Staff Publications

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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    Uncertainties in Predicting Debris Flow Hazards Following Wildfire
    Hyde, K.D. ; Riley, Karin ; Stoof, C.R. - \ 2017
    In: Natural Hazard Uncertainty Assessment: Modeling and Decision Support / Riley, Karin, Webley , Peter, Thompson, Matthew, American Geophysical Union (Geophysical Monograph Series ) - ISBN 9781119027867 - p. 287 - 299.
    Wildfire increases the probability of debris flows posing hazardous conditions where values-at-risk exist downstream of burned areas. Conditions and processes leading to postfire debris flows usually follow a general sequence defined here as the postfire debris flow hazard cascade: biophysical setting, fire processes, fire effects, rainfall, debris flow, and values-at-risk. Prediction of postfire debris flow hazards is a problem of identifying and understanding the spatial and temporal interactions within this cascade. This chapter summarizes present knowledge of the processes involved in this postfire debris flow hazard cascade and identify uncertainties in terms of knowledge gaps, contradictions in current process understanding, stochastic system variables, and limits to data to support hazard prediction. Understanding these uncertainties can improve delineation of areas threatened by postfire debris flows, can guide future research, and, when addressed, contribute to development of comprehensive and robust modeling and prediction systems that may ultimately reduce threats to values-at-risk.
    Neotypification and phylogeny of Kalmusia
    Zhang, Y. ; Zhang, J.Q. ; Wang, Z.D. ; Fournier, J. ; Crous, P.W. ; Zhang, X.D. ; Li, W.J. ; Ariyawansa, H.A. ; Hyde, K.D. - \ 2014
    Phytotaxa 176 (2014)1. - ISSN 1179-3155 - p. 164 - 173.
    pleosporales - likelihood
    Kalmusia ebuli, the type species of Kalmusia, lacks type material and therefore its phylogenetic position remains unresolved. As a consequence the familial position of Kalmusia is based on morphology and molecular phylogeny of species other than the type. A fresh collection of K. ebuli, recently obtained from decorticated wood of Populus tremula in the foothills of the French Pyrenees is, therefore, designated as neotype to stabilize the application of the species and/or genus name. The holotype of K. ebuli f. sarothamni represents a synonym of K. ebuli. The genus Kalmusia is shown to be polyphyletic within the family Montagnulaceae, with K. ebuli being distant from K. brevispora and K. scabrispora, which appear to represent a different genus.
    The genus Bipolaris
    Manamgoda, D.S. ; Rossman, A.Y. ; Castlebury, L.A. ; Crous, P.W. ; Madrid, H. ; Chukeatirote, E. ; Hyde, K.D. - \ 2014
    Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 221 - 288.
    plant-pathogenic fungi - ascomycota pleosporales-pleosporaceae - phylogenetic species recognition - cochliobolus-sativus - leaf-spot - perfect stage - north-dakota - helminthosporium - sorokiniana - curvularia
    The genus Bipolaris includes important plant pathogens with worldwide distribution. Species recognition in the genus has been uncertain due to the lack of molecular data from ex-type cultures as well as overlapping morphological characteristics. In this study, we revise the genus Bipolaris based on DNA sequence data derived from living cultures of fresh isolates, available ex-type cultures from worldwide collections and observation of type and additional specimens. Combined analyses of ITS, GPDH and TEF gene sequences were used to reconstruct the molecular phylogeny of the genus Bipolaris for species with living cultures. The GPDH gene is determined to be the best single marker for species of Bipolaris. Generic boundaries between Bipolaris and Curvularia are revised and presented in an updated combined ITS and GPDH phylogenetic tree. We accept 47 species in the genus Bipolaris and clarify the taxonomy, host associations, geographic distributions and species’ synonymies. Modern descriptions and illustrations are provided for 38 species in the genus with notes provided for the other taxa when recent descriptions are available. Bipolaris cynodontis, B. oryzae, B. victoriae, B. yamadae and B. zeicola are epi- or neotypified and a lectotype is designated for B. stenospila. Excluded and doubtful species are listed with notes on taxonomy and phylogeny. Seven new combinations are introduced in the genus Curvularia to accomodate the species of Bipolaris transferred based on the phylogenetic analysis. A taxonomic key is provided for the morphological identification of species within the genus.
