Doassansiopsis Tomasii, an Aquatic Smut New to Uganda
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Axpcoords & Parallel Axparafit: Statistical Co-Phylogenetic Analyses
BMC Bioinformatics BioMed Central Software Open Access AxPcoords & parallel AxParafit: statistical co-phylogenetic analyses on thousands of taxa Alexandros Stamatakis*1,2, Alexander F Auch3, Jan Meier-Kolthoff3 and Markus Göker4 Address: 1École Polytechnique Fédérale de Lausanne, School of Computer & Communication Sciences, Laboratory for Computational Biology and Bioinformatics STATION 14, CH-1015 Lausanne, Switzerland, 2Swiss Institute of Bioinformatics, 3Center for Bioinformatics (ZBIT), Sand 14, Tübingen, University of Tübingen, Germany and 4Organismic Botany/Mycology, Auf der Morgenstelle 1, Tübingen, University of Tübingen, Germany Email: Alexandros Stamatakis* - [email protected]; Alexander F Auch - [email protected]; Jan Meier- Kolthoff - [email protected]; Markus Göker - [email protected] * Corresponding author Published: 22 October 2007 Received: 26 June 2007 Accepted: 22 October 2007 BMC Bioinformatics 2007, 8:405 doi:10.1186/1471-2105-8-405 This article is available from: http://www.biomedcentral.com/1471-2105/8/405 © 2007 Stamatakis et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented in Parafit does not allow it to handle large datasets in reasonable times. The Parafit and DistPCoA programs are the by far most compute-intensive components of the Parafit analysis pipeline. -
Competing Sexual and Asexual Generic Names in <I
doi:10.5598/imafungus.2018.09.01.06 IMA FUNGUS · 9(1): 75–89 (2018) Competing sexual and asexual generic names in Pucciniomycotina and ARTICLE Ustilaginomycotina (Basidiomycota) and recommendations for use M. Catherine Aime1, Lisa A. Castlebury2, Mehrdad Abbasi1, Dominik Begerow3, Reinhard Berndt4, Roland Kirschner5, Ludmila Marvanová6, Yoshitaka Ono7, Mahajabeen Padamsee8, Markus Scholler9, Marco Thines10, and Amy Y. Rossman11 1Purdue University, Department of Botany and Plant Pathology, West Lafayette, IN 47901, USA; corresponding author e-mail: maime@purdue. edu 2Mycology & Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705, USA 3Ruhr-Universität Bochum, Geobotanik, ND 03/174, D-44801 Bochum, Germany 4ETH Zürich, Plant Ecological Genetics, Universitätstrasse 16, 8092 Zürich, Switzerland 5Department of Biomedical Sciences and Engineering, National Central University, 320 Taoyuan City, Taiwan 6Czech Collection of Microoorganisms, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic 7Faculty of Education, Ibaraki University, Mito, Ibaraki 310-8512, Japan 8Systematics Team, Manaaki Whenua Landcare Research, Auckland 1072, New Zealand 9Staatliches Museum f. Naturkunde Karlsruhe, Erbprinzenstr. 13, D-76133 Karlsruhe, Germany 10Senckenberg Gesellschaft für Naturforschung, Frankfurt (Main), Germany 11Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97333, USA Abstract: With the change to one scientific name for pleomorphic fungi, generic names typified by sexual and Key words: asexual morphs have been evaluated to recommend which name to use when two names represent the same genus Basidiomycetes and thus compete for use. In this paper, generic names in Pucciniomycotina and Ustilaginomycotina are evaluated pleomorphic fungi based on their type species to determine which names are synonyms. Twenty-one sets of sexually and asexually taxonomy typified names in Pucciniomycotina and eight sets in Ustilaginomycotina were determined to be congeneric and protected names compete for use. -
Phylogenetic Studies on Nuclear Large Subunit Ribosomal DNA Sequences of Smut Fungi and Related Taxar
