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Samerpitak K, Van der Linde E, Choi HJ, Gerrits van den Ende AHG, Machouart M, Gueidan C, de Hoog GS. Taxonomy of Ochroconis, genus including opportunistic pathogens on humans and animals. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0253-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Ruibal C, Gueidan C, Selbmann L, Gorbushina AA, Crous PW, Groenewald JZ, Muggia L, Grube M, Isola D, Schoch CL, Staley JT, Lutzoni F, de Hoog GS. Phylogeny of rock-inhabiting fungi related to Dothideomycetes. Stud Mycol 2011; 64:123-133S7. [PMID: 20169026 PMCID: PMC2816969 DOI: 10.3114/sim.2009.64.06] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The class Dothideomycetes (along with Eurotiomycetes)
includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that
tolerates surprisingly well harsh conditions prevailing on rock surfaces.
Despite their convergent morphology and physiology, RIF are phylogenetically
highly diverse in Dothideomycetes. However, the positions of main
groups of RIF in this class remain unclear due to the lack of a strong
phylogenetic framework. Moreover, connections between rock-dwelling habit and
other lifestyles found in Dothideomycetes such as plant pathogens,
saprobes and lichen-forming fungi are still unexplored. Based on multigene
phylogenetic analyses, we report that RIF belong to Capnodiales
(particularly to the family Teratosphaeriaceae s.l.),
Dothideales, Pleosporales, and Myriangiales, as
well as some uncharacterised groups with affinities to
Dothideomycetes. Moreover, one lineage consisting exclusively of RIF
proved to be closely related to Arthoniomycetes, the sister class of
Dothideomycetes. The broad phylogenetic amplitude of RIF in
Dothideomycetes suggests that total species richness in this class
remains underestimated. Composition of some RIF-rich lineages suggests that
rock surfaces are reservoirs for plant-associated fungi or saprobes, although
other data also agree with rocks as a primary substrate for ancient fungal
lineages. According to the current sampling, long distance dispersal seems to
be common for RIF. Dothideomycetes lineages comprising lichens also
include RIF, suggesting a possible link between rock-dwelling habit and
lichenisation.
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Affiliation(s)
- C Ruibal
- Departamento de Ingeniería y Ciencia de los Materiales, Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (UPM), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Summerbell RC, Gueidan C, Schroers HJ, de Hoog GS, Starink M, Rosete YA, Guarro J, Scott JA. Acremonium phylogenetic overview and revision of Gliomastix, Sarocladium, and Trichothecium. Stud Mycol 2011; 68:139-62. [PMID: 21523192 PMCID: PMC3065988 DOI: 10.3114/sim.2011.68.06] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Over 200 new sequences are generated for members of the genus
Acremonium and related taxa including ribosomal small subunit
sequences (SSU) for phylogenetic analysis and large subunit (LSU) sequences
for phylogeny and DNA-based identification. Phylogenetic analysis reveals that
within the Hypocreales, there are two major clusters containing
multiple Acremonium species. One clade contains Acremonium
sclerotigenum, the genus Emericellopsis, and the genus
Geosmithia as prominent elements. The second clade contains the
genera Gliomastixsensu stricto and Bionectria. In
addition, there are numerous smaller clades plus two multi-species clades, one
containing Acremonium strictum and the type species of the genus
Sarocladium, and, as seen in the combined SSU/LSU analysis, one
associated subclade containing Acremonium breve and related species
plus Acremonium curvulum and related species. This sequence
information allows the revision of three genera. Gliomastix is
revived for five species, G. murorum, G. polychroma, G. tumulicola, G.
roseogrisea, and G. masseei. Sarocladium is extended to
include all members of the phylogenetically distinct A. strictum
clade including the medically important A. kiliense and the
protective maize endophyte A. zeae. Also included in
Sarocladium are members of the phylogenetically delimited
Acremonium bacillisporum clade, closely linked to the A.
strictum clade. The genus Trichothecium is revised following the
principles of unitary nomenclature based on the oldest valid anamorph or
teleomorph name, and new combinations are made in Trichothecium for
the tightly interrelated Acremonium crotocinigenum, Spicellum
roseum, and teleomorph Leucosphaerinaindica. Outside
the Hypocreales, numerous Acremonium-like species fall into
the Plectosphaerellaceae, and A. atrogriseum falls into the
Cephalothecaceae.
