Phylogeny of Yeasts and Related Filamentous Fungi Within
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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. -
Bodenmikrobiologie (Version: 07/2019)
Langzeitmonitoring von Ökosystemprozessen - Methoden-Handbuch Modul 04: Bodenmikrobiologie (Version: 07/2019) www.hohetauern.at Impressum Impressum Für den Inhalt verantwortlich: Dr. Fernando Fernández Mendoza & Prof. Mag Dr. Martin Grube Institut für Biologie, Bereich Pflanzenwissenschaften, Universität Graz, Holteigasse 6, 8010 Graz Nationalparkrat Hohe Tauern, Kirchplatz 2, 9971 Matrei i.O. Titelbild: Ein Transekt im Untersuchungsgebiet Innergschlöss (2350 m üNN) wird im Jahr 2017 beprobt. © Newesely Zitiervorschlag: Fernández Mendoza F, Grube M (2019) Langzeitmonitoring von Ökosystemprozessen im Nationalpark Hohe Tauern. Modul 04: Mikrobiologie. Methoden-Handbuch. Verlag der Österreichischen Akademie der Wissenschaften, Wien. ISBN-Online: 978-3-7001-8752-3, doi: 10.1553/GCP_LZM_NPHT_Modul04 Weblink: https://verlag.oeaw.ac.at und http://www.parcs.at/npht/mmd_fullentry.php?docu_id=38612 Inhaltsverzeichnis Zielsetzung ...................................................................................................................................................... 1 Inhalt Vorbereitungsarbeit und benötigtes Material ................................................................................................... 2 a. Materialien für die Probenahme und Probenaufbewahrung ................................................................ 2 b. Materialien und Geräte für die Laboranalyse ...................................................................................... 2 Arbeitsablauf ................................................................................................................................................... -
The Flora Mycologica Iberica Project Fungi Occurrence Dataset
A peer-reviewed open-access journal MycoKeys 15: 59–72 (2016)The Flora Mycologica Iberica Project fungi occurrence dataset 59 doi: 10.3897/mycokeys.15.9765 DATA PAPER MycoKeys http://mycokeys.pensoft.net Launched to accelerate biodiversity research The Flora Mycologica Iberica Project fungi occurrence dataset Francisco Pando1, Margarita Dueñas1, Carlos Lado1, María Teresa Telleria1 1 Real Jardín Botánico-CSIC, Claudio Moyano 1, 28014, Madrid, Spain Corresponding author: Francisco Pando ([email protected]) Academic editor: C. Gueidan | Received 5 July 2016 | Accepted 25 August 2016 | Published 13 September 2016 Citation: Pando F, Dueñas M, Lado C, Telleria MT (2016) The Flora Mycologica Iberica Project fungi occurrence dataset. MycoKeys 15: 59–72. doi: 10.3897/mycokeys.15.9765 Resource citation: Pando F, Dueñas M, Lado C, Telleria MT (2016) Flora Mycologica Iberica Project fungi occurrence dataset. v1.18. Real Jardín Botánico (CSIC). Dataset/Occurrence. http://www.gbif.es/ipt/resource?r=floramicologicaiberi ca&v=1.18, http://doi.org/10.15468/sssx1e Abstract The dataset contains detailed distribution information on several fungal groups. The information has been revised, and in many times compiled, by expert mycologist(s) working on the monographs for the Flora Mycologica Iberica Project (FMI). Records comprise both collection and observational data, obtained from a variety of sources including field work, herbaria, and the literature. The dataset contains 59,235 records, of which 21,393 are georeferenced. These correspond to 2,445 species, grouped in 18 classes. The geographical scope of the dataset is Iberian Peninsula (Continental Portugal and Spain, and Andorra) and Balearic Islands. The complete dataset is available in Darwin Core Archive format via the Global Biodi- versity Information Facility (GBIF). -
