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Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    Pestalotiopsis revisited
    Maharachchikumbura, S.S.N. ; Hyde, K.D. ; Groenewald, J.Z. ; Xu, J. ; Crous, P.W. - \ 2014
    Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 121 - 186.
    ribosomal dna-sequences - sp-nov - morphological characters - conidial structure - camellia-sinensis - natural-products - twig blight - primer sets - leaf-spot - disease
    Species of Pestalotiopsis occur commonly as plant pathogens, and represent a fungal group known to produce a wide range of chemically novel, diverse metabolites. In the present study, we investigated 91 Pestalotiopsis isolates from the CBS-KNAW Fungal Biodiversity Centre (CBS) culture collection. The phylogeny of the Amphisphaeriaceae was constructed based on analysis of 28S nrRNA gene (LSU) sequence data, and taxonomic changes are proposed to reflect more natural groupings. We combined morphological and DNA data, and segregated two novel genera from Pestalotiopsis, namely Neopestalotiopsis and Pseudopestalotiopsis. The three genera are easily distinguishable on the basis of their conidiogenous cells and colour of their median conidial cells. We coupled morphological and combined sequence data of internal transcribed spacer (ITS), partial ß-tubulin (TUB) and partial translation elongation factor 1-alpha (TEF) gene regions, which revealed 30 clades in Neopestalotiopsis and 43 clades in Pestalotiopsis. Based on these data, 11 new species are introduced in Neopestalotiopsis, 24 in Pestalotiopsis, and two in Pseudopestalotiopsis. Several new combinations are proposed to emend monophyly of Neopestalotiopsis, Pestalotiopsis and Pseudopestalotiopsis.
    One stop shop: backbones trees for important phytopathogenic genera: I (2014)
    Hyde, K.D. ; Nilsson, R.H. ; Alias, S.A. ; Ariyawansa, H.A. ; Blair, J.E. ; Cai, L. ; Cock, A.W.A.M. de; Dissanayake, A.J. ; Glockling, S.L. ; Goonasekara, I.D. ; Gorczak, M. ; Hahn, M. ; Jayawardena, R.S. ; Kan, J.A.L. van; Laurence, M.H. ; Lévesque, C.A. ; Li, X. ; Liu, J.K. ; Maharachchikumbura, S.S.N. ; Manamgoda, D.S. ; Martin, F.N. ; McKenzie, E.H.C. ; McTaggart, A.R. ; Mortimer, P.E. ; Nair, P.V.R. ; Pawlowska, J. ; Rintoul, T.L. ; Shivas, R.G. ; Spies, C.F.J. ; Summerell, B.A. ; Taylor, P.W.J. ; Terhem, R.B. ; Udayanga, D. ; Vaghefi, N. ; Walther, G. ; Wilk, M. ; Wrzosek, M. ; Xu, J.C. ; Yan, J.Y. ; Zhou, N. - \ 2014
    Fungal Diversity 67 (2014). - ISSN 1560-2745 - p. 21 - 125.
    internal transcribed spacer - ribosomal dna-sequences - vegetative compatibility groups - plant-pathogenic fungi - citrus black spot - spored graminicolous colletotrichum - sporisorium-macalpinomyces complex - fragment-length-polymorphisms - botrytis-cinerea popu
    Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineage-specific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae, Botryosphaeria, Botrytis, Choanephora, Colletotrichum, Curvularia, Diaporthe, Diplodia, Dothiorella, Fusarium, Gilbertella, Lasiodiplodia, Mucor, Neofusicoccum, Pestalotiopsis, Phyllosticta, Phytophthora, Puccinia, Pyrenophora, Pythium, Rhizopus, Stagonosporopsis, Ustilago and Verticillium are dealt with in this paper.
