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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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.
The Ascomycota tree of life: a phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits
Schoch, C.L. ; Sung, G.H. ; López-Giráldez, F. ; Townsend, J.P. ; Miadlikowska, J. ; Hofstetter, V. ; Robbertse, B. ; Brandon Matheny, P. ; Kauff, F. ; Wang, Z. ; Gueidan, C. ; Andrie, R.M. ; Trippe, K. ; Ciufetti, L.M. ; Wynns, A. ; Fraker, E. ; Hodkinson, B.P. ; Bonito, G. ; Groenewald, J.Z. ; Arzanlou, M. ; Hoog, G.S. de; Crous, P.W. ; Hewitt, D. ; Pfister, D.H. ; Peterson, K. ; Gryzenhout, M. ; Wingfield, M.J. ; Aptroot, A. ; Suh, S.O. ; Blackwell, M. ; Hillis, D.M. ; Griffith, G.W. ; Castlebury, L.A. ; Rossman, A.Y. ; Lumbsch, H.T. ; Lücking, R. ; Büdel, B. ; Rauhut, A. ; Diederich, P. ; Ertz, D. ; Geiser, D.M. ; Hosaka, K. ; Inderbitzin, P. ; Kohlmeyer, J. ; Volkmann-Kohlmeyer, B. ; Mostert, L. ; O'Donnell, K. ; Sipman, H. ; Rogers, J.D. ; Shoemaker, R.A. ; Sugiyama, J. ; Summerbell, R.C. ; Untereiner, W. ; Johnston, P.R. ; Stenroos, S. ; Zuccaro, A. ; Dyer, P.S. ; Crittenden, P.D. ; Cole, M.S. ; Hansen, K. ; Trappe, J.M. ; Yahr, R. ; Lutzoni, F. ; Spatafora, J.W. - \ 2009
Systematic Biology 58 (2009)2. - ISSN 1063-5157 - p. 224 - 239.
rna-polymerase-ii - multiple sequence alignment - fungal lineages - cleistothecial fungi - classification - subunit - pezizomycotina - divergence - morphology - eukaryotes
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.
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.
Reconstructing the early evolution of the fungi using a six gene phylogeny
James, T.Y. ; Kauff, F. ; Schoch, C.L. ; Matheny, P.B. ; Hofstetter, V. ; Cox, C.J. ; Celio, G. ; Gueidan, C. ; Fraker, E. ; Miadlikowska, J. ; Lumbsch, H.T. ; Rauhut, A. ; Reeb, V. ; Arnold, A.E. ; Amtoft, A. ; Stajich, J.E. ; Hosaka, K. ; Sung, G.H. ; Johnson, D. ; O'Rourke, B. ; Binder, M. ; Curtis, J.M. ; Slot, J.C. ; Wang, Z. ; Wilson, A.W. ; Schüßler, A. ; Longcore, J.E. ; O'Donnell, K. ; Mozley-Standridge, S. ; Porter, D. ; Letcher, P.M. ; Powell, M.J. ; Taylor, J.W. ; White, M.M. ; Griffith, G.W. ; Davies, D.R. ; Sugiyama, J. ; Rossman, A.Y. ; Rogers, J.D. ; Pfister, D.H. ; Hewitt, D. ; Hansen, K. ; Hambleton, S. ; Shoemaker, R.A. ; Kohlmeyer, J. ; Volkmann-Kohlmeyer, B. ; Spotts, R.A. ; Serdani, M. ; Crous, P.W. ; Hughes, K.W. ; Matsuura, K. ; Langer, E. ; Langer, G. ; Untereiner, W.A. ; Lücking, R. ; Büdel, B. ; Geiser, D.M. ; Aptroot, A. ; Diederich, P. ; Schmitt, I. ; Schultz, M. ; Yahr, R. ; Hibbett, D.S. ; Lutzoni, F. ; McLaughlin, D.J. ; Spatafora, J.W. ; Vilgalys, R. - \ 2006
Nature 443 (2006)7113. - ISSN 0028-0836 - p. 818 - 822.
arbuscular mycorrhizal fungi - molecular phylogeny - maximum-likelihood - land plants - tree - microsporidia - sequences - animals - chytridiomycota - glomeromycota
The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree
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