    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.
    Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
    Schoch, C.L. ; Robbertse, B. ; Robert, V. ; Vu, D. ; Cardinali, G. ; Irinyi, L. ; Meyer, W. ; Nilsson, R.H. ; Hughes, K. ; Miller, A.N. ; Kirk, P.M. ; Abarenkov, K. ; Aime, M.C. ; Ariyawansa, H.A. ; Bidartondo, M. ; Boekhout, T. ; Buyck, B. ; Cai, Q. ; Chen, J. ; Crespo, A. ; Crous, P.W. ; Damm, U. ; Beer, Z.W. de; Dentinger, B.T.M. ; Divakar, P.K. ; Duenas, M. ; Feau, N. ; Fliegerova, K. ; Garcia, M.A. ; Ge, Z.W. ; Griffith, G.W. ; Groenewald, J.Z. ; Groenewald, M. ; Grube, M. ; Gryzenhout, M. ; Gueidan, C. ; Guo, L. ; Hambleton, S. ; Hamelin, R. ; Hansen, K. ; Hofstetter, V. ; Hong, S.B. ; Houbraken, J. ; Hyde, K.D. ; Inderbitzin, P. ; Johnston, P.A. ; Karunarathna, S.C. ; Koljalg, U. ; Kovacs, G.M. ; Kraichak, E. ; Krizsan, K. ; Kurtzman, C.P. ; Larsson, K.H. ; Leavitt, S. ; Letcher, P.M. ; Liimatainen, K. ; Liu, J.K. ; Lodge, D.J. ; Luangsa-ard, J.J. ; Lumbsch, H.T. ; Maharachchikumbura, S.S.N. ; Manamgoda, D. ; Martin, M.P. ; Minnis, A.M. ; Moncalvo, J.M. ; Mule, G. ; Nakasone, K.K. ; Niskanen, T. ; Olariaga, I. ; Papp, T. ; Petkovits, T. ; Pino-Bodas, R. ; Powell, M.J. ; Raja, H.A. ; Redecker, D. ; Sarmiento-Ramirez, J.M. ; Seifert, K.A. ; Shrestha, B. ; Stenroos, S. ; Stielow, B. ; Suh, S.O. ; Tanaka, K. ; Tedersoo, L. ; Telleria, M.T. ; Udayanga, D. ; Untereiner, W.A. ; Dieguez Uribeondo, J. ; Subbarao, K.V. ; Vagvolgyi, C. ; Visagie, C. ; Voigt, K. ; Walker, D.M. ; Weir, B.S. ; Weiss, M. ; Wijayawardene, N.N. ; Wingfield, M.J. ; Xu, J.P. ; Yang, Z.L. ; Zhang, N. ; Zhuang, W.Y. ; Federhen, S. - \ 2014
    Database : the Journal of Biological Databases and Curation 2014 (2014). - ISSN 1758-0463 - 21 p.
    internal transcribed spacer - arbuscular mycorrhizal fungi - ribosomal dna - interspecific hybridization - sequence analyses - species complex - identification - evolution - barcode - life
    DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
    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.
