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.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Fat, fibre and cancer risk in African Americans and rural Africans
O'Keefe, S.J. ; Li, J.V. ; Lahti, Leo ; Ou, J. ; Carbonero, F. ; Khaled, M. ; Postma, J.M. ; Kinross, J. ; Wahl, E. ; Ruder, E. ; Vipperla, K. ; Naidoo, V. ; Mtshali, L. ; Tims, S. ; Puylaert, P.G.B. ; DeLany, J. ; Krasinskas, A. ; Benefiel, A.C. ; Kaseb, H.O. ; Newton, K. ; Nicholson, J.K. ; Vos, W.M. De; Gaskins, H.R. ; Zoetendal, E.G. - \ 2015
microbiota - HITChip - genera
Rates of colon cancer are much higher in African Americans (65:100,000) than in rural South Africans (<5:100,000). The higher rates are associated with higher animal protein and fat, and lower fibre consumption, higher colonic secondary bile acids, lower colonic short-chain fatty acid quantities and higher mucosal proliferative biomarkers of cancer risk in otherwise healthy middle-aged volunteers. Here we investigate further the role of fat and fibre in this association. We performed 2-week food exchanges in subjects from the same populations, where African Americans were fed a high-fibre, low-fat African-style diet and rural Africans a high-fat, low-fibre western-style diet, under close supervision. In comparison with their usual diets, the food changes resulted in remarkable reciprocal changes in mucosal biomarkers of cancer risk and in aspects of the microbiota and metabolome known to affect cancer risk, best illustrated by increased saccharolytic fermentation and butyrogenesis, and suppressed secondary bile acid synthesis in the African Americans.
Resolving the polyphyletic nature of Pyricularia (Pyriculariaceae)
Klaubauf, S. ; Tharreau, D. ; Fournier, E. ; Groenewald, J.Z. ; Crous, P.W. ; Vries, R.P. de; Lebrun, M.H. - \ 2014
Studies in Mycology 79 (2014). - ISSN 0166-0616 - p. 85 - 120.
rice blast fungus - magnaporthe-oryzae - juncus-roemerianus - molecular-data - fresh-water - grisea - phylogeny - genera - specificity - resistance
Species of Pyricularia (magnaporthe-like sexual morphs) are responsible for major diseases on grasses. Pyricularia oryzae (sexual morph Magnaporthe oryzae) is responsible for the major disease of rice called rice blast disease, and foliar diseases of wheat and millet, while Pyricularia grisea (sexual morph Magnaporthe grisea) is responsible for foliar diseases of Digitaria. Magnaporthe salvinii, M. poae and M. rhizophila produce asexual spores that differ from those of Pyricularia sensu stricto that has pyriform, 2-septate conidia produced on conidiophores with sympodial proliferation. Magnaporthe salvinii was recently allocated to Nakataea, while M. poae and M. rhizophila were placed in Magnaporthiopsis. To clarify the taxonomic relationships among species that are magnaporthe- or pyricularia-like in morphology, we analysed phylogenetic relationships among isolates representing a wide range of host plants by using partial DNA sequences of multiple genes such as LSU, ITS, RPB1, actin and calmodulin. Species of Pyricularia s. str. belong to a monophyletic clade that includes all P. oryzae/P. grisea isolates tested, defining the Pyriculariaceae, which is sister to the Ophioceraceae, representing two novel families. These clades are clearly distinct from species belonging to the Gaeumannomyces pro parte/Magnaporthiopsis/Nakataea generic complex that are monophyletic and define the Magnaporthaceae. A few magnaporthe- and pyricularia-like species are unrelated to Magnaporthaceae and Pyriculariaceae. Pyricularia oryzae/P. grisea isolates cluster into two related clades. Host plants such as Eleusine, Oryza, Setaria or Triticum were exclusively infected by isolates from P. oryzae, while some host plant such as Cenchrus, Echinochloa, Lolium, Pennisetum or Zingiber were infected by different Pyricularia species. This demonstrates that host range cannot be used as taxonomic criterion without extensive pathotyping. Our results also show that the typical pyriform, 2-septate conidium morphology of P. grisea/P. oryzae is restricted to Pyricularia and Neopyricularia, while most other genera have obclavate to more ellipsoid 2-septate conidia. Some related genera (Deightoniella, Macgarvieomyces) have evolved 1-septate conidia. Therefore, conidium morphology cannot be used as taxonomic criterion at generic level without phylogenetic data. We also identified 10 novel genera, and seven novel species. A re-evaluation of generic and species concepts within Pyriculariaceae is presented, and novelties are proposed based on morphological and phylogenetic data.
