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 genera of Fungi: fixing the application of type species of generic names
Crous, P.W. ; Giraldo, A. ; Hawksworth, D.L. ; Robert, V. ; Kirk, P.M. ; Guarro, J. ; Robbertse, B. ; Schoch, C.L. ; Damm, U. ; Trakunyingcharoen, T. ; Groenewald, J.Z. - \ 2014
IMA fungus 5 (2014)1. - ISSN 2210-6340 - p. 141 - 160.
To ensure a stable platform for fungal taxonomy, it is of paramount importance that the genetic application of generic names be based on their DNA sequence data, and wherever possible, not morphology or ecology alone. To facilitate this process, a new database, accessible at www.GeneraofFungi.org (GoF) was established, which will allow deposition of metadata linked to holo-, lecto-, neo- or epitype specimens, cultures and DNA sequence data of the type species of genera. Although there are presently more than 18 000 fungal genera described, we aim to initially focus on the subset of names that have been placed on the “Without-prejudice List of Protected Generic Names of Fungi” (see IMA Fungus 4 (2): 381–443, 2013). To enable the global mycological community to keep track of typification events and avoid duplication, special MycoBank Typification identfiers (MBT) will be issued upon deposit of metadata in MycoBank. MycoBank is linked to GoF, thus deposited metadata of generic type species will be displayed in GoF (and vice versa), but will also be linked to Index Fungorum (IF) and the curated RefSeq Targeted Loci (RTL) database in GenBank at the National Center for Biotechnology Information (NCBI). This initial paper focuses on eight genera of appendaged coelomycetes, the type species of which are neo- or epitypified here: Bartalinia (Bartalinia robillardoides; Amphisphaeriaceae, Xylariales), Chaetospermum (Chaetospermum chaetosporum, incertae sedis, Sebacinales), Coniella (Coniella fragariae, Schizoparmaceae, Diaporthales), Crinitospora (Crinitospora pulchra, Melanconidaceae, Diaporthales), Eleutheromyces (Eleutheromyces subulatus, Helotiales), Kellermania (Kellermania yuccigena, Planistromataceae, Botryosphaeriales), Mastigosporium (Mastigosporium album, Helotiales), and Mycotribulus (Mycotribulus mirabilis, Agaricales). Authors interested in contributing accounts of individual genera to larger multi-authored papers to be published in IMA Fungus, should contact the associate editors listed below for the major groups of fungi on the List of Protected Generic Names for Fungi.
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Ohm, R.A. ; Feau, N. ; Henrissat, B. ; Schoch, C.L. ; Horwitz, B.A. ; Bradshaw, R.E. ; Ciuffetti, L. ; Hamelin, R.C. ; Kema, G.H.J. ; Lawrence, C. ; Scott, J.A. ; Spatafora, J.W. ; Turgeon, B.G. ; Wit, P.J.G.M. de; Zhong, S. ; Goodwin, S.B. ; Grigoriev, I.V. - \ 2013
In: Book of Abstracts 27th Fungal Genetics Conference, Asilomar, Pacific Grove, California, USA, 12-17 March 2013. - - p. 203 - 203.
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi
Ohm, R.A. ; Feau, N. ; Henrissat, B. ; Schoch, C.L. ; Horwitz, B.A. ; Barry, K.W. ; Condon, B.J. ; Copeland, A.C. ; Dhillon, B. ; Glaser, F. ; Hesse, C.N. ; Kosti, I. ; LaButti, K. ; Lindquist, E.A. ; Lucas, S. ; Salamov, A.A. ; Bradshaw, R.E. ; Ciuffetti, L. ; Hamelin, R.C. ; Kema, G.H.J. ; Lawrence, C. ; Scott, J.A. ; Spatafora, J.W. ; Turgeon, B.G. ; Wit, P.J.G.M. de; Zhong, S. ; Goodwin, S.B. ; Grigoriev, I.V. - \ 2012
PLoS Pathogens 8 (2012)12. - ISSN 1553-7366
ascomycete leptosphaeria-maculans - nonribosomal peptide synthetases - induced point mutations - polyketide synthase - cochliobolus-heterostrophus - colletotrichum-graminicola - fusarium-graminearum - stagonospora-nodorum - phylogenetic trees - neurospora-crassa
The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Schoch, C.L. ; Seifert, K.A. ; Huhndorf, S. ; Robert, V. ; Spouge, J.L. ; Levesque, C.A. ; Chen, W. ; Crous, P.W. ; Boekhout, T. ; Damm, U. ; Hoog, G.S. de; Eberhardt, U. ; Groenewald, J.Z. ; Groenewald, M. ; Hagen, F. ; Houbraken, J. ; Quaedvlieg, W. ; Stielow, B. ; Vu, T.D. ; Walther, G. - \ 2012
Proceedings of the National Academy of Sciences of the United States of America 109 (2012)16. - ISSN 0027-8424 - p. 6241 - 6246.