Jason Stajich UC Riverside Fungidb Supported by Sloan Foundation
FungiDB and 1000 Fungal genomes Jason Stajich UC Riverside FungiDB supported by Sloan Foundation • Data coordinating center - Knight, Sogin, Meyer labs • Fungal microbiome support - Stajich Lab (Greg Gu, Steven Ahrendt) --> Scott Bates, Jon Leff Fierer Lab Fungal genome sequencing * ** 10-15 “Zygos” + Chytrids + Cryptomycota 400-500+ genomes of Fungi http://www.diark.org/diark/statistics http://1000.fungalgenomes.org Addressing the phylogenetic diversity: 1000 Fungal genomes project !"#$%&'%()*+#+,- !"#$%&'%()*+#+,- .%#$'/+%()*+#+,- .%#$'/+%()*+#+,- 01"%2%()*+#+,- 01"%2%()*+#+,- D+%E8%,,%()*+#+,- D+%E8%,,%()*+#+,- F+G'G%()*%2&4- 3&*+"#4+-,+/',- F+G'G%()*%2&4- 3&*+"#4+-,+/',- 547%187+&'%()*+#+,- 547%187+&'%()*+#+,- 5+*4&%"%()*+#+,- 5+*4&%"%()*+#+,- 5+%2%()*+#+,- 5+%2%()*+#+,- 5'*$'&%()*+#+,- 5'*$'&%()*+#+,- 6"7'8'%()*+#+,- 6"7'8'%()*+#+,- F+G'G%()*+#+,- F+G'G%()*+#+,- H4**$4"%()*%2&4- H%"/4"'%()*+#+,- H4**$4"%()*%2&4- H%"/4"'%()*+#+,- H4**$4"%()*+#+,- H4**$4"%()*+#+,- I+%8+*#%()*+#+,- I+%8+*#%()*+#+,- J4K$"'&%()*%2&4- F&+1(%*),2/'%()*+#+,- J4K$"'&%()*%2&4- F&+1(%*),2/'%()*+#+,- H*$'G%,4**$4"%()*+#+,- H*$'G%,4**$4"%()*+#+,- J4K$"'&%()*+#+,- J4K$"'&%()*+#+,- M,284E'&%()*%2&4- 0L%74,'/'%()*+#+,- M,284E'&%()*%2&4- 0L%74,'/'%()*+#+,- M,284E'&%()*+#+,- M,284E'&%()*+#+,- !E4"'*%,287%()*+#+,- !E4"'*%,287%()*+#+,- !#"4*2+88%()*+#+,- !#"4*2+88%()*+#+,- N84,,'*18%()*+#+,- N84,,'*18%()*+#+,- F1**'&'%()*%2&4- N")K#%()*%*%84*%()*+#+,- F1**'&'%()*%2&4- N")K#%()*%*%84*%()*+#+,- N),#%74,'/'%()*+#+,- N),#%74,'/'%()*+#+,- O'*"%7%#")%()*+#+,- O'*"%7%#")%()*+#+,- -
Crittendenia Gen. Nov., a New Lichenicolous Lineage in the Agaricostilbomycetes (Pucciniomycotina), and a Review of the Biology
The Lichenologist (2021), 53, 103–116 doi:10.1017/S002428292000033X Standard Paper Crittendenia gen. nov., a new lichenicolous lineage in the Agaricostilbomycetes (Pucciniomycotina), and a review of the biology, phylogeny and classification of lichenicolous heterobasidiomycetes Ana M. Millanes1, Paul Diederich2, Martin Westberg3 and Mats Wedin4 1Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain; 2Musée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg; 3Museum of Evolution, Norbyvägen 16, SE-75236 Uppsala, Sweden and 4Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden Abstract The lichenicolous ‘heterobasidiomycetes’ belong in the Tremellomycetes (Agaricomycotina) and in the Pucciniomycotina. In this paper, we provide an introduction and review of these lichenicolous taxa, focusing on recent studies and novelties of their classification, phylogeny and evolution. Lichen-inhabiting fungi in the Pucciniomycotina are represented by only a small number of species included in the genera Chionosphaera, Cyphobasidium and Lichenozyma. The phylogenetic position of the lichenicolous representatives of Chionosphaera has, however, never been investigated by molecular methods. Phylogenetic analyses using the nuclear SSU, ITS, and LSU ribosomal DNA mar- kers reveal that the lichenicolous members of Chionosphaera