, such as rhizoids and sporangiola, traditionally used in mucoralean taxonomy are plesiomorphic traits. The ITS region turned out to be an appropriate barcoding marker in Mucorales. It could be sequenced directly in 82 % of the strains and its variability was sufficient to resolve most of the morphospecies. Molecular identification turned out to be problematic only for the species complexes of Mucor circinelloides, M. flavus, M. piriformis and Zygorhynchus moelleri. As many as 12 possibly undescribed species were detected. Intraspecific variability differed widely among mucorealean species ranging from 0 % in Backusella circina to 13.3 % in Cunninghamella echinulata. A high proportion of clinical strains was included for molecular identification. Clinical isolates of Cunninghamella elegans were identified molecularly for the first time. As a result of the phylogenetic analyses several taxonomic and nomenclatural changes became necessary. The genus Backusella was emended to include all species with transitorily recurved sporangiophores. Since this matched molecular data all Mucor species possessing this character were transferred to Backusella. The genus Zygorhynchus was shown to be polyphyletic based on ITS and LSU data. Consequently, Zygorhynchus was abandoned and all species were reclassified in Mucor. Our phylogenetic analyses showed, furthermore, that all non-thermophilic Rhizomucor species belong to Mucor. Accordingly, Rhizomucor endophyticus was transferred to Mucor and Rhizomucor chlamydosporus was synonymised with Mucor indicus. Lecto-, epi- or neotypes were designated for several taxa.
    Keywords: Backusella ; biodiversity ; clinical relevance ; DNA barcoding ; intraspecific variability ; ITS ; LSU ; Mucor ; Mucorales ; nomenclature ; Rhizomucor ; taxonomy ; Zygorhynchus
    Repository Name: National Museum of Natural History, Netherlands
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