arbuscular mycorrhizal fungi - phylogenetic-relationships - basidiomycetous yeasts - intragenomic variation - ectomycorrhizal fungi - species recognition - sequence-analysis - rpb1 sequences - rdna - subunit
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
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.
Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations
Rouxel, T. ; Grandaubert, J. ; Hane, J.K. ; Hoede, C. ; Wouw, A. ; Couloux, A. ; Dominguez, V. ; Anthouard, V. ; Bally, P. ; Bourras, S. ; Cozijnsen, A.J. ; Ciuffetti, L.M. ; Degrave, A. ; Dilmaghani, A. ; Duret, L. ; Fudal, L. ; Goodwin, S.B. ; Gout, L. ; Glaser, N. ; Linglin, J. ; Kema, G.H.J. ; Lapalu, N. ; Lawrence, C.B. ; May, K. ; Meyer, M. ; Ollivier, B. ; Poulain, J. ; Schoch, C.L. ; Simon, A. ; Spatafora, J.W. ; Stachowiak, A. ; Turgeon, B.G. ; Tyler, B.M. ; Vincent, D. ; Weissenbach, J. ; Amselem, J. ; Quesneville, H. ; Oliver, R.P. ; Wincker, P. ; Balesdent, M.H. ; Howlett, B.J. - \ 2011
Nature Communications 2 (2011). - ISSN 2041-1723 - p. 202 - 202.
transposable elements - molecular evolution - pathogen effectors - brassica-napus - gene-transfer - oilseed rape - stem canker - avirulence - plant - fungal
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints
Phylogeny of rock-inhabiting fungi related to Dothideomycetes
Ruibal, C. ; Gueidan, C. ; Selbmann, L. ; Gorbushina, A.A. ; Crous, P.W. ; Groenewald, J.Z. ; Muggia, L. ; Grube, M. ; Isola, D. ; Schoch, C.L. ; Staley, J.T. ; Lutzoni, F. ; Hoog, G.S. de - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 123 - 133.
subunit ribosomal dna - microcolonial fungi - meristematic fungi - lichenized fungi - antique marbles - black yeasts - pcr primers - evolution - ascomycota - life
The class Dothideomycetes (along with Eurotiomycetes) includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that tolerates surprisingly well harsh conditions prevailing on rock surfaces. Despite their convergent morphology and physiology, RIF are phylogenetically highly diverse in Dothideomycetes. However, the positions of main groups of RIF in this class remain unclear due to the lack of a strong phylogenetic framework. Moreover, connections between rock-dwelling habit and other lifestyles found in Dothideomycetes such as plant pathogens, saprobes and lichen-forming fungi are still unexplored. Based on multigene phylogenetic analyses, we report that RIF belong to Capnodiales (particularly to the family Teratosphaeriaceae s.l.), Dothideales, Pleosporales, and Myriangiales, as well as some uncharacterised groups with affinities to Dothideomycetes. Moreover, one lineage consisting exclusively of RIF proved to be closely related to Arthoniomycetes, the sister class of Dothideomycetes. The broad phylogenetic amplitude of RIF in Dothideomycetes suggests that total species richness in this class remains underestimated. Composition of some RIF-rich lineages suggests that rock surfaces are reservoirs for plant-associated fungi or saprobes, although other data also agree with rocks as a primary substrate for ancient fungal lineages. According to the current sampling, long distance dispersal seems to be common for RIF. Dothideomycetes lineages comprising lichens also include RIF, suggesting a possible link between rock-dwelling habit and lichenisation
Multi-locus phylogeny of Pleosporales: a taxonomic, ecological and evolutionary re-evaluation
Zhang, Y. ; Schoch, C.L. ; Fournier, J. ; Crous, P.W. ; Gruyter, J. de; Woudenberg, J.H.C. ; Hirayama, K. ; Tanaka, K. ; Pointing, S.B. ; Spatafora, J.W. ; Hyde, K.D. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 85 - 102.