    Introducing Chaetothyriothecium, a new genus of Microthyriales
    Hongsanan, S. ; Chomnunti, P. ; Crous, P.W. ; Chukeatirote, E. ; Hyde, K.D. - \ 2014
    Phytotaxa 161 (2014)2. - ISSN 1179-3155 - p. 157 - 164.
    probability - sequences - bootstrap - inference - alignment - genera - trees - tools
    The order Microthyriales comprises foliar biotrophs, epiphytes, pathogens or saprobes that occur on plant leaves and stems. The order is relatively poorly known due to limited sampling and few in-depth studies. There is also a lack of phylogenetic data for these fungi, which form small black spots on plant host surfaces, but rarely cause any damage to the host. A "Microthyriaceae"-like fungus collected in central Thailand is described as a new genus, Chaetothyriothecium (type species Chaetothyriothecium elegans sp. nov.). Phylogenetic analyses of LSU gene data showed this species to cluster with other members of Microthyriales, where it is related to Microthyrium microscopicum the type of the order. The description of the new species is supplemented by DNA sequence data, which resolves its placement in the order. Little molecular data is available for this order, stressing the need for further collections and molecular data.
    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.
    A phylogenetic re-evaluation of Phyllosticta (Botryosphaeriales)
    Wikee, S. ; Lombard, L. ; Nakashima, C. ; Motohashi, K. ; Chukeatirote, E. ; Cheewangkoon, R. ; McKenzie, E.H.C. ; Hyde, K.D. ; Crous, P.W. - \ 2013
    Studies in Mycology 76 (2013)1. - ISSN 0166-0616 - p. 1 - 29.
    citrus black spot - ribosomal dna - south-africa - fungus - banana - identification - eucalyptus - anamorph - vaccinii - nuclear
    Phyllosticta is a geographically widespread genus of plant pathogenic fungi with a diverse host range. This study redefines Phyllosticta, and shows that it clusters sister to the Botryosphaeriaceae (Botryosphaeriales, Dothideomycetes), for which the older family name Phyllostictaceae is resurrected. In moving to a unit nomenclature for fungi, the generic name Phyllosticta was chosen over Guignardia in previous studies, an approach that we support here. We use a multigene DNA dataset of the ITS, LSU, ACT, TEF and GPDH gene regions to investigate 129 isolates of Phyllosticta, representing about 170 species names, many of which are shown to be synonyms of the ubiquitous endophyte P. capitalensis. Based on the data generated here, 12 new species are introduced, while epitype and neotype specimens are designated for a further seven species. One species of interest is P. citrimaxima associated with tan spot of Citrus maxima fruit in Thailand, which adds a fifth species to the citrus black spot complex. Previous morphological studies lumped many taxa under single names that represent complexes. In spite of this Phyllosticta is a species-rich genus, and many of these taxa need to be recollected in order to resolve their phylogeny and taxonomy.
    Fungal Planet description sheets: 154–213
    Crous, P.W. ; Wingfield, M.J. ; Guarro, J. ; Cheewangkoon, R. ; Bank, M. van der; Swart, W.J. ; Stchigel, A.M. ; Cano-Lira, J.F. ; Roux, J. ; Madrid, H. ; Damm, U. ; Wood, A.R. ; Shuttleworth, L.A. ; Hodges, C.S. ; Munster, M. ; Jesús Yáñez-Morales, M. de; Zúñiga-Estrada, L. ; Cruywagen, E.M. ; Hoog, G.S. de; Silvera, C. ; Najafzadeh, J. ; Davison, E.M. ; Davison, P.J.N. ; Barrett, M.D. ; Barrett, R.L. ; Manamgoda, D.S. ; Minnis, A.M. ; Kleczewski, N.M. ; Flory, S.L. ; Castlebury, L.A. ; Clay, K. ; Hyde, K.D. ; Maússe-Sitoe, S.N.D. ; Chen, S. ; Lechat, C. ; Hairaud, M. ; Lesage-Meessen, L. ; Pawlowska, J. ; Wilk, M. ; Sliwinska-Wyrzychowska, A. ; Metrak, M. ; Wrzosek, M. ; Pavlic-Zupanc, D. ; Maleme, H.M. ; Slippers, B. ; Mac Cormack, W.P. ; Archuby, D.I. ; Grünwald, N.J. ; Tellería, M.T. ; Dueñas, M. ; Martín, M.P. ; Marincowitz, S. ; Beer, Z.W. de; Perez, C.A. ; Gené, J. ; Marin-Felix, Y. ; Groenewald, J.Z. - \ 2013
    Persoonia 31 (2013). - ISSN 0031-5850 - p. 188 - 296.