2045 Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxar Dominik Begerow, Robert Bauer, and Franz Oberwinkler Abstract: To show phylogenetic relationships among the smut fungi and thcir relatives. we sequenced a part of the nuclear LSU rDNA from 43 different species of smut fungi and related taxa. Our data were combined with the existing sequences of seven further smut fungi and 17 other basidiomycetes. Two sets of sequences were analyzed. The first set with a representative number of simple septate basidiomycetes, complex scptate basidiomycetes, and smut fungi was analyzed with the neighbor-joining method to estimate the general topology of the basidiomycetes phylogeny and the positions of the smut fungi. The tripartite subclassification of the basidiomycetes into the Urediniomycetes, Ustilaginomycetes, and Hymcnomycetes was confirmed and two groups of smut fungi appeared. Thc smut genera Aurantiosporiurn, Microbotrl-unr, Fulvisporium, and Ustilentr-loma are members of the Urediniomycetes, whereas the other smut species tested are members of the Ustilaginomycetes wrth Entorrhiz.a as a basal taxon. The second set of 46 Ustilaginomycetes was analyzed using the neighbor-joining and the maximum parsimony methods to show the inner topology of the Ustilaginomycetes. The results indicated three major lineages among Ustilaginomycetes corresponding to the Entorrhizomycetidae, Exobasidiomycetidae, and Ustilaginomycetidae. The Entorrhizomycetidae are represented by Entorrhiza species. The Ustilaginomycctidae contain at least two groups, thc Urocystales and Ustilaginales. The Exobasidiomycetidae include five orders, i.e., Doassansiales, Entylomatales, Exobasidiales. Georgefischeriales. and Tilletiales, and Graphiola phoenicis and Microstroma juglandis. Our results support a classification mainly based on ultrastructure. The description of the Glomosporiaceae is emended. -
A Higher-Level Phylogenetic Classification of the Fungi
mycological research 111 (2007) 509–547 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycres A higher-level phylogenetic classification of the Fungi David S. HIBBETTa,*, Manfred BINDERa, Joseph F. BISCHOFFb, Meredith BLACKWELLc, Paul F. CANNONd, Ove E. ERIKSSONe, Sabine HUHNDORFf, Timothy JAMESg, Paul M. KIRKd, Robert LU¨ CKINGf, H. THORSTEN LUMBSCHf, Franc¸ois LUTZONIg, P. Brandon MATHENYa, David J. MCLAUGHLINh, Martha J. POWELLi, Scott REDHEAD j, Conrad L. SCHOCHk, Joseph W. SPATAFORAk, Joost A. STALPERSl, Rytas VILGALYSg, M. Catherine AIMEm, Andre´ APTROOTn, Robert BAUERo, Dominik BEGEROWp, Gerald L. BENNYq, Lisa A. CASTLEBURYm, Pedro W. CROUSl, Yu-Cheng DAIr, Walter GAMSl, David M. GEISERs, Gareth W. GRIFFITHt,Ce´cile GUEIDANg, David L. HAWKSWORTHu, Geir HESTMARKv, Kentaro HOSAKAw, Richard A. HUMBERx, Kevin D. HYDEy, Joseph E. IRONSIDEt, Urmas KO˜ LJALGz, Cletus P. KURTZMANaa, Karl-Henrik LARSSONab, Robert LICHTWARDTac, Joyce LONGCOREad, Jolanta MIA˛ DLIKOWSKAg, Andrew MILLERae, Jean-Marc MONCALVOaf, Sharon MOZLEY-STANDRIDGEag, Franz OBERWINKLERo, Erast PARMASTOah, Vale´rie REEBg, Jack D. ROGERSai, Claude ROUXaj, Leif RYVARDENak, Jose´ Paulo SAMPAIOal, Arthur SCHU¨ ßLERam, Junta SUGIYAMAan, R. Greg THORNao, Leif TIBELLap, Wendy A. UNTEREINERaq, Christopher WALKERar, Zheng WANGa, Alex WEIRas, Michael WEISSo, Merlin M. WHITEat, Katarina WINKAe, Yi-Jian YAOau, Ning ZHANGav aBiology Department, Clark University, Worcester, MA 01610, USA bNational Library of Medicine, National Center for Biotechnology Information, -
A Survey of Ballistosporic Phylloplane Yeasts in Baton Rouge, Louisiana
Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 2012 A survey of ballistosporic phylloplane yeasts in Baton Rouge, Louisiana Sebastian Albu Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Plant Sciences Commons Recommended Citation Albu, Sebastian, "A survey of ballistosporic phylloplane yeasts in Baton Rouge, Louisiana" (2012). LSU Master's Theses. 3017. https://digitalcommons.lsu.edu/gradschool_theses/3017 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. A SURVEY OF BALLISTOSPORIC PHYLLOPLANE YEASTS IN BATON ROUGE, LOUISIANA A Thesis Submitted to the Graduate Faculty of the Louisiana Sate University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Department of Plant Pathology by Sebastian Albu B.A., University of Pittsburgh, 2001 B.S., Metropolitan University of Denver, 2005 December 2012 Acknowledgments It would not have been possible to write this thesis without the guidance and support of many people. I would like to thank my major professor Dr. M. Catherine Aime for her incredible generosity and for imparting to me some of her vast knowledge and expertise of mycology and phylogenetics. Her unflagging dedication to the field has been an inspiration and continues to motivate me to do my best work. -