form a monophyletic group in the Pucciniomycotina, distinct from Chionosphaera and outside the Chionosphaeraceae. The new genus Crittendenia is described to accommodate these lichen-inhabiting spe- cies. Crittendenia is characterized by minute synnemata-like basidiomata, the presence of clamp connections and aseptate tubular basidia from which 4–7 spores discharge passively, often in groups. Crittendenia, Cyphobasidium and Lichenozyma are the only lichenicolous lineages known so far in the Pucciniomycotina, whereas Chionosphaera does not include any lichenicolous taxa. -
9B Taxonomy to Genus
Fungus and Lichen Genera in the NEMF Database Taxonomic hierarchy: phyllum > class (-etes) > order (-ales) > family (-ceae) > genus. Total number of genera in the database: 526 Anamorphic fungi (see p. 4), which are disseminated by propagules not formed from cells where meiosis has occurred, are presently not grouped by class, order, etc. Most propagules can be referred to as "conidia," but some are derived from unspecialized vegetative mycelium. A significant number are correlated with fungal states that produce spores derived from cells where meiosis has, or is assumed to have, occurred. These are, where known, members of the ascomycetes or basidiomycetes. However, in many cases, they are still undescribed, unrecognized or poorly known. (Explanation paraphrased from "Dictionary of the Fungi, 9th Edition.") Principal authority for this taxonomy is the Dictionary of the Fungi and its online database, www.indexfungorum.org. For lichens, see Lecanoromycetes on p. 3. Basidiomycota Aegerita Poria Macrolepiota Grandinia Poronidulus Melanophyllum Agaricomycetes Hyphoderma Postia Amanitaceae Cantharellales Meripilaceae Pycnoporellus Amanita Cantharellaceae Abortiporus Skeletocutis Bolbitiaceae Cantharellus Antrodia Trichaptum Agrocybe Craterellus Grifola Tyromyces Bolbitius Clavulinaceae Meripilus Sistotremataceae Conocybe Clavulina Physisporinus Trechispora Hebeloma Hydnaceae Meruliaceae Sparassidaceae Panaeolina Hydnum Climacodon Sparassis Clavariaceae Polyporales Gloeoporus Steccherinaceae Clavaria Albatrellaceae Hyphodermopsis Antrodiella -
The Isolation and Characterization of Resident Yeasts from the Phylloplane of Arabidopsis Thaliana Received: 12 July 2016 Kai Wang, Timo P
www.nature.com/scientificreports OPEN The isolation and characterization of resident yeasts from the phylloplane of Arabidopsis thaliana Received: 12 July 2016 Kai Wang, Timo P. Sipilä & Kirk Overmyer Accepted: 23 November 2016 The genetic model plant Arabidopsis thaliana (arabidopsis) has been instrumental to recent advances in Published: 22 December 2016 our understanding of the molecular function of the plant immune system. However, this work has not yet included plant associated and phytopathogenic yeasts largely due to a lack of yeast species known to interact with arabidopsis. The plant phylloplane is a significant habitat for neutral-residents, plant- growth and health-promoting species, and latent-pathogenic species. However, yeast phylloplane residents of arabidopsis remain underexplored. To address this, resident yeasts from the phyllosphere of wild arabidopsis collected in field conditions have been isolated and characterized. A total of 95 yeast strains representing 23 species in 9 genera were discovered, including potentially psychrophilic and pathogenic strains. Physiological characterization