    sp-nov - colletotrichum-sansevieriae - anamorph genus - south-africa - 1st report - phytophthora-ipomoeae - leaf-blight - genera - phylogeny - botryosphaeriaceae
    Novel species of microfungi described in the present study include the following from South Africa: Camarosporium aloes, Phaeococcomyces aloes and Phoma aloes from Aloe, C. psoraleae, Diaporthe psoraleae and D. psoraleae-pinnatae from Psoralea, Colletotrichum euphorbiae from Euphorbia, Coniothyrium prosopidis and Peyronellaea prosopidis from Prosopis, Diaporthe cassines from Cassine, D. diospyricola from Diospyros, Diaporthe maytenicola from Maytenus, Harknessia proteae from Protea, Neofusicoccum ursorum and N. cryptoaustrale from Eucalyptus, Ochrocladosporium adansoniae from Adansonia, Pilidium pseudoconcavum from Greyia radlkoferi, Stagonospora pseudopaludosa from Phragmites and Toxicocladosporium ficiniae from Ficinia. Several species were also described from Thailand, namely: Chaetopsina pini and C. pinicola from Pinus spp., Myrmecridium thailandicum from reed litter, Passalora pseudotithoniae from Tithonia, Pallidocercospora ventilago from Ventilago, Pyricularia bothriochloae from Bothriochloa and Sphaerulina rhododendricola from Rhododendron. Novelties from Spain include Cladophialophora multiseptata, Knufia tsunedae and Pleuroascus rectipilus from soil and Cyphellophora catalaunica from river sediments. Species from the USA include Bipolaris drechsleri from Microstegium, Calonectria blephiliae from Blephilia, Kellermania macrospora (epitype) and K. pseudoyuccigena from Yucca. Three new species are described from Mexico, namely Neophaeosphaeria agaves and K. agaves from Agave and Phytophthora ipomoeae from Ipomoea. Other African species include Calonectria mossambicensis from Eucalyptus (Mozambique), Harzia cameroonensis from an unknown creeper (Cameroon), Mastigosporella anisophylleae from Anisophyllea (Zambia) and Teratosphaeria terminaliae from Terminalia (Zimbabwe). Species from Europe include Auxarthron longisporum from forest soil (Portugal), Discosia pseudoartocreas from Tilia (Austria), Paraconiothyrium polonense and P. lycopodinum from Lycopodium (Poland) and Stachybotrys oleronensis from Iris (France). Two species of Chrysosporium are described from Antarctica, namely C. magnasporum and C. oceanitesii. Finally, Licea xanthospora is described from Australia, Hypochnicium huinayensis from Chile and Custingophora blanchettei from Uruguay. Novel genera of Ascomycetes include Neomycosphaerella from Pseudopentameris macrantha (South Africa), and Paramycosphaerella from Brachystegia sp. (Zimbabwe). Novel hyphomycete genera include Pseudocatenomycopsis from Rothmannia (Zambia), Neopseudocercospora from Terminalia (Zambia) and Neodeightoniella from Phragmites (South Africa), while Dimorphiopsis from Brachystegia (Zambia) represents a novel coelomycetous genus. Furthermore, Alanphillipsia is introduced as a new genus in the Botryosphaeriaceae with four species, A. aloes, A. aloeigena and A. aloetica from Aloe spp. and A. euphorbiae from Euphorbia sp. (South Africa). A new combination is also proposed for Brachysporium torulosum (Deightoniella black tip of banana) as Corynespora torulosa. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
    A without-prejudice list of generic names of fungi for protection under the International Code of Nomenclature for algae, fungi, and plants
    Kirk, P.M. ; Stalpers, J.A. ; Braun, U. ; Crous, P.W. ; Hansen, K. ; Hawksworth, D.L. ; Hyde, K.D. ; Lücking, R. ; Lumbsch, T.H. ; Rossman, A.Y. ; Seifert, K.A. ; Stadler, M. - \ 2013
    IMA fungus 4 (2013)2. - ISSN 2210-6340 - p. 381 - 443.