    Families of Dothideomycetes
    Hyde, K.D. ; Gareth Jones, E.B. ; Liu, J.K. ; Ariyawansa, H. ; Boehm, E. ; Boonmee, S. ; Braun, U. ; Chomnunti, P. ; Crous, P.W. ; Dai, D.Q. ; Diederich, P. ; Dissanayake, A. ; Doilom, M. ; Doveri, F. ; Hongsanan, S. ; Jayawardena, R. ; Lawrey, J.D. ; Li, Y.M. ; Liu, Y.X. ; Lücking, R. ; Monkai, J. ; Muggia, L. ; Nelsen, M.P. ; Pang, K.L. ; Phookamsak, R. ; Senanayake, I.C. ; Shearer, C.A. ; Suetrong, S. ; Tanaka, K. ; Thambugala, K.M. ; Wijayawardene, N.N. ; Wikee, S. ; Wu, H.X. ; Zhang, Y. ; Aguirre-Hudson, B. ; Alias, S.A. ; Aptroot, A. ; Bahkali, A.H. ; Berezza, J.L. ; Bhat, D.J. ; Camporesi, E. ; Chukeatirote, E. ; Gueidan, C. ; Hawksworth, D.L. ; Hirayama, K. ; Hoog, S. de; Kang, J.C. ; Knudsen, K. ; Li, W.J. ; Li, X.H. ; Liu, Z.Y. ; Mapook, A. ; McKenzie, E.H.C. ; Miller, A.N. ; Mortimer, P.E. ; Phillips, A.J.L. ; Raja, H.A. ; Scheuer, C. ; Schumm, F. ; Taylor, J.E. ; Tian, Q. ; Tibpromma, S. ; Wanasinghe, D.N. ; Wang, Y. ; Xu, J.C. ; Yacharoen, S. ; Yan, J.Y. ; Zhang, M. - \ 2013
    Fungal Diversity 63 (2013)1. - ISSN 1560-2745 - p. 1 - 313.
    ribosomal dna-sequences - morphologically similar genera - foliicolous lichenized fungi - intertidal mangrove wood - leaf-inhabiting fungi - fresh-water habitats - new-zealand fungi - russian far-east - papua-new-guinea - sp-nov
    Dothideomycetes comprise a highly diverse range of fungi characterized mainly by asci with two wall layers (bitunicate asci) and often with fissitunicate dehiscence. Many species are saprobes, with many asexual states comprising important plant pathogens. They are also endophytes, epiphytes, fungicolous, lichenized, or lichenicolous fungi. They occur in terrestrial, freshwater and marine habitats in almost every part of the world. We accept 105 families in Dothideomycetes with the new families Anteagloniaceae, Bambusicolaceae, Biatriosporaceae, Lichenoconiaceae, Muyocopronaceae, Paranectriellaceae, Roussoellaceae, Salsugineaceae, Seynesiopeltidaceae and Thyridariaceae introduced in this paper. Each family is provided with a description and notes, including asexual and asexual states, and if more than one genus is included, the type genus is also characterized. Each family is provided with at least one figure-plate, usually illustrating the type genus, a list of accepted genera, including asexual genera, and a key to these genera. A phylogenetic tree based on four gene combined analysis add support for 64 of the families and 22 orders, including the novel orders, Dyfrolomycetales, Lichenoconiales, Lichenotheliales, Monoblastiales, Natipusillales, Phaeotrichales and Strigulales. The paper is expected to provide a working document on Dothideomycetes which can be modified as new data comes to light. It is hoped that by illustrating types we provide stimulation and interest so that more work is carried out in this remarkable group of fungi.
    Redisposition of Phoma-like anamorphs in Pleosporales
    Gruyter, J. de; Woudenberg, J.H.C. ; Aveskamp, M.M. ; Verkley, G.J.M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
    Studies in Mycology 75 (2013). - ISSN 0166-0616 - p. 1 - 36.
    ribosomal dna-sequences - winter oilseed rape - 7 mu-m - leptosphaeria-maculans - stem canker - molecular phylogeny - section plenodomus - small conidia - monograph - taxa
    The anamorphic genus Phoma was subdivided into nine sections based on morphological characters, and included teleomorphs in Didymella, Leptosphaeria, Pleospora and Mycosphaerella, suggesting the polyphyly of the genus. Recent molecular, phylogenetic studies led to the conclusion that Phoma should be restricted to Didymellaceae. The present study focuses on the taxonomy of excluded Phoma species, currently classified in Phoma sections Plenodomus, Heterospora and Pilosa. Species of Leptosphaeria and Phoma section Plenodomus are reclassified in Plenodomus, Subplenodomus gen. nov., Leptosphaeria and Paraleptosphaeria gen. nov., based on the phylogeny determined by analysis of sequence data of the large subunit 28S nrDNA (LSU) and Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS). Phoma heteromorphospora, type species of Phoma section Heterospora, and its allied species Phoma dimorphospora, are transferred to the genus Heterospora stat. nov. The Phoma acuta complex (teleomorph Leptosphaeria doliolum), is revised based on a multilocus sequence analysis of the LSU, ITS, small subunit 18S nrDNA (SSU), ß-tubulin (TUB), and chitin synthase 1 (CHS-1) regions. Species of Phoma section Pilosa and allied Ascochyta species were determined to belong to Pleosporaceae based on analysis of actin (ACT) sequence data. Anamorphs that are similar morphologically to Phoma and described in Ascochyta, Asteromella, Coniothyrium, Plectophomella, Pleurophoma and Pyrenochaeta are included in this study. Phoma-like species, which grouped outside the Pleosporineae based on a LSU sequence analysis, are transferred to the genera Aposphaeria, Paraconiothyrium and Westerdykella. The genera Medicopsis gen. nov. and Nigrograna gen. nov. are introduced to accommodate the medically important species formerly known as Pyrenochaeta romeroi and Pyrenochaeta mackinnonii, respectively.