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.
Annonaceae substitution rates - a codon model perspective
Chatrou, L.W. ; Pirie, M.D. ; Velzen, R. van; Bakker, F.T. - \ 2014
Revista Brasileira de Fruticultura 36 (2014)edição especial, e.. - ISSN 0100-2945 - p. 108 - 117.
molecular evolution - flowering plants - phylogeny reconstruction - historical biogeography - nucleotide substitution - maximum-likelihood - genera - diversification - characters - patterns
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.
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.
Integrative systematics supports the establishment of Winitia, a new genus of Annonaceae (Malmeoideae, Miliuseae) allied to Stelechocarpus and Sageraea
Chaowasku, T. ; Ham, R.W.J.M. van der; Chatrou, L.W. - \ 2013
Systematics and Biodiversity 11 (2013)2. - ISSN 1477-2000 - p. 195 - 207.
molecular phylogenetics - uvaria annonaceae - historical biogeography - pseuduvaria annonaceae - pollen morphology - polyalthia - revision - delimitation - genera - clade
The generic circumscriptions of Stelechocarpus and Sageraea (Annonaceae) are assessed using molecular phylogenetic, macromorphological, and pollen morphological evidence. For molecular phylogenetic analysis the combined seven plastid markers: rbcL exon, trnL intron, trnL-F spacer, matK exon, ndhF exon, psbA-trnH spacer, and ycf1 exon constituting c. 7 kb are used. The results corroborate the recognition of a maximally supported clade as a new genus, Winitia. It is weakly to moderately supported as sister to Stelechocarpus burahol, the type and only species of Stelechocarpus. A clade consisting of Winitia and Stelechocarpus is strongly supported as sister to Sageraea, which is monophyletic with strong support. Winitia consists of two species, one of which (W. expansa) is proposed as a new species endemic to Thailand, whereas one new combination (W. cauliflora) is made. The new genus is primarily characterized by (1) multicolumellar stigmas (= 5 columns per stigma) and (2) pollen grains with a very thin tectum, a more or less columellate/coarsely granular infratectum, and a very distinct basal layer. The macromorphology and pollen morphology of the three genera (Stelechocarpus, Winitia, and Sageraea) are highlighted.
Sizing up Septoria
Quaedvlieg, W. ; Verkley, G.J.M. ; Shin, H.D. ; Barreto, R.W. ; Alfenas, A.C. ; Swart, W.J. ; Groenewald, J.Z. ; Crous, P.W. - \ 2013
Studies in Mycology 75 (2013). - ISSN 0166-0616 - p. 307 - 390.
molecular-data sets - systematic reappraisal - phylogenetic lineages - genus septoria - ribosomal dna - similar fungi - sooty blotch - south-africa - mycosphaerella - genera
Septoria represents a genus of plant pathogenic fungi with a wide geographic distribution, commonly associated with leaf spots and stem cankers of a broad range of plant hosts. A major aim of this study was to resolve the phylogenetic generic limits of Septoria, Stagonospora, and other related genera such as Sphaerulina, Phaeosphaeria and Phaeoseptoria using sequences of the the partial 28S nuclear ribosomal RNA and RPB2 genes of a large set of isolates. Based on these results Septoria is shown to be a distinct genus in the Mycosphaerellaceae, which has mycosphaerella-like sexual morphs. Several septoria-like species are now accommodated in Sphaerulina, a genus previously linked to this complex. Phaeosphaeria (based on P. oryzae) is shown to be congeneric with Phaeoseptoria (based on P. papayae), which is reduced to synonymy under the former. Depazea nodorum (causal agent of nodorum blotch of cereals) and Septoria avenae (causal agent of avenae blotch of barley and rye) are placed in a new genus, Parastagonospora, which is shown to be distinct from Stagonospora (based on S. paludosa) and Phaeosphaeria. Partial nucleotide sequence data for five gene loci, ITS, LSU, EF-1a, RPB2 and Btub were generated for all of these isolates. A total of 47 clades or genera were resolved, leading to the introduction of 14 new genera, 36 new species, and 19 new combinations
Letter to the Editor : One Fungus, One Name: Defining the Genus Fusarium in a Scientifically Robust Way That Preserves Longstanding Use
Geiser, D.M. ; Aoki, T. ; Bacon, C.W. ; Baker, S.E. ; Bhattacharyya, M.K. ; Brandt, M.E. ; Brown, D.W. ; Burgess, L.W. ; Chulze, S. ; Coleman, J.J. ; Correll, J.C. ; Covert, S.F. ; Crous, P.W. ; Waalwijk, C. - \ 2013
Phytopathology 103 (2013). - ISSN 0031-949X - p. 400 - 408.