    As a first step towards the production of a List of Protected Generic Names for Fungi, a without-prejudice list is presented here as a basis for future discussion and the production of a List for formal adoption. We include 6995 generic names out of the 17072 validly published names proposed for fungi and invite comments from all interested mycologists by 31 March 2014. The selection of names for inclusion takes note of recent major publications on different groups of fungi, and further the decisions reached so far by international working groups concerned with particular families or genera. Changes will be sought in the Code to provide for this and lists at other ranks to be protected against any competing unlisted names, and to permit the inclusion of names of lichen-forming fungi. A revised draft will be made available for further discussion at the 10th International Mycological Congress in Bangkok in August 2014. A schedule is suggested for the steps needed to produce a list for adoption by the International Botanical Congress in August 2017. This initiative provides mycologists with an opportunity to place nomenclature at the generic level on a more secure and stable base.
    Phyllosticta capitalensis, a widespread endophyte of plants
    Wikee, S. ; Lombard, L. ; Crous, P.W. ; Nakashima, C. ; Motohashi, K. ; Chukeatirote, E. ; Alias, S.A. ; McKenzie, E.H.C. ; Hyde, K.D. - \ 2013
    Fungal Diversity 60 (2013)1. - ISSN 1560-2745 - p. 91 - 105.
    citrus black spot - guignardia-citricarpa - fungal endophytes - natural-products - latent pathogens - musa-acuminata - woody-plants - diversity - thailand - banana
    Phyllosticta capitalensis is an endophyte and weak plant pathogen with a worldwide distribution presently known from 70 plant families. This study isolated P. capitalensis from different host plants in northern Thailand, and determined their different life modes. Thirty strains of P. capitalensis were isolated as endophytes from 20 hosts. An additional 30 strains of P. capitalensis from other hosts and geographic locations were also obtained from established culture collections. Phylogenetic analysis using ITS, ACT and TEF gene data confirmed the identity of all isolates. Pathogenicity tests with five strains of P. capitalensis originating from different hosts were completed on their respective host plants. In all cases there was no infection of healthy leaves, indicating that this endophyte does not cause disease on healthy, unstressed host plants. That P. capitalensis is often isolated as an endophyte has important implications in fungal biology and plant health. Due to its endophytic nature, P. capitalensis is commonly found associated with lesions of plants, and often incorrectly identified as a species of quarantine importance, which again has implications for trade in agricultural and forestry production.
    A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species
    Maharachchikumbura, S.S.N. ; Guo, L.D. ; Cai, L. ; Chukeatirote, E. ; Wu, W.P. ; Sun, X. ; Crous, P.W. ; Bhat, D.J. ; McKenzie, E.H.C. ; Bahkali, A.H. ; Hyde, K.D. - \ 2012
    Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 95 - 129.