    Phylogenetic lineages in Pseudocercospora
    Crous, P.W. ; Braun, U. ; Hunter, G.C. ; Wingfield, M.J. ; Verkley, G.J.M. ; Shin, H.D. ; Nakashima, C. ; Groenewald, J.Z. - \ 2013
    Studies in Mycology 75 (2013). - ISSN 0166-0616 - p. 37 - 114.
    ribosomal dna-sequences - eucalyptus leaves - mycosphaerella-spp. - leaf-spot - genus mycosphaerella - korean cercosporae - taxonomic notes - rdna sequence - allied genera - sooty blotch
    Pseudocercospora is a large cosmopolitan genus of plant pathogenic fungi that are commonly associated with leaf and fruit spots as well as blights on a wide range of plant hosts. They occur in arid as well as wet environments and in a wide range of climates including cool temperate, sub-tropical and tropical regions. Pseudocercospora is now treated as a genus in its own right, although formerly recognised as either an anamorphic state of Mycosphaerella or having Mycosphaerella-like teleomorphs. The aim of this study was to sequence the partial 28S nuclear ribosomal RNA gene of a selected set of isolates to resolve phylogenetic generic limits within the Pseudocercospora complex. From these data, 14 clades are recognised, six of which cluster in Mycosphaerellaceae. Pseudocercospora s. str. represents a distinct clade, sister to Passalora eucalypti, and a clade representing the genera Scolecostigmina, Trochophora and Pallidocercospora gen. nov., taxa formerly accommodated in the Mycosphaerella heimii complex and characterised by smooth, pale brown conidia, as well as the formation of red crystals in agar media. Other clades in Mycosphaerellaceae include Sonderhenia, Microcyclosporella, and Paracercospora. Pseudocercosporella resides in a large clade along with Phloeospora, Miuraea, Cercospora and Septoria. Additional clades represent Dissoconiaceae, Teratosphaeriaceae, Cladosporiaceae, and the genera Xenostigmina, Strelitziana, Cyphellophora and Thedgonia. The genus Phaeomycocentrospora is introduced to accommodate Mycocentrospora cantuariensis, primarily distinguished from Pseudocercospora based on its hyaline hyphae, broad conidiogenous loci and hila. Host specificity was considered for 146 species of Pseudocercospora occurring on 115 host genera from 33 countries. Partial nucleotide sequence data for three gene loci, ITS, EF-1a, and ACT suggest that the majority of these species are host specific. Species identified on the basis of host, symptomatology and general morphology, within the same geographic region, frequently differed phylogenetically, indicating that the application of European and American names to Asian taxa, and vice versa, was often not warranted.
    Mycosphaerella and Teratosphaeria species associated with leaf diseases on Eucalyptus globulus in southern Brazil
    Teodoro, M.G. ; Ferreira, M.A. ; Guimarães, L.M.S. ; Mafia, R.G. ; Groenewald, J.Z. ; Crous, P.W. ; Alfenas, A.C. - \ 2012
    Phytopathologia Mediterranea 51 (2012)2. - ISSN 0031-9465 - p. 355 - 364.
    ribosomal dna-sequences - phylogenetic reassessment - anamorphs - nubilosa - spp. - identification - dissoconium - plantations - lateralis - australia
    Leaf blight and defoliation caused by Teratosphaeria species is one of the most important leaf diseases of Eucalyptus globulus. Due to the importance of this tree species for the production of pulp and paper, and recent reports of severe leaf disease symptoms in Brazil, the present study was conducted to identify the pathogen(s) involved. Symptomatic leaves were collected in the Brazilian states of Paraná and Rio Grande do Sul, single ascospore cultures established, and isolates were investigated using DNA-based molecular tools. A species-specific PCR and sequence data from the nuclear ribosomal DNA operon were used for species identification. The following seven species were identified: Mycosphaerella scytalidii, Dissoconium dekkeri (=M. lateralis), Teratosphaeria ohnowa, T. perpendicularis, T. pseudafricana, T. flexuosa and T.nubilosa. Of the recorded species, T. nubilosa is regarded as the most serious threat to the cultivation of E. globulus in the states surveyed.