solani species complex - sudden-death syndrome - phylogeny - tucumaniae - taxonomy - reveals - genera
In this letter, we advocate recognizing the genus Fusarium as the sole name for a group that includes virtually all Fusarium species of importance in plant pathology, mycotoxicology, medicine, and basic research. This phylogenetically guided circumscription will free scientists from any obligation to use other genus names, including teleomorphs, for species nested within this clade, and preserve the application of the name Fusarium in the way it has been used for almost a century. Due to recent changes in the International Code of Nomenclature for algae, fungi, and plants, this is an urgent matter that requires community attention. The alternative is to break the longstanding concept of Fusarium into nine or more genera, and remove important taxa such as those in the F. solani species complex from the genus, a move we believe is unnecessary. Here we present taxonomic and nomenclatural proposals that will preserve established research connections and facilitate communication within and between research communities, and at the same time support strong scientific principles and good taxonomic practice.
Dissoconiaceae associated with sooty blotch and flyspeck on fruits in China and the United States
Li, H.Y. ; Sun, G.Y. ; Zhai, X.R. ; Batzer, J.C. ; Mayfield, D.A. ; Crous, P.W. ; Groenewald, J.Z. ; Gleason, M.L. - \ 2012
Persoonia 28 (2012). - ISSN 0031-5850 - p. 113 - 125.
complex davidiellaceae - clustal-w - mycosphaerella - eucalyptus - apple - anamorphs - teratosphaeria - capnodiales - taxonomy - genera
Zasmidium angulare, a novel species of Mycosphaerellaceae, and several novel taxa that reside in Dissoconiaceae, were identified from a collection of apples and Cucurbita maxima (cv. Blue Hubbard) from China and the USA that exhibited sooty blotch and flyspeck (SBFS) signs on their host substrata. Morphology on fruit surfaces and in culture, and phylogenetic analyses of the nuclear ribosomal DNAs 28S and internal transcribed spacer regions, as well as partial translation elongation factor 1-alpha gene sequences in some cases, were used to delineate seven previously unidentified species and three known species. Pseudoveronaea was established as a new genus of Dissoconiaceae, represented by two species, P. ellipsoidea and P. obclavata. Although Pseudoveronaea was morphologically similar to Veronaea, these fungi clustered with Dissoconiaceae (Capnodiales) rather than Chaetothyriales (Herpotrichiellaceae). Ramichloridium mali comb. nov., and three novel species, R. cucurbitae, R. luteum and R. punctatum were closely related with R. apiculatum, which together formed a distinct subclade in Dissoconiaceae. Species of Dissoconium s.lat. clustered in two well-supported clades supported by distinct morphological and cultural features. Subsequently Uwebraunia, a former synonym of Dissoconium, was resurrected for the one clade, with new combinations proposed for U. australiensis, U. commune, U. dekkeri and U. musae. Furthermore, we also reported that D. aciculare, Dissoconium sp., U. commune and U. dekkeri were associated with SBFS on apples.
Stagonosporopsis spp. associated with ray blight disease of Asteraceae
Vaghefi, N. ; Pethybridge, S.J. ; Ford, R. ; Nicolas, M.E. ; Crous, P.W. ; Taylor, P.W.J. - \ 2012
Australasian Plant Pathology 41 (2012)6. - ISSN 0815-3191 - p. 675 - 686.
phoma-ligulicola - phylogenetic analyses - ribosomal dna - mixed models - host-range - pyrethrum - sequences - complex - genera - taxa
Ray blight disease of pyrethrum (Tanacetum cinerariifolium) is shown to be caused by more than one species of Stagonosporopsis. The Australian pathogen, previously identified as Phoma ligulicola var. inoxydabilis, represents a new species described as Stagonosporopsis tanaceti based on morphological characters and a five-gene phylogeny employing partial sequences of the actin, translation elongation factor 1-alpha, internal transcribed spacers and 5.8S of the nrDNA, 28S large subunit and beta-tubulin 2 gene sequences. Furthermore, the two varieties of Stagonosporopsis ligulicola are elevated to species level as S. chrysanthemi and S. inoxydabilis based on their DNA phylogeny and morphology.