    dna-sequence database - rna-polymerase-ii - endophytic fungus - beta-tubulin - antifungal metabolites - primer sets - sp-nov - phylogeny - diversity - plant
    Pestalotiopsis is a taxonomically confused, pathogenic and chemically creative genus requiring a critical re-examination using a multi-gene phylogeny based on ex-type and ex-epitype cultures. In this study 40 isolates of Pestalotiopsis, comprised of 28 strains collected from living and dead plant material of various host plants from China were studied by means of morphology and analysis of ITS, ß–tubulin and tef1 gene sequence data. Based on molecular and morphological data we describe 14 new species (Pestalotiopsis asiatica, P. chinensis, P. chrysea, P. clavata, P. diversiseta, P. ellipsospora, P. inflexa, P. intermedia, P. linearis, P. rosea, P. saprophyta, P. umberspora, P. unicolor and P. verruculosa) and three species are epitypified (P. adusta, P. clavispora and P. foedans). Of the 10 gene regions (ACT, ß-tubulin, CAL, GPDH, GS, ITS, LSU, RPB 1, SSU and tef1) utilized to resolve cryptic Pestalotiopsis species, ITS, ß–tubulin and tef1 proved to be the better markers. The other gene regions were less useful due to poor success in PCR amplification and/or in their ability to resolve species boundaries. As a single gene tef1 met the requirements for an ideal candidate and functions well for species delimitation due to its better species resolution and PCR success. Although ß-tubulin showed fairly good differences among species, a combination of ITS, ß-tubulin and tef1 gene data gave the best resolution as compared to single gene analysis. This work provides a backbone tree for 22 ex-type/epitypified species of Pestalotiopsis and can be used in future studies of the genus.
    A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis)
    Udayanga, D. ; Liu, X. ; Crous, P.W. ; McKenzie, E.H.C. ; Chukeatirote, E. ; Hyde, K.D. - \ 2012
    Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 157 - 171.
    multiple sequence alignment - plant-pathogenic fungi - species concepts - south-africa - primer sets - genes - phaseolorum - longicolla - pcr - phylogeography
    The genus Diaporthe (Phomopsis) includes important plant pathogenic fungi with wide host ranges and geographic distributions. In the present study, phylogenetic species recognition in Diaporthe is re-evaluated using a multi-locus phylogeny based on a combined data matrix of rDNA ITS, and partial sequences from the translation elongation factor 1-a (EF 1-a), ß tubulin (TUB) and calmodulin (CAL) molecular markers. DNA sequences of available ex-type cultures have been included, providing a multi-locus backbone tree for future studies on Diaporthe. Four utilizable loci were analyzed individually and in combination, and ITS, EF 1-a and multi-locus phylogenetic trees are presented. The phylogenetic tree inferred by combined analysis of four loci provided the best resolution for species as compared to single gene analysis. Notes are provided for nine species previously known in Phomopsis that are transferred to Diaporthe in the present study. The unraveling of cryptic species complexes of Diaporthe based on Genealogical Concordance Phylogenetic Species Recognition (GCPSR) is emphasized.
    A phylogenetic and taxonomic re-evaluation of the Bipolaris - Cochliobolus - Curvularia Complex
    Manamgoda, D.S. ; Cai, L. ; McKenzie, E.H.C. ; Crous, P.W. ; Madrid, H. ; Chukeatirote, E. ; Shivas, R.G. ; Tan, Y.P. ; Hyde, K.D. - \ 2012
    Fungal Diversity 56 (2012)1. - ISSN 1560-2745 - p. 131 - 144.
    species concepts - sequences - pseudocochliobolus - helminthosporium - pathogens - alignment - genes - fungi - genus - rdna
    Three genera, Cochliobolus, Bipolaris and Curvularia form a complex that contains many plant pathogens, mostly on grasses (Poaceae) with a worldwide distribution. The taxonomy of this complex is confusing as frequent nomenclatural changes and refinements have occurred. There is no clear morphological boundary between the asexual genera Bipolaris and Curvularia, and some species show intermediate morphology. We investigated this complex based on a set of ex-type cultures and collections from northern Thailand. Combined gene analysis of rDNA ITS (internal transcribed spacer), GPDH (glyceraldehyde 3-phosphate dehydrogenase), LSU (large subunit) and EF1-a (translation elongation factor 1-a) shows that this generic complex divides into two groups. Bipolaris and Cochliobolus species clustered in Group 1 along with their type species, whereas Curvularia species (including species named as Bipolaris, Cochliobolus and Curvularia) clustered in Group 2, with its generic type. The nomenclatural conflict in this complex is resolved giving priority to the more commonly used established generic names Bipolaris and Curvularia. Modern descriptions of the genera Bipolaris and Curvularia are provided and species resolved in this study are transferred to one of these genera based on their phylogeny.