    Pleosporales
    Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. - \ 2012
    Fungal Diversity 53 (2012)1. - ISSN 1560-2745 - p. 1 - 221.
    ribosomal dna-sequences - australian fresh-water - intertidal mangrove wood - sp-nov - north-america - marine fungi - molecular phylogeny - trematosphaeria-circinans - shiraia-bambusicola - multigene phylogeny
    One hundred and five generic types of Pleosporales are described and illustrated. A brief introduction and detailed history with short notes on morphology, molecular phylogeny as well as a general conclusion of each genus are provided. For those genera where the type or a representative specimen is unavailable, a brief note is given. Altogether 174 genera of Pleosporales are treated. Phaeotrichaceae as well as Kriegeriella, Zeuctomorpha and Muroia are excluded from Pleosporales. Based on the multigene phylogenetic analysis, the suborder Massarineae is emended to accommodate five families, viz. Lentitheciaceae, Massarinaceae, Montagnulaceae, Morosphaeriaceae and Trematosphaeriaceae.
    Re-evaluation of Cryptosporiopsis eucalypti and Cryptosporiopsis-like species occurring on Eucalyptus
    Cheewangkoon, R. ; Groenewald, J.Z. ; Verkley, G.J.M. ; Hyde, K.D. ; Wingfield, M.J. ; Gryzenhout, M. ; Summerell, B.A. ; Denman, S. ; Toanan, C. ; Crous, P.W. - \ 2010
    Fungal Diversity 44 (2010)1. - ISSN 1560-2745 - p. 89 - 105.
    ribosomal dna-sequences - diaporthales - mycosphaerella - phylogeny - anamorphs - taxonomy - genera
    Cryptosporiopsis eucalypti is a common follicolous pathogen of Eucalyptus species in tropical and temperate regions where these trees are grown in plantations. The taxonomy of C. eucalypti is confused by the fact that it is phylogenetically unrelated to the type species of Cryptosporiopsis (Cryptosporiopsis nigra = C. scutellata, Helotiales). The aim of this study was to resolve the taxonomic position of C. eucalypti based on morphology and phylogenetic inference. Thirty-two Eucalyptus leaf samples with symptoms typical of C. eucalypti infection were collected from 10 tropical and temperate countries across four continents. Cultures were established from single conidia, as well as from ascospores of a previously unreported teleomorph state. DNA sequences were obtained for the 28 S nrDNA, the internal transcribed spacers of the nrDNA operon, and beta-tubulin regions to determine generic and species-level relationships. DNA-sequence analysis showed that conidial and ascospore isolates of C. eucalypti have low intraspecific variation, although two collections from Australia and one from Uruguay represented two novel taxa. Based on the newly collected teleomorph stage, as well as the phylogenetic data, C. eucalypti is shown to represent a new genus closely related to Plagiostoma (Gnomoniaceae, Diaporthales) for which the names Pseudoplagiostoma gen. nov. and Pseudoplagiostomaceae fam. nov. (Diaporthales) are introduced. Two new species of Cryptosporiopsis (Dermateaceae, Helotiales) on Eucalyptus from Australia and California (USA) are also described.
    Highlights of the Didymellaceae: A polyphasic approach to characterise Phoma and related pleosporalean genera
    Aveskamp, M.M. ; Gruyter, J. de; Woudenberg, J.H.C. ; Verkley, G.J.M. ; Crous, P.W. - \ 2010
    Studies in Mycology 65 (2010)1. - ISSN 0166-0616 - p. 1 - 60.
    ribosomal dna-sequences - powdery mildew fungi - transcribed spacer sequences - medicaginis var pinodella - maculans species complex - 7 mu-m - leptosphaeria-maculans - sp-nov - genetic diversity - ascochyta-rabiei
    Fungal taxonomists routinely encounter problems when dealing with asexual fungal species due to poly- and paraphyletic generic phylogenies, and unclear species boundaries. These problems are aptly illustrated in the genus Phoma. This phytopathologically significant fungal genus is currently subdivided into nine sections which are mainly based on a single or just a few morphological characters. However, this subdivision is ambiguous as several of the section-specific characters can occur within a single species. In addition, many teleomorph genera have been linked to Phoma, three of which are recognised here. In this study it is attempted to delineate generic boundaries, and to come to a generic circumscription which is more correct from an evolutionary point of view by means of multilocus sequence typing. Therefore, multiple analyses were conducted utilising sequences obtained from 28S nrDNA (Large Subunit - LSU), 18S nrDNA (Small Subunit - SSU), the Internal Transcribed Spacer regions 1 & 2 and 5.8S nrDNA (ITS), and part of the ß-tubulin (TUB) gene region. A total of 324 strains were included in the analyses of which most belonged to Phoma taxa, whilst 54 to related pleosporalean fungi. In total, 206 taxa were investigated, of which 159 are known to have affinities to Phoma. The phylogenetic analysis revealed that the current Boeremaean subdivision is incorrect from an evolutionary point of view, revealing the genus to be highly polyphyletic. Phoma species are retrieved in six distinct clades within the Pleosporales, and appear to reside in different families. The majority of the species, however, including the generic type, clustered in a recently established family, Didymellaceae. In the second part of this study, the phylogenetic variation of the species and varieties in this clade was further assessed. Next to the genus Didymella, which is considered to be the sole teleomorph of Phoma s. str., we also retrieved taxa belonging to the teleomorph genera Leptosphaerulina and Macroventuria in this clade. Based on the sequence data obtained, the Didymellaceae segregate into at least 18 distinct clusters, of which many can be associated with several specific taxonomic characters. Four of these clusters were defined well enough by means of phylogeny and morphology, so that the associated taxa could be transferred to separate genera. Aditionally, this study addresses the taxonomic description of eight species and two varieties that are novel to science, and the recombination of 61 additional taxa.
    Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
    Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
    Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
    ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
    Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
    Phylogenetic lineages in the Capnodiales
    Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. ; Wood, A.R. ; Gueidan, C. ; Hoog, G.S. de; Groenewald, J.Z. - \ 2009
    Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 17 - 47.
    ribosomal dna-sequences - leaf spots - gen-nov - fungal pathogens - lichenized fungi - blotch-disease - crofton weed - south-africa - mycosphaerella - eucalyptus
    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
    A class-wide phylogenetic assessment of Dothideomycetes
    Schoch, C.L. ; Crous, P.W. ; Groenewald, J.Z. ; Boehm, E.W.A. ; Burgess, T.I. ; Gruyter, J. de; Hoog, G.S. de; Dixon, L.J. ; Grube, M. ; Gueidan, C. ; Harada, Y. ; Hatakeyama, S. ; Hirayama, K. ; Hosoya, T. ; Huhndorf, S.M. ; Hyde, K.D. ; Jones, E.B.G. ; Kohlmeyer, J. ; Kruys, Å. ; Li, Y.M. ; Lücking, R. ; Lumbsch, H.T. ; Marvanová, L. ; Mbatchou, J.S. ; McVay, A.H. ; Miller, A.N. ; Mugambi, G.K. ; Muggia, L. ; Nelsen, M.P. ; Nelson, P. ; Owensby, C.A. ; Phillips, A.J.L. ; Phongpaichit, S. ; Pointing, S.B. ; Pujade-Renaud, V. ; Raja, H.A. ; Rivas Plata, E. ; Robbertse, B. ; Ruibal, C. ; Sakayaroj, J. ; Sano, T. ; Selbmann, L. ; Shearer, C.A. ; Shirouzu, T. ; Slippers, B. ; Suetrong, S. ; Tanaka, K. ; Volkmann-Kohlmeyer, B. ; Wingfield, M.J. ; Wood, A.R. ; Woudenberg, J.H.C. ; Yonezawa, H. ; Zhang, Y. ; Spatafora, J.W. - \ 2009
    Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 1 - 15.
    ribosomal dna-sequences - multigene phylogenies - molecular phylogeny - maximum-likelihood - multiple alignment - marine ascomycota - rdna sequences - fungi - evolution - classification
    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
    Molecular phylogeny of Phoma and allied anamorph genera: towards a reclassification of the Phoma complex
    Gruyter, J. de; Aveskamp, M.M. ; Woudenberg, J.H.C. ; Verkley, G.J.M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2009
    Mycological Research 113 (2009)4. - ISSN 0953-7562 - p. 508 - 519.
    ribosomal dna-sequences - sirococcus-conigenus - mycosphaerella - genus - pleosporales - botryosphaeriaceae - paraconiothyrium - classification - diaporthales - gnomoniaceae
    The present generic concept of Phoma is broadly defined, with nine sections being recognised based on morphological characters. Teleomorph states of Phoma have been described in the genera Didymella, Leptosphaeria, Pleospora and Mycosphaerella, indicating that Phoma anamorphs represent a polyphyletic group. In an attempt to delineate generic boundaries, representative strains of the various Phoma sections and allied coelomycetous genera were included for study. Sequence data of the 18S nrDNA (SSU) and the 28S nrDNA (LSU) regions of 18 Phoma strains included were compared with those of representative strains of 39 allied anamorph genera, including Ascochyta, Coniothyrium, Deuterophoma, Microsphaeropsis, Pleurophoma, Pyrenochaeta, and 11 teleomorph genera. The type species of the Phoma sections Phoma, Phyllostictoides, Sclerophomella, Macrospora and Peyronellaea grouped in a subclade in the Pleosporales with the type species of Ascochyta and Microsphaeropsis. The new family Didymellaceae is proposed to accommodate these Phoma sections and related anamorph genera. The present study demonstrated that Phoma radicina, the type species of Phoma sect. Paraphoma and Phoma heteromorphospora, the type species of Phoma sect. Heterospora can be assigned to the Phaeosphaeriaceae and Leptosphaeriaceae respectively.