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Affiliation(s)
- R C Summerbell
- Sporometrics, Inc. 219 Dufferin Street, Suite 20C, Toronto, Ont., Canada M6K 1Y9
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Schoch CL, Crous PW, Groenewald JZ, Boehm EWA, Burgess TI, de Gruyter J, de Hoog GS, Dixon LJ, Grube M, Gueidan C, Harada Y, Hatakeyama S, Hirayama K, Hosoya T, Huhndorf SM, Hyde KD, Jones EBG, Kohlmeyer J, Kruys A, Li YM, Lücking R, Lumbsch HT, Marvanová L, Mbatchou JS, McVay AH, Miller AN, Mugambi GK, Muggia L, Nelsen MP, Nelson P, Owensby CA, Phillips AJL, Phongpaichit S, Pointing SB, Pujade-Renaud V, Raja HA, Plata ER, Robbertse B, Ruibal C, Sakayaroj J, Sano T, Selbmann L, Shearer CA, Shirouzu T, Slippers B, Suetrong S, Tanaka K, Volkmann-Kohlmeyer B, Wingfield MJ, Wood AR, Woudenberg JHC, Yonezawa H, Zhang Y, Spatafora JW. A class-wide phylogenetic assessment of Dothideomycetes. Stud Mycol 2011; 64:1-15S10. [PMID: 20169021 PMCID: PMC2816964 DOI: 10.3114/sim.2009.64.01] [Citation(s) in RCA: 344] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon.
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Affiliation(s)
- C L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, Maryland 20892-6510, U.S.A
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Abstract
The Capnodiales incorporates plant and human pathogens, endophytes, saprobes and epiphytes, with a wide range of nutritional modes. Several species are lichenised, or occur as parasites on fungi, or animals. The aim of the present study was to use DNA sequence data of the nuclear ribosomal small and large subunit RNA genes to test the monophyly of the Capnodiales, and resolve families within the order. We designed primers to allow the amplification and sequencing of almost the complete nuclear ribosomal small and large subunit RNA genes. Other than the Capnodiaceae (sooty moulds), and the Davidiellaceae, which contains saprobes and plant pathogens, the order presently incorporates families of major plant pathological importance such as the Mycosphaerellaceae, Teratosphaeriaceae and Schizothyriaceae. The Piedraiaceae was not supported, but resolves in the Teratosphaeriaceae. The Dissoconiaceae is introduced as a new family to accommodate Dissoconium and Ramichloridium. Lichenisation, as well as the ability to be saprobic or plant pathogenic evolved more than once in several families, though the taxa in the upper clades of the tree lead us to conclude that the strictly plant pathogenic, nectrotrophic families evolved from saprobic ancestors (Capnodiaceae), which is the more primitive state.
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Affiliation(s)
- P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The
Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of
Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The
Netherlands
| | - C.L. Schoch
- National Center for Biotechnology Information, National Library of
Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda,
Maryland 20892-6510, U.S.A.
| | - K.D. Hyde
- School of Science, Mae Fah Luang University, Tasud, Muang, Chiang Rai
57100, Thailand
| | - A.R. Wood
- ARC – Plant Protection Research Institute, P. Bag X5017,
Stellenbosch, 7599, South Africa
| | - C. Gueidan
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The
Netherlands
| | - G.S. de Hoog
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The
Netherlands
| | - J.Z. Groenewald
- CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The
Netherlands
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Najafzadeh MJ, Gueidan C, Badali H, Van Den Ende AHGG, Xi L, De Hoog GS. Genetic diversity and species delimitation in the opportunistic genus Fonsecaea. Med Mycol 2008; 47:17-25. [PMID: 19107635 DOI: 10.1080/13693780802527178] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Genetic diversity and species delimitation were investigated among 39 isolates recovered from clinical and environmental sources in Central and South America, Africa, East Asia and Europe. All had been morphologically identified as Fonsecaea spp. Molecular analyses were based on sequences of the ribosomal internal transcribed spacers (ITS), -tubulin (TUB1) and actin (ACT1) regions. A phylogenetic approach using haplotype networks was used to evaluate species delimitation and genetic diversity. The presence and the modes of reproductive isolation were tested by measuring the index of differentiation (ID) and the index of association (IA). Based on the sequence data, the 39 Fonsecaea strains were classified into three major entities: (i) a group representing Fonsecaea pedrosoi, (ii) a second composed of F. monophora, and (iii) a third group including mostly strains from South America. The two major, clinically relevant Fonsecaea species, F. monophora and F. pedrosoi, also differed in the pathological symptoms found in patients. Moreover, F. pedrosoi is mostly recovered in clinical settings, whereas F. monophora is commonly isolated from the environment. One environmental strain with Fonsecaea-like appearance was shown to belong to a different species, only distantly related to the core-group of Fonsecaea.