    Chocolate spot of Eucalyptus
    Cheewangkoon, R. ; Groenewald, J.Z. ; Hyde, K.D. ; To-anun, C. ; Crous, P.W. - \ 2012
    Mycological Progress 11 (2012)2. - ISSN 1617-416X - p. 61 - 69.
    leaf-inhabiting fungi - ribosomal dna - genera nova - heteroconium - proteaceae - anamorphs - culture
    Chocolate Spot leaf disease of Eucalyptus is associated with several Heteroconium-like species of hyphomycetes that resemble Heteroconium s.str. in morphology. They differ, however, in their ecology, with the former being plant pathogenic, while Heteroconium s.str. is a genus of sooty moulds. Results of molecular analyses, inferred from DNA sequences of the large subunit (LSU) and internal transcribed spacers (ITS) region of nrDNA, delineated four Heteroconium-like species on Eucalyptus, namely H. eucalypti, H. kleinziense, Alysidiella parasitica, and one isolate resembling a novel species in a clade separate from the holotype of Heteroconium, H. citharexyli. Based on molecular phylogeny, morphology and ecology, the Heteroconium-like species associated with Chocolate Spot disease are reclassified in the genus Alysidiella, which is shown to have mycelium that is immersed in and superficial on the host tissue and conidiogenous cells that can have loci that are either inconspicuous or proliferating percurrently. Furthermore, conidiogenous cells can either occur solitary on hyphae, or be sporodochial, arranged on a weakly developed stroma, which further distinguishes Alysidiella from Heteroconium
    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.
    A molecular, morphological and ecological re-appraisal of Venturiales¿a new order of Dothideomycetes
    Zhang, Y. ; Crous, P.W. ; Schoch, C.L. ; Bahkali, A.H. ; Guo, L.D. ; Hyde, K.D. - \ 2011
    Fungal Diversity 51 (2011)1. - ISSN 1560-2745 - p. 249 - 277.
    phylogenetic trees - bayesian-inference - sequence-data - apple scab - sp-nov - venturiaceae - genera - fungi - herpotrichiellaceae - classification
    The Venturiaceae was traditionally assigned to Pleosporales although its diagnostic characters readily distinguish it from other pleosporalean families. These include a parasitic or saprobic lifestyle, occurring on leaves or stems of dicotyledons; small to medium-sized ascomata, often with setae; deliquescing pseudoparaphyses; 8-spored, broadly cylindrical to obclavate asci; 1-septate, yellowish, greenish or pale brown to brown ascospores; and hyphomycetous anamorphs. Phylogenetically, core genera of Venturiaceae form a monophyletic clade within Dothideomycetes, and represent a separate sister lineage from current orders, thus a new order—Venturiales is introduced. A new family, Sympoventuriaceae, is introduced to accommodate taxa of a well-supported subclade within Venturiales, which contains Sympoventuria, Veronaeopsis simplex and Fusicladium-like species. Based on morphology and DNA sequence analysis, eight genera are included in Venturiaceae, viz. Acantharia, Apiosporina (including Dibotryon), Caproventuria, Coleroa, Pseudoparodiella, Metacoleroa, Tyrannosorus and Venturia. Molecular phylogenetic information is lacking for seven genera previously included in Venturiales, namely Arkoola, Atopospora, Botryostroma, Lasiobotrys, Trichodothella, Trichodothis and Rhizogenee and these are discussed, but their inclusion in Venturiaceae is doubtful. Crotone, Gibbera, Lineostroma, Phaeocryptopus, Phragmogibbera, Platychora, Polyrhizon, Rosenscheldiella, Uleodothis and Xenomeris are excluded from Venturiales, and their ordinal placement needs further investigation. Zeuctomorpha is treated as a synonym of Acantharia.