ribosomal dna-sequences - stagonospora-nodorum - molecular phylogeny - leptosphaeria-maculans - phaeosphaeria-nodorum - multigene phylogeny - multiple alignment - endophytic fungi - sp-nov - ascomycota
Five loci, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, are used for analysing 129 pleosporalean taxa representing 59 genera and 15 families in the current classification of Pleosporales. The suborder Pleosporineae is emended to include four families, viz. Didymellaceae, Leptosphaeriaceae, Phaeosphaeriaceae and Pleosporaceae. In addition, two new families are introduced, i.e. Amniculicolaceae and Lentitheciaceae. Pleomassariaceae is treated as a synonym of Melanommataceae, and new circumscriptions of Lophiostomataceae s. str, Massarinaceae and Lophiotrema are proposed. Familial positions of Entodesmium and Setomelanomma in Phaeosphaeriaceae, Neophaeosphaeria in Leptosphaeriaceae, Leptosphaerulina, Macroventuria and Platychora in Didymellaceae, Pleomassaria in Melanommataceae and Bimuria, Didymocrea, Karstenula and Paraphaeosphaeria in Montagnulaceae are clarified. Both ecological and morphological characters show varying degrees of phylogenetic significance. Pleosporales is most likely derived from a saprobic ancestor with fissitunicate asci containing conspicuous ocular chambers and apical rings. Nutritional shifts in Pleosporales likely occured from saprotrophic to hemibiotrophic or biotrophic.
Phylogenetic lineages in the Capnodiales
Crous, P.W. ; Schoch, C.L. ; Hyde, K.D. ; Wood, A.R. ; Gueidan, C. ; Hoog, G.S. de; Groenewald, J.Z. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 17 - 47.
ribosomal dna-sequences - leaf spots - gen-nov - fungal pathogens - lichenized fungi - blotch-disease - crofton weed - south-africa - mycosphaerella - eucalyptus
The Capnodiales incorporates plant and human pathogens, endophytes, saprobes and epiphytes, with a wide range of nutritional modes. Several species are lichenised, or occur as parasites on fungi, or animals. The aim of the present study was to use DNA sequence data of the nuclear ribosomal small and large subunit RNA genes to test the monophyly of the Capnodiales, and resolve families within the order. We designed primers to allow the amplification and sequencing of almost the complete nuclear ribosomal small and large subunit RNA genes. Other than the Capnodiaceae (sooty moulds), and the Davidiellaceae, which contains saprobes and plant pathogens, the order presently incorporates families of major plant pathological importance such as the Mycosphaerellaceae, Teratosphaeriaceae and Schizothyriaceae. The Piedraiaceae was not supported, but resolves in the Teratosphaeriaceae. The Dissoconiaceae is introduced as a new family to accommodate Dissoconium and Ramichloridium. Lichenisation, as well as the ability to be saprobic or plant pathogenic evolved more than once in several families, though the taxa in the upper clades of the tree lead us to conclude that the strictly plant pathogenic, nectrotrophic families evolved from saprobic ancestors (Capnodiaceae), which is the more primitive state
A class-wide phylogenetic assessment of Dothideomycetes
Schoch, C.L. ; Crous, P.W. ; Groenewald, J.Z. ; Boehm, E.W.A. ; Burgess, T.I. ; Gruyter, J. de; Hoog, G.S. de; Dixon, L.J. ; Grube, M. ; Gueidan, C. ; Harada, Y. ; Hatakeyama, S. ; Hirayama, K. ; Hosoya, T. ; Huhndorf, S.M. ; Hyde, K.D. ; Jones, E.B.G. ; Kohlmeyer, J. ; Kruys, Å. ; Li, Y.M. ; Lücking, R. ; Lumbsch, H.T. ; Marvanová, L. ; Mbatchou, J.S. ; McVay, A.H. ; Miller, A.N. ; Mugambi, G.K. ; Muggia, L. ; Nelsen, M.P. ; Nelson, P. ; Owensby, C.A. ; Phillips, A.J.L. ; Phongpaichit, S. ; Pointing, S.B. ; Pujade-Renaud, V. ; Raja, H.A. ; Rivas Plata, E. ; Robbertse, B. ; Ruibal, C. ; Sakayaroj, J. ; Sano, T. ; Selbmann, L. ; Shearer, C.A. ; Shirouzu, T. ; Slippers, B. ; Suetrong, S. ; Tanaka, K. ; Volkmann-Kohlmeyer, B. ; Wingfield, M.J. ; Wood, A.R. ; Woudenberg, J.H.C. ; Yonezawa, H. ; Zhang, Y. ; Spatafora, J.W. - \ 2009
Studies in Mycology 64 (2009)1. - ISSN 0166-0616 - p. 1 - 15.