Characterization of Hubera (Annonaceae), a new genus segregated from Polyalthia and allied to Miliusa.
Chaowasku, T. ; Johnson, D.M. ; Ham, R.W.J.M. van der; Chatrou, L.W. - \ 2012
Phytotaxa 69 (2012). - ISSN 1179-3155 - p. 33 - 56.
molecular phylogenetics - uvaria annonaceae - pollen morphology - chloroplast dna - evolution - genera - reconstruction - hypotheses - sequences - revision
On the basis of molecular phylogenetics, pollen morphology and macromorphology, a new genus of the tribe Miliuseae, Hubera, segregrated from Polyalthia and allied to Miliusa, is established and described. It is characterized by the combination of reticulate tertiary venation of the leaves, axillary inflorescences, a single ovule per ovary and therefore single-seeded monocarps, seeds with a flat to slightly raised raphe, spiniform(-flattened peg) ruminations of the endosperm, and pollen with a finely and densely granular infratectum. Twenty-seven species are accordingly transferred to this new genus.
Macrophotographic wood atlas of Annonaceae.
Koek-Noorman, J. ; Westra, L.I.T. - \ 2012
Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 135 - 189.
flowering plants - genera - classification - evolution - families - genus
In this article, a general description of the microscopic wood anatomy of Annonaceae is given. We provide a description of the wood anatomical features of the family and of all subfamilies and tribes, all from material in the Utrecht Wood collection. Hand-lens images can be an important help in identification, not only at the family level, but also at the level of genera or below, notwithstanding the fact that the number of characters that can be easily observed in end-grain photographs is restricted. The differences are often slight and difficult to summarize in a few words, making illustrations an indispensable tool. Therefore, we provide end-grain photographs of cross-sections of wood of 66 genera and > 90 species of Annonaceae. The variation seen in lens key characters is discussed against the framework of the current phylogenetic tree of the family. Additional remarks on microscopic features are given when appropriate
Editorial: The natural history of Annonaceae.
Chatrou, L.W. ; Erkens, R.H.J. ; Richardson, J.E. ; Saunders, R.M.K. ; Fay, M.F. - \ 2012
Botanical Journal of the Linnean Society 169 (2012)1. - ISSN 0024-4074 - p. 1 - 4.
phylogeny group classification - cladistic-analysis - uvaria annonaceae - flowering plants - apg iii - families - genera - genus - update - orders
One fungus, one name promotes progressive plant pathology
Wingfield, M.J. ; Beer, Z.W. de; Slippers, B. ; Wingfield, B.D. ; Groenewald, J.Z. ; Lombard, L. ; Crous, P.W. - \ 2012
Molecular Plant Pathology 13 (2012)6. - ISSN 1464-6722 - p. 604 - 613.
phylogenetic lineages - amsterdam declaration - calonectria-morganii - gen. nov. - nomenclature - anamorphs - revision - genera - cylindrocladium - fusarium
The robust and reliable identification of fungi underpins virtually every element of plant pathology, from disease diagnosis to studies of biology, management/control, quarantine and, even more recently, comparative genomics. Most plant diseases are caused by fungi, typically pleomorphic organisms, for which the taxonomy and, in particular, a dual nomenclature system have frustrated and confused practitioners of plant pathology. The emergence of DNA sequencing has revealed cryptic taxa and revolutionized our understanding of relationships in the fungi. The impacts on plant pathology at every level are already immense and will continue to grow rapidly as new DNA sequencing technologies continue to emerge. DNA sequence comparisons, used to resolve a dual nomenclature problem for the first time only 19 years ago, have made it possible to approach a natural classification for the fungi and to abandon the confusing dual nomenclature system. The journey to a one fungus, one name taxonomic reality has been long and arduous, but its time has come. This will inevitably have a positive impact on plant pathology, plant pathologists and future students of this hugely important discipline on which the world depends for food security and plant health in general. This contemporary review highlights the problems of a dual nomenclature, especially its impact on plant pathogenic fungi, and charts the road to a one fungus, one name system that is rapidly drawing near.