    The Amsterdam Declaration on Fungal Nomenclature
    Hawksworth, D.L. ; Crous, P.W. ; Redhead, S.A. ; Reynolds, D.R. ; Samson, R.A. ; Seifert, K.A. ; Taylor, J.W. ; Wingfield, M.J. ; Abaci, Ö. ; Aime, C. ; Asan, A. ; Bai, F.Y. ; Beer, W. de; Begerow, D. ; Berikten, D. ; Boekhout, T. ; Buchanan, P.K. ; Burgess, T. ; Buzina, W. ; Cai, L. ; Cannon, P.F. ; Crane, J.L. ; Damm, U. ; Daniel, H.M. ; Diepeningen, A.D. van; Druzhinina, I. ; Dyer, P.S. ; Eberhardt, U. ; Fell, J.W. ; Frisvad, J.C. ; Geiser, D.M. ; Geml, J. ; Glienke, C. ; Gräfenhan, T. ; Groenewald, J.Z. ; Groenewald, M. ; Gruyter, J. de; Guého-Kellemann, E. ; Guo, L.D. ; Hibbett, D.S. ; Hong, S.B. ; Hoog, G.S. de; Houbraken, J. ; Huhndorf, S.M. ; Hyde, K.D. ; Ismail, A. ; Johnston, P.R. ; Kadaifciler, D.G. ; Kirk, P.M. ; Köljalg, U. ; Kurtzman, C.P. ; Lagneau, P.E. ; Lévesque, C.A. ; Liu, X. ; Lombard, L. ; Meyer, W. ; Miller, A. ; Minter, D.W. ; Najafzadeh, M.J. ; Norvell, L. ; Ozerskaya, S.M. ; Öziç, R. ; Pennycook, S.R. ; Peterson, S.W. ; Pettersson, O.V. ; Quaedvlieg, W. ; Robert, V.A. ; Ruibal, C. ; Schnürer, J. ; Schroers, H.J. ; Shivas, R. ; Slippers, B. ; Spierenburg, H. ; Takashima, M. ; Taskin, E. ; Thines, M. ; Thrane, U. ; Uztan, A.H. ; Raak, M. van; Varga, J. ; Vasco, A. ; Verkley, G. ; Videira, S.I.R. ; Vries, R.P. de; Weir, B.S. ; Yilmaz, N. ; Yurkov, A. ; Zhang, N. - \ 2011
    IMA fungus 2 (2011)1. - ISSN 2210-6340 - p. 105 - 112.
    The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19-20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature offungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented.
    Nomenclature - Formal reports, proposals, and opinion
    Senkardesler, A. ; Buyck, B. ; Hofstetter, V. ; Verbeken, A. ; Walleyn, R. ; Thorsten Lumbsch, H. ; Ahti, T. ; Parnmen, S. ; Vellinga, E.C. ; Pennycook, S.R. ; Hawksworth, D.L. ; Cooper, J.A. ; Crous, P.W. ; Hyde, K.D. ; Iturriaga, T. ; Kirk, P.M. ; Lumbsch, H.T. ; May, T.W. ; Minter, D.W. ; Misra, J.K. ; Norvell, L. ; Redhead, S.A. ; Rossman, A.Y. ; Seifert, K.A. ; Stalpers, J.A. ; Taylor, J.W. ; Wingfield, M.J. - \ 2010
    Mycotaxon 111 (2010). - ISSN 0093-4666 - p. 501 - 520.
    Formal proposals to conserve or protect fungal names as well as proposals to amend the International Code of Nomenclature of immediate interest to mycologists are now published concurrently in Mycotaxon and Taxon. Conservation proposals include Prop. 1918 (to conserve the name Dermatocarpon bucekii against Placidium steineri), Prop. 1919 (to conserve the name Lactarius with a conserved type), Prop. 1926 (to conserve the name Cladia against Heterodea, and Prop.1927 (to conserve the name Agaricus rachodes with that spelling). Props. 117-119 to amend the Code ask for pre-publication deposit of nomenclatural information in a recognized repository for valid publication of fungal names.
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