ribosomal dna-sequences - multigene phylogenies - molecular phylogeny - maximum-likelihood - multiple alignment - marine ascomycota - rdna sequences - fungi - evolution - classification
We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae is expanded to include the aquatic order Jahnulales. An ancestral reconstruction of basic nutritional modes supports numerous transitions from saprobic life histories to plant associated and lichenised modes and a transition from terrestrial to aquatic habitats are confirmed. Finally, a genomic comparison of 6 dothideomycete genomes with other fungi finds a high level of unique protein associated with the class, supporting its delineation as a separate taxon
A phylogenetic re-evaluation of Dothideomycetes
Schoch, C.L. ; Spatafora, J.W. ; Lumbsch, H.T. ; Huhndorf, S.M. ; Hyde, K.D. ; Groenewald, J.Z. ; Crous, P.W. - \ 2009
Utrecht, the Netherlands : CBS-KNAW (Studies in mycology 64) - ISBN 9789070351786 - 220
pezizomycotina - fylogenetica - fylogenie - evolutie - taxonomie - moleculaire taxonomie - phylogenetics - phylogeny - evolution - taxonomy - molecular taxonomy
This volume presents a re-evaluation of phylogenetic relationships within the class Dothideomycetes, which is by far the largest and arguably most phylogenetically diverse class within the largest fungal phylum, Ascomycota.
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.
Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum
Hane, J.K. ; Lowe, R.G.T. ; Solomon, P.S. ; Tan, K.C. ; Schoch, C.L. ; Spatafora, J.W. ; Crous, P.W. ; Kodira, C. ; Birren, B.W. ; Galagan, J.E. ; Torriani, S.F.F. ; McDonald, B.A. ; Oliver, R.P. - \ 2007
The Plant Cell 19 (2007)11. - ISSN 1040-4651 - p. 3347 - 3368.
polyketide synthase genes - rice blast fungus - anamorph fusarium-graminearum - pyrenophora-tritici-repentis - peptide synthetase gene - complete dna-sequence - magnaporthe-grisea - leptosphaeria-maculans - mitochondrial genome - functional-analysis
Stagonospora nodorum is a major necrotrophic fungal pathogen of wheat (Triticum aestivum) and a member of the Dothideomycetes, a large fungal taxon that includes many important plant pathogens affecting all major crop plant families. Here, we report the acquisition and initial analysis of a draft genome sequence for this fungus. The assembly comprises 37,164,227 bp of nuclear DNA contained in 107 scaffolds. The circular mitochondrial genome comprises 49,761 bp encoding 46 genes, including four that are intron encoded. The nuclear genome assembly contains 26 classes of repetitive DNA, comprising 4.5% of the genome. Some of the repeats show evidence of repeat-induced point mutations consistent with a frequent sexual cycle. ESTs and gene prediction models support a minimum of 10,762 nuclear genes. Extensive orthology was found between the polyketide synthase family in S. nodorum and Cochliobolus heterostrophus, suggesting an ancient origin and conserved functions for these genes. A striking feature of the gene catalog was the large number of genes predicted to encode secreted proteins; the majority has no meaningful similarity to any other known genes. It is likely that genes for host-specific toxins, in addition to ToxA, will be found among this group. ESTs obtained from axenic mycelium grown on oleate (chosen to mimic early infection) and late-stage lesions sporulating on wheat leaves were obtained. Statistical analysis shows that transcripts encoding proteins involved in protein synthesis and in the production of extracellular proteases, cellulases, and xylanases predominate in the infection library. This suggests that the fungus is dependant on the degradation of wheat macromolecular constituents to provide the carbon skeletons and energy for the synthesis of proteins and other components destined for the developing pycnidiospores.
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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