Notes, Outline and Divergence Times of Basidiomycota
Fungal Diversity (2019) 99:105–367 https://doi.org/10.1007/s13225-019-00435-4 (0123456789().,-volV)(0123456789().,- volV) Notes, outline and divergence times of Basidiomycota 1,2,3 1,4 3 5 5 Mao-Qiang He • Rui-Lin Zhao • Kevin D. Hyde • Dominik Begerow • Martin Kemler • 6 7 8,9 10 11 Andrey Yurkov • Eric H. C. McKenzie • Olivier Raspe´ • Makoto Kakishima • Santiago Sa´nchez-Ramı´rez • 12 13 14 15 16 Else C. Vellinga • Roy Halling • Viktor Papp • Ivan V. Zmitrovich • Bart Buyck • 8,9 3 17 18 1 Damien Ertz • Nalin N. Wijayawardene • Bao-Kai Cui • Nathan Schoutteten • Xin-Zhan Liu • 19 1 1,3 1 1 1 Tai-Hui Li • Yi-Jian Yao • Xin-Yu Zhu • An-Qi Liu • Guo-Jie Li • Ming-Zhe Zhang • 1 1 20 21,22 23 Zhi-Lin Ling • Bin Cao • Vladimı´r Antonı´n • Teun Boekhout • Bianca Denise Barbosa da Silva • 18 24 25 26 27 Eske De Crop • Cony Decock • Ba´lint Dima • Arun Kumar Dutta • Jack W. Fell • 28 29 30 31 Jo´ zsef Geml • Masoomeh Ghobad-Nejhad • Admir J. Giachini • Tatiana B. Gibertoni • 32 33,34 17 35 Sergio P. Gorjo´ n • Danny Haelewaters • Shuang-Hui He • Brendan P. Hodkinson • 36 37 38 39 40,41 Egon Horak • Tamotsu Hoshino • Alfredo Justo • Young Woon Lim • Nelson Menolli Jr. • 42 43,44 45 46 47 Armin Mesˇic´ • Jean-Marc Moncalvo • Gregory M. Mueller • La´szlo´ G. Nagy • R. Henrik Nilsson • 48 48 49 2 Machiel Noordeloos • Jorinde Nuytinck • Takamichi Orihara • Cheewangkoon Ratchadawan • 50,51 52 53 Mario Rajchenberg • Alexandre G. -
The Phylocode Applied to <I>Cintractiellales</I>, a New Order
VOLUME 6 DECEMBER 2020 Fungal Systematics and Evolution PAGES 55–64 doi.org/10.3114/fuse.2020.06.04 The PhyloCode applied to Cintractiellales, a new order of smut fungi with unresolved phylogenetic relationships in theUstilaginomycotina A.R. McTaggart1,2, C.J. Prychid3,4, J.J. Bruhl3, R.G. Shivas5* 1Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, GPO Box 267, Brisbane 4001, Australia 2Department of Plant and Soil Sciences, Tree Protection Co-operative Programme (TPCP), Forestry and Agricultural Biotechnology Institute (FABI), Private Bag X20, University of Pretoria, Pretoria, Gauteng, South Africa 3School of Environmental and Rural Science, University of New England, Armidale 2351, New South Wales, Australia 4Current address: Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK 5Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia *Corresponding author: [email protected] The first two authors contributed equally to the manuscript Key words: Abstract: The PhyloCode is used to classify taxa based on their relation to a most recent common ancestor as recovered Cyperaceae pathogens from a phylogenetic analysis. We examined the first specimen of Cintractiella (Ustilaginomycotina) collected from fungal systematics Australia and determined its systematic relationship to other Fungi. Three ribosomal DNA loci were analysed both ITS with and without constraint to a phylogenomic hypothesis of the Ustilaginomycotina. Cintractiella did not share a LSU most recent common ancestor with other orders of smut fungi. We used the PhyloCode to define theCintractiellales , new taxa a monogeneric order with four species of Cintractiella, including C. scirpodendri sp. nov. on Scirpodendron ghaeri. -
SIM55 6Jul06.Indd