Cylindrocarpon root rot: multi-gene analysis reveals novel species within the Ilyonectria radicicola species complex
Cabral, A. ; Groenewald, J.Z. ; Rego, C. ; Oliveira, H. ; Crous, P.W. - \ 2012
Mycological Progress 11 (2012)3. - ISSN 1617-416X - p. 655 - 688.
black foot disease - phylogenetic-relationships - neonectria - anamorphs - fusarium - destructans - hypocreales - nectriaceae - ginseng - genera
Ilyonectria radicicola and its Cylindrocarpon-like anamorph represent a species complex that is commonly associated with root rot disease symptoms on a range of hosts. During the course of this study, several species could be distinguished from I. radicicola sensu stricto based on morphological and culture characteristics. DNA sequence analysis of the partial ß-tubulin, histone H3, translation elongation factor 1-a and nuclear ribosomal RNA-Internal Transcribed Spacer (nrRNA-ITS) genes were employed to provide further support for the morphological species resolved among 68 isolates associated with root rot disease symptoms. Of the various loci screened, nrRNA-ITS sequences were the least informative, while histone H3 sequences were the most informative, resolving the same number of species as the combined dataset across the four genes. Within the Ilyonectria radicicola species complex, 12 new taxa are delineated occurring on a diverse range of hosts, the most common being Cyclamen, Lilium, Panax, Pseudotsuga, Quercus and Vitis.
Fungal Planet description sheets: 69–91
Crous, P.W. ; Groenewald, J.Z. ; Shivas, R.G. ; Edwards, J. ; Seifert, K.A. ; Alfenas, A.C. ; Alfenas, R.F. ; Burgess, T.I. ; Carnegie, A.J. ; Hardy, G.E.S.T.J. ; Hiscock, N. ; Hüberli, D. ; Jung, T. ; Louis-Seize, G. ; Okada, G. ; Pereira, O.L. ; Stukely, M.J.C. ; Wang, W. ; White, G.P. ; Young, A.J. ; McTaggart, A.R. ; Pascoe, I.G. ; Porter, I.J. ; Quaedvlieg, W. - \ 2011
Persoonia 26 (2011). - ISSN 0031-5850 - p. 108 - 156.
ribosomal dna - eucalyptus - genera - dictyosporium - microfungi - phylogeny - china - genus - spot - nov
Novel species of microfungi described in the present study include the following from Australia: Bagadiella victoriae and Bagadiella koalae on Eucalyptus spp., Catenulostroma eucalyptorum on Eucalyptus laevopinea, Cercospora eremochloae on Eremochloa bimaculata, Devriesia queenslandica on Scaevola taccada, Diaporthe musigena on Musa sp., Diaporthe acaciigena on Acacia retinodes, Leptoxyphium kurandae on Eucalyptus sp., Neofusicoccum grevilleae on Grevillea aurea, Phytophthora fluvialis from water in native bushland, Pseudocercospora cyathicola on Cyathea australis, and Teratosphaeria mareebensis on Eucalyptus sp. Other species include Passalora leptophlebiae on Eucalyptus leptophlebia (Brazil), Exophiala tremulae on Populus tremuloides and Dictyosporium stellatum from submerged wood (Canada), Mycosphaerella valgourgensis on Yucca sp. (France), Sclerostagonospora cycadis on Cycas revoluta (Japan), Rachicladosporium pini on Pinus monophylla (Netherlands), Mycosphaerella wachendorfiae on Wachendorfia thyrsifolia and Diaporthe rhusicola on Rhus pendulina (South Africa). Novel genera of hyphomycetes include Noosia banksiae on Banksia aemula (Australia), Utrechtiana cibiessia on Phragmites australis (Netherlands), and Funbolia dimorpha on blackened stem bark of an unidentified tree (USA). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.
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.
Fungal pathogens of Proteaceae
Crous, P.W. ; Summerell, B.A. ; Swart, L. ; Denman, S. ; Taylor, J.E. ; Bezuidenhout, C.M. ; Palm, M.E. ; Marincowitz, S. ; Groenewald, J.Z. - \ 2011
Persoonia 27 (2011). - ISSN 0031-5850 - p. 20 - 45.