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Affiliation(s)
- M J Najafzadeh
- Centraalbureau voor Schimmelcultures Fungal Biodiversity Centre, Utrecht, The Netherlands
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Abstract
Cladophialophora is a genus of black yeast-like fungi comprising a number of clinically highly significant species in addition to environmental taxa. The genus has previously been characterized by branched chains of ellipsoidal to fusiform conidia. However, this character was shown to have evolved several times independently in the order Chaetothyriales. On the basis of a multigene phylogeny (nucLSU, nucSSU, RPB1), most of the species of Cladophialophora (including its generic type C. carrionii) belong to a monophyletic group comprising two main clades (carrionii- and bantiana-clades). The genus includes species causing chromoblastomycosis and other skin infections, as well as disseminated and cerebral infections, often in immunocompetent individuals. In the present study, multilocus phylogenetic analyses were combined to a morphological study to characterize phenetically similar Cladophialophora strains. Sequences of the ITS region, partial Translation Elongation Factor 1-alpha and beta-Tubulin genes were analysed for a set of 48 strains. Four novel species were discovered, originating from soft drinks, alkylbenzene-polluted soil, and infected patients. Membership of the both carrionii and bantiana clades might be indicative of potential virulence to humans.
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Affiliation(s)
- H Badali
- CBS Fungal Biodiversity Centre, P.O. Box 85167, NL-3508 AD Utrecht, The Netherlands
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Gueidan C, Villaseñor CR, de Hoog GS, Gorbushina AA, Untereiner WA, Lutzoni F. A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages. Stud Mycol 2008; 61:111-9. [PMID: 19287533 PMCID: PMC2610302 DOI: 10.3114/sim.2008.61.11] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare rocks. Multigene phylogenetic analyses were used to study relationships of ascomycetes from a variety of substrates, with a dataset including a broad sampling of rock dwellers from different geographical locations. Rock-inhabiting fungi appear particularly diverse in the early diverging lineages of the orders Chaetothyriales and Verrucariales. Although these orders share a most recent common ancestor, their lifestyles are strikingly different. Verrucariales are mostly lichen-forming fungi, while Chaetothyriales, by contrast, are best known as opportunistic pathogens of vertebrates (e.g. Cladophialophora bantiana and Exophiala dermatitidis, both agents of fatal brain infections) and saprophytes. The rock-dwelling habit is shown here to be key to the evolution of these two ecologically disparate orders. The most recent common ancestor of Verrucariales and Chaetothyriales is reconstructed as a non-lichenised rock-inhabitant. Ancestral state reconstructions suggest Verrucariales as one of the independent ascomycetes group where lichenisation has evolved on a hostile rock surface that might have favored this shift to a symbiotic lifestyle. Rock-inhabiting fungi are also ancestral to opportunistic pathogens, as they are found in the early diverging lineages of Chaetothyriales. In Chaetothyriales and Verrucariales, specific morphological and physiological traits (here referred to as extremotolerance) evolved in response to stresses in extreme conditions prevailing on rock surfaces. These factors facilitated colonisation of various substrates including the brains of vertebrates by opportunistic fungal pathogens, as well as helped establishment of a stable lichen symbiosis.
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Affiliation(s)
- C Gueidan
- Department of Biology, Duke University, Box 90338, Durham NC, 27708 U.S.A
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Miadlikowska J, Kauff F, Hofstetter V, Fraker E, Grube M, Hafellner J, Reeb V, Hodkinson BP, Kukwa M, Lucking R, Hestmark G, Otalora MG, Rauhut A, Budel B, Scheidegger C, Timdal E, Stenroos S, Brodo I, Perlmutter GB, Ertz D, Diederich P, Lendemer JC, May P, Schoch CL, Arnold AE, Gueidan C, Tripp E, Yahr R, Robertson C, Lutzoni F. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 2007. [DOI: 10.3852/mycologia.98.6.1088] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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