STUDIES IN MYCOLOGY 55: 289–298. 2006. Phylogeny of the Quambalariaceae fam. nov., including important Eucalyptus pathogens in South Africa and Australia Z. Wilhelm de Beer1*, Dominik Begerow2, Robert Bauer2, Geoff S. Pegg3, Pedro W. Crous4 and Michael J. Wingfield1 1Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa; 2Lehrstuhl Spezielle Botanik und Mykologie, Institut für Biologie I, Universität Tübingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germany; 3Department of Primary Industries and Fisheries, Horticulture and Forestry Science, Indooroopilly, Brisbane 4068; 4Centraalbureau voor Schimmelcultures, Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD, Utrecht, The Netherlands *Correspondence: Wilhelm de Beer, [email protected] Abstract: The genus Quambalaria consists of plant-pathogenic fungi causing disease on leaves and shoots of species of Eucalyptus and its close relative, Corymbia. The phylogenetic relationship of Quambalaria spp., previously classified in genera such as Sporothrix and Ramularia, has never been addressed. It has, however, been suggested that they belong to the basidiomycete orders Exobasidiales or Ustilaginales. The aim of this study was thus to consider the ordinal relationships of Q. eucalypti and Q. pitereka using ribosomal LSU sequences. Sequence data from the ITS nrDNA were used to determine the phylogenetic relationship of the two Quambalaria species together with Fugomyces (= Cerinosterus) cyanescens. In addition to sequence data, the ultrastructure of the septal pores of the species in question was compared. From the LSU sequence data it was concluded that Quambalaria spp. and F. cyanescens form a monophyletic clade in the Microstromatales, an order of the Ustilaginomycetes. -
A Higher Level Classification of All Living Organisms
RESEARCH ARTICLE A Higher Level Classification of All Living Organisms Michael A. Ruggiero1*, Dennis P. Gordon2, Thomas M. Orrell1, Nicolas Bailly3, Thierry Bourgoin4, Richard C. Brusca5, Thomas Cavalier-Smith6, Michael D. Guiry7, Paul M. Kirk8 1 Integrated Taxonomic Information System, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, United States of America, 2 National Institute of Water & Atmospheric Research, Wellington, New Zealand, 3 WorldFish—FIN, Los Baños, Philippines, 4 Institut Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 MNHN-CNRS-UPMC-EPHE, Sorbonne Universités, Museum National d'Histoire Naturelle, 57, rue Cuvier, CP 50, F-75005, Paris, France, 5 Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America, 6 Department of Zoology, University of Oxford, Oxford, United Kingdom, 7 The AlgaeBase Foundation & Irish Seaweed Research Group, Ryan Institute, National University of Ireland, Galway, Ireland, 8 Mycology Section, Royal Botanic Gardens, Kew, London, United Kingdom * [email protected] Abstract We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, OPEN ACCESS hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collab- orative effort is to provide a hierarchical classification serving not only the needs of the Citation: Ruggiero MA, Gordon DP, Orrell TM, Bailly CoL’s database providers but also the diverse public-domain user community, most of N, Bourgoin T, Brusca RC, et al. (2015) A Higher Level Classification of All Living Organisms. PLoS whom are familiar with the Linnaean conceptual system of ordering taxon relationships. -
Zusammenfassungen Der Arbeitskreisbeiträge
Deutsche Phytomedizinische Gesellschaft Zusammenfassungen der Arbeitskreisbeiträge 2011 Impressum Redaktion: Dr. Falko Feldmann, Dr. Christian Carstensen Deutsche Phytomedizinische Gesellschaft e. V. Messeweg 11/12 D-38104 Braunschweig Tel.: 0531 / 299-3213, Fax 0531 / 299-3019 E-mail: [email protected] www.phytomedizin.org ii INHALT DPG Symposium Plant Protection and Plant Health in Europe 2011 ......................................... 1 AK Herbologie ............................................................................................................................ 6 AK Mykologie........................................................................................................................... 10 AK Nematologie ....................................................................................................................... 21 AK Nutzarthropoden und Entomopathogene Nematoden ........................................................ 39 AK Pflanzenschutztechnik ........................................................................................................ 51 AK Phytobakteriologie .............................................................................................................. 59 AK Phytomedizin in Ackerbau und Grünland PG Schädlinge in Getreide und Mais ........................................................................... 65 PG Krankheiten an Getreide ............................................................................................... 68 AK Phytomedizin in Gartenbau -