south-africa - primer sets - sp nov. - phylogeny - mycosphaerella - genera - phoma - genus - calonectria - morphology
Species of Leucadendron, Leucospermum and Protea (Proteaceae) are in high demand for the international floriculture market due to their brightly coloured and textured flowers or bracts. Fungal pathogens, however, create a serious problem in cultivating flawless blooms. The aim of the present study was to characterise several of these pathogens using morphology, culture characteristics, and DNA sequence data of the rRNA-ITS and LSU genes. In some cases additional genes such as TEF 1-a and CHS were also sequenced. Based on the results of this study, several novel species and genera are described. Brunneosphaerella leaf blight is shown to be caused by three species, namely B. jonkershoekensis on Protea repens, B. nitidae sp. nov. on Protea nitida and B. protearum on a wide host range of Protea spp. (South Africa). Coniothyrium-like species associated with Coniothyrium leaf spot are allocated to other genera, namely Curreya grandicipis on Protea grandiceps, and Microsphaeropsis proteae on P. nitida (South Africa). Diaporthe leucospermi is described on Leucospermum sp. (Australia), and Diplodina microsperma newly reported on Protea sp. (New Zealand). Pyrenophora blight is caused by a novel species, Pyrenophora leucospermi, and not Drechslera biseptata or D. dematoidea as previously reported. Fusicladium proteae is described on Protea sp. (South Africa), Pestalotiopsis protearum on Leucospermum cuneiforme (Zimbabwe), Ramularia vizellae and R. stellenboschensis on Protea spp. (South Africa), and Teratosphaeria capensis on Protea spp. (Portugal, South Africa). Aureobasidium leaf spot is shown to be caused by two species, namelyA.proteaecomb. nov. on Protea spp. (South Africa), and A. leucospermi sp. nov. on Leucospermum spp. (Indonesia, Portugal, South Africa). Novel genera and species elucidated in this study include Gordonomyces mucovaginatus and Pseudopassalora gouriqua (hyphomycetes), and Xenoconiothyrium catenata (coelomycete), all on Protea spp. (South Africa).
Systematic reappraisal of species in Phoma section Paraphoma, Pyrenochaeta and Pleurophoma
Gruyter, J. de; Woudenberg, J.H.C. ; Aveskamp, M.M. ; Verkley, G.J.M. ; Groenewald, J.Z. ; Crous, P.W. - \ 2010
Mycologia 102 (2010)5. - ISSN 0027-5514 - p. 1066 - 1081.
molecular phylogeny - ribosomal dna - monograph - genus - peyronellaea - complex - genera
Sequence data from the 18S nrDNA (SSU) and 28S nrDNA (LSU) regions of isolates of Phoma section Paraphoma were compared with those of representative isolates of the morphologically similar anamorph genera Pleurophoma and Pyrenochaeta and of the type species of Phoma sections Phoma, Pilosa and Plenodomus. Phoma section Paraphoma was found to be highly polyphyletic within the Pleosporales and only distantly related to Phoma section Phoma. The genus Paraphoma, which is based on Paraphoma radicina, is reintroduced in the Phaeosphaeriaceae with two additional taxa. The new genera Setophoma and Neosetophoma, type species Setophoma terrestris comb. nov. and Neosetophoma samarorum comb. nov., are introduced and represent species that are closely related to Paraphoma but differ based on morphological characters and molecular phylogeny. Phoma coonsii is transferred to genus Chaetosphaeronema that also belongs to the Phaeosphaeriaceae. Pyrenochaetopsis gen. nov. is introduced to accommodate the type species Pyrenochaetopsis leptospora comb. nov., as well as several other species formerly accommodated in Phoma and Pyrenochaeta. Pyrenochaetopsis is closely related to Pyrenochaeta and classified in the Cucurbitariaceae. Pleurophoma cava is transferred to genus Pyrenochaeta. The new genera elucidate the confusing taxonomy of species in genera Phoma, Pyrenochaeta and Pleurophoma and recognize monophyletic genera with distinct teleomorph affinities.
Ooencyrtus marcelloi sp. nov. (Hymenoptera: Encyrtidae), an egg parasitoid of Heliconiini (Lepidoptera: Nymphalidae: Heliconiinae) on passion vines (Malpighiales: Passifloraceae) in Central America
Guerrieri, E. ; Huigens, M.E. ; Estrada, C. ; Woelke, J.B. ; Rijk, M. de; Fatouros, N.E. ; Aiello, A. ; Noyes, J.S. - \ 2010
Journal of Natural History 44 (2010)1-2. - ISSN 0022-2933 - p. 81 - 87.
genera
A new species belonging to the genus Ooencyrtus Ashmead is described. Ooencyrtus marcelloi sp. nov. has been reared from eggs of Heliconiini (Lepidoptera: Nymphalidae, Heliconiinae) collected in Panama on Passiflora spp. The new species is compared with its closest Ooencyrtus species, i.e. O. caligo Noyes, O. neustriae Mercet, O. flavipes (Timberlake), O. camerounensis (Risbec), O. endymion Huang and Noyes and Ooencyrtus sp. “undet. C.” (from India). This represents the second record of Ooencyrtus from Heliconinae and the first record of this genus from Panama.
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