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.
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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