Additions and Amendments to the List of British Smut Fungi
mycologist 20 (2006) 90– 96 available at www.sciencedirect.com journal homepage: www.elsevier.com/locate/mycol Additions and amendments to the list of British smut fungi B. M. SPOONER*, N. W. LEGON Mycology Section, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, U.K. abstract Keywords: Investigation of material of British smut fungi held in the national collections at kew (k) un- British Isles dertaken during preparation of the new checklist of British and Irish Basidiomycota (Legon New records et al. 2005) identified several species not hitherto known from the British Isles. These in- Smut fungi clude taxa not previously recognised due to earlier, broader species concepts, as well as Urediniomycetes others based on earlier misidentifications or discovered during examination of herbarium Ustilaginomycetes material of their host plants. These taxa are fully reported here. In addition, amendments to nomenclature and taxonomy of other British species which have occurred since the monography by Mordue & Ainsworth (1984) are summarised. ª 2006 The British Mycological Society. Published by Elsevier Ltd. All rights reserved. 1. Introduction taxonomy, to the extent that some taxa have been linked more closely with the rusts (Urediniomycetes). Furthermore, The first monographic treatment of the British smut fungi extensive revisions of some genera, e.g. Cintractia (Pie- (Ustilaginomycetes) was published by Plowright (1889) and in- penbring 2000), have been undertaken, and monographic re- cluded just 51 species. Enormous progress since then with visions of European taxa published by Va´nky (1994) and by regard both to taxonomic concepts and to study of the British Zogg (1985). species has resulted in extensive amendments and additions During preparation of the new Checklist of the British and to the list. -
Smut Fungi (Ustilaginomycetes and Microbotryales, Basidiomycota) in Panama
Rev. Biol. Trop., 49(2): 411-428, 2001 www.ucr.ac.cr www.ots.ac.cr www.ots.duke.edu Smut fungi (Ustilaginomycetes and Microbotryales, Basidiomycota) in Panama Meike Piepenbring Lehrstuhl Spezielle Botanik/Mykologie, Botanisches Institut, Universität Tübingen, Auf der Morgenstelle 1, 72076 Tübingen, Germany. Fax: 0049 7071 295344 E-mail: [email protected] Received 6-V-2000. Corrected 30-X-2000. Accepted 31-X-2000. Abstract: This is the first publication dedicated to the diversity of smut fungi in Panama based on field work, the study of herbarium specimens, and references taken from literature. It includes smuts parasitizing cultivated and wild plants. The latter are mostly found in rural vegetation. Among the 24 species cited here, 14 species are recorded for the first time for Panama. One of them, Sporisorium ovarium, is observed for the first time in Central America. Entyloma spilanthis is found on the host species Acmella papposa var. macrophylla (Asteraceae) for the first time. Entyloma costaricense and Entyloma ecuadorense are considered synonyms of Entyloma compositarum and Entyloma spilanthis respectively. For the new conbination Sponsorium panamensis see note at the end of this publication. Descriptions of the species are complemented by some illustrations, a checklist, and a key. Key words: Checklist, neotropics, Panama, smut fungi, Sponsorium panamensis, Tilletiales, Ustilaginales Smut fungi (Ustilaginomycetes and Micro- literature (Zundel 1939, 1953, Toler et al. 1959, botryales, Urediniomycetes; Basidiomycota; Dennis 1970, Comstock et al. 1983). Bauer et al. 1997, 2001) are parasites of plants, The check list in the present publication is especially herbs belonging to the Poaceae and far from complete, being based on only about Cyperaceae.