    Ectomycorrhizal fungal diversity: seperating the wheat from the chaff
    Rinaldi, A.C. ; Comandini, O. ; Kuyper, T.W. - \ 2008
    Fungal Diversity 33 (2008). - ISSN 1560-2745 - p. 1 - 45.
    truffle-like fungi - n-15 isotopic fractionation - ribosomal dna-sequences - pure culture synthesis - mixed-conifer forest - picea-abies - norway spruce - molecular phylogeny - douglas-fir - new-zealand
    Thousands of ectomycorrhizal (ECM) fungal species exist, but estimates of global species richness of ECM fungi differ widely. Many genera have been proposed as being ECM, but ill a number of studies evidence for the hypothesized ECM habit is lacking. Progress in estimating ECM species richness is therefore slow. Ill this paper we have retrieved studies providing evidence for the ECM habit of fungal species and For the identification of the mycobiont(s) ill specific ECM associations, using published and web-based mycorrhiza literature. The identification methods considered are morpho-anatomical, characterization or naturally occurring ECMs, pure Culture synthesis, molecular identification, and isotopic evidence. In addition, phylogenetic information is also considered as a relevant criterion to assess ECM habit. OF 343 fungal genera for which all ECM status has been alleged, about two thirds have Supportive published evidence or ECM Status can be at least hypothesized. For the remaining taxa, Currently no indication exists as for their I-CM nutritional habit, besides field observations or associations with putative hosts. Our survey clearly indicates that current knowledge of ECM fungal diversity, as Supported by experimental evidence, is only partly complete, and that inclusion of many Funga genera in this trophic and ecological category is not verified at this stage. Care must thus be used when compiling lists of ECM and saprotrophic full studies oil the basis of published information only. On the basis of our literature search we conservatively estimate ECM species richness around 7750 species. However, oil the basis of estimates of knowns and unknowns in macromycete diversity, a final estimate or ECM species richness Would likely be between 20000 and 25000.
    The Culicoides 'snapshot': a novel approach used to assess vector densities widely and rapidly during the 2006 outbreak of bluetongue in The Netherlands
    Meiswinkel, R. ; Goffredo, M. ; Leijs, P. ; Conte, M. - \ 2008
    Preventive Veterinary Medicine 87 (2008)1-2. - ISSN 0167-5877 - p. 98 - 118.
    ribosomal dna-sequences - subgenus avaritia fox - obsoletus complex - virus - ceratopogonidae - diptera - identification - europe - epidemiology - infection
    A novel method was developed and implemented during the recent outbreak of bluetongue (BT) in sheep and cattle in The Netherlands to obtain rapidly a `snapshot¿ of Culicoides vector densities at the national level. The country was divided into 110 raster cells, each measuring 20 km × 20 km; within 106 of these cells, a farm was selected with a minimum of 10 cattle and sampled for Culicoides for one night only using the Onderstepoort-type blacklight trap. Prior to deployment of the light traps in the field, local veterinarians were trained in their use and in the preservation of captured Culicoides. The collections were despatched daily by courier to a field laboratory where the Culicoides were counted and identified. The `snapshot¿ commenced on 12 September 2006 and was completed on 28 September coinciding with the 5¿7 weeks of BT virus (BTV) activity in The Netherlands and when the number of weekly cases of disease was on the rise. Analysis of the 106 collections was completed on 5 October. The number of grid cells in which a taxon occurred is represented by the index 202 gFR (=20 km × 20 km grid Frequency Rate); this index essentially reflects the percentage of examined raster cells found to contain the potential vector in question. The `snapshot¿ results can be summarised as follows:
    Oidium neolycopersici: Intra-specific variability inferred from AFLP analysis and relationship with closely related powdery mildew fungi infecting various plant species
    Jankovics, T. ; Bai, Y. ; Kovacs, G.M. ; Bardin, M. ; Nicot, P.C. ; Toyoda, H. ; Matsuda, Y. ; Niks, R.E. ; Kiss, L. - \ 2008
    Phytopathology 98 (2008). - ISSN 0031-949X - p. 529 - 540.
    ribosomal dna-sequences - nuclear rdna sequences - host-range - evolutionary analysis - nucleotide-sequences - blumeria-graminis - genetic-variation - tomato - identification - resistance
    Previous works indicated a considerable variation in the pathogenicity, virulence, and host range of Oidium neolycopersici isolates causing tomato powdery mildew epidemics in many parts of the world. In this study, rDNA internal transcribed spacer (ITS) sequences, and amplified fragment length polymorphism (AFLP) patterns were analyzed in 17 O. neolycopersici samples collected in Europe, North America, and Japan, including those which overcame some of the tomato major resistance genes. The ITS sequences were identical in all 10 samples tested and were also identical to ITS sequences of eight previously studied O. neolycopersici specimens. The AFLP analysis revealed a high genetic diversity in O. neolycopersici and indicated that all 17 samples represented different genotypes. This might suggest the existence of either a yet unrevealed sexual reproduction or other genetic mechanisms that maintain a high genetic variability in O. neolycopersici. No clear correlation was found between the virulence and the AFLP patterns of the O. neolycopersici isolates studied. The relationship between O. neolycopersici and powdery mildew anamorphs infecting Aquilegia vulgaris, Chelidonium majus, Passiflora caerulea, and Sedum alboroseum was also investigated. These anamorphs are morphologically indistinguishable from and phylogenetically closely related to O. neolycopersici. The cross-inoculation tests and the analyses of ITS sequences and AFLP patterns jointly indicated that the powdery mildew anamorphs collected from the above mentioned plant species all represent distinct, but closely related species according to the phylogenetic species recognition. All these species were pathogenic only to their original host plant species, except O. neolycopersici which infected S. alboroseum, tobacco, petunia, and Arabidopsis thaliana, in addition to tomato, in cross-inoculation tests. This is the first genome-wide study that investigates the relationships among powdery mildews that are closely related based on ITS sequences and morphology. The results indicate that morphologically indistinguishable powdery mildews that differed in only one to five single nucleotide positions in their ITS region are to be considered as different taxa with distinct host ranges
    Mycosphaerella is polophyletic
    Crous, P.W. ; Braun, U. ; Groenewald, J.Z. - \ 2007
    Studies in Mycology 58 (2007)1. - ISSN 0166-0616 - p. 1 - 32.
    ribosomal dna-sequences - rdna sequence - gen-nov - phylogenetic reassessment - black fungi - leaf-spot - eucalyptus - anamorphs - cladosporium - spp.
    Mycosphaerella, one of the largest genera of ascomycetes, encompasses several thousand species and has anamorphs residing in more than 30 form genera. Although previous phylogenetic studies based on the ITS rDNA locus supported the monophyly of the genus, DNA sequence data derived from the LSU gene distinguish several clades and families in what has hitherto been considered to represent the Mycosphaerellaceae. Several important leaf spotting and extremotolerant species need to be disposed to the genus Teratosphaeria, for which a new family, the Teratosphaeriaceae, is introduced. Other distinct clades represent the Schizothyriaceae, Davidiellaceae, Capnodiaceae, and the Mycosphaerellaceae. Within the two major clades, namely Teratosphaeriaceae and Mycosphaerellaceae, most anamorph genera are polyphyletic, and new anamorph concepts need to be derived to cope with dual nomenclature within the Mycosphaerella complex.
    A higher-level phylogenetic classification of the Fungi
    Hibbett, D.S. ; Binder, M. ; Bischoff, J.F. ; Blackwell, M. ; Cannon, P.F. ; Eriksson, O.E. ; Huhndorf, S. ; James, T. ; Kirk, P.M. ; Lücking, R. ; Thorsten Lumbsch, H. ; Lutzoni, F. ; Brandon Matheny, P. ; McLaughlin, D.J. ; Powell, M.J. ; Redhead, S. ; Schoch, C.L. ; Spatafora, J.W. ; Stalpers, J.A. ; Vilgalys, R. ; Aime, M.C. ; Aptroot, A. ; Bauer, R. ; Begerow, D. ; Benny, G.L. ; Castlebury, L.A. ; Crous, P.W. ; Dai, Y.C. ; Gams, W. ; Geiser, D.M. ; Griffith, G.W. ; Gueidan, C. ; Hawksworth, D.L. ; Hestmark, G. ; Hosaka, K. ; Humber, R.A. ; Hyde, K.D. ; Ironside, J.E. ; Koljalg, U. ; Kurtzman, C.P. ; Larsson, K.H. ; Lichtwardt, R. ; Longcore, J. ; Miadlikowska, J. ; Miller, A. ; Moncalvo, J.M. ; Mozley-Standridge, S. ; Oberwinkler, F. ; Parmasto, E. ; Reeb, V. ; Rogers, J.D. ; Roux, C. Le; Ryvarden, L. ; Sampaio, J.P. ; Schüssler, A. ; Sugiyama, J. ; Thorn, R.G. ; Tibell, L. ; Untereiner, W.A. ; Walker, C. ; Wang, Z. ; Weir, A. ; Weiss, M. ; White, M.M. ; Winka, K. ; Yao, Y.J. ; Zhang, N. - \ 2007
    Mycological Research 111 (2007)5. - ISSN 0953-7562 - p. 509 - 547.
    ribosomal dna-sequences - lsu rdna sequences - molecular phylogeny - ord-nov - mitochondrial sequences - natural classification - basidiomycetous yeasts - bayesian-analysis - large subunits - nuclear rdna
    A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecarioromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotiria. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. (c) 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.
    Cladosporium leaf-blotch and stem rot of Paeonia spp. caused by Dichocladosporium chlorocephalum gen. nov.
    Schubert, K. ; Braun, U. ; Groenewald, J.Z. ; Crous, P.W. - \ 2007
    Studies in Mycology 58 (2007)1. - ISSN 0166-0616 - p. 95 - 104.
    ribosomal dna-sequences - organism - peony
    Cladosporium chlorocephalum (= C. paeoniae) is a common, widespread leaf-spotting hyphomycete of peony (Paeonia spp.), characterised by having dimorphic conidiophores. During the season, one stage of this fungus causes distinct, necrotic leaf-blotch symptoms on living leaves of Paeonia spp. In late autumn, winter or after overwintering, a second morphologically distinct conidiophore type occurs on dead, blackish, rotting stems. Conspecificity of the two morphs, previously proposed on the basis of observations in culture, was supported by DNA sequence data from the ITS and LSU gene regions, using cultures obtained from leaf-blotch symptoms on living leaves, as well as from dead stems of Paeonia spp. Sequence data were identical, indicating a single species with two morphs. On account of its distinct conidiogenous loci and conidial hila, as well as its sequence-based phylogenetic position separate from the Davidiella/Cladosporium clade, the peony fungus has to be excluded from Cladosporium s. str., but still belongs to the Davidiellaceae (Capnodiales). The leaf-blotching (cladosporioid) morph of this fungus morphologically resembles species of Fusicladium, but differs in having dimorphic fruiting, and is phylogenetically distant from the Venturiaceae. The macronematous (periconioid) morph resembles Metulocladosporiella (Chaetothyriales), but lacks rhizoid conidiophore hyphae, and has 0-5-septate conidia. Hence, C. chlorocephalum is assigned to the new genus Dichocladosporium.
    Delimiting Cladosporium from morphologically similar genera
    Crous, P.W. ; Braun, U. ; Schubert, K. ; Groenewald, J.Z. - \ 2007
    Studies in Mycology 58 (2007)1. - ISSN 0166-0616 - p. 33 - 56.
    ribosomal dna-sequences - taxonomic revision - phylogenetic reassessment - molecular diagnostics - mycosphaerella spp. - causal organism - gen.-nov - anamorphs - eucalyptus - stenella
    The genus Cladosporium is restricted to dematiaceous hyphomycetes with a coronate scar type, and Davidiella teleomorphs. In the present study numerous cladosporium-like taxa are treated, and allocated to different genera based on their morphology and DNA phylogeny derived from the LSU nrRNA gene. Several species are introduced in new genera such as Hyalodendriella, Ochrocladosporium, Rachicladosporium, Rhizocladosporium, Toxicocladosporium and Verrucocladosporium. A further new taxon is described in Devriesia (Teratosphaeriaceae). Furthermore, Cladosporium castellanii, the etiological agent of tinea nigra in humans, is confirmed as synonym of Stenella araguata, while the type species of Stenella is shown to be linked to the Teratosphaeriaceae (Capnodiales), and not the Mycosphaerellaceae as formerly presumed. Taxonomic novelties: Devriesia americana Crous & Dugan, sp. nov., Hyalodendriella Crous, gen. nov., Hyalodendriella betulae Crous sp. nov., Ochrocladosporium Crous & U. Braun, gen. nov., Ochrocladosporium elatum (Harz) Crous & U. Braun, comb. nov., Ochrocladosporium frigidarii Crous & U. Braun, sp. nov., Rachicladosporium Crous, U. Braun & Hill, gen. nov., Rachicladosporium luculiae Crous, U. Braun & Hill, sp. nov., Rhizocladosporium Crous & U. Braun, gen. nov., Rhizocladosporium argillaceum (Minoura) Crous & U. Braun, comb. nov., Toxicocladosporium Crous & U. Braun, gen. nov., Toxicocladosporium irritans Crous & U. Braun, sp. nov., Verrucocladosporium K. Schub., Aptroot & Crous, gen. nov., Verrucocladosporium dirinae K. Schub., Aptroot & Crous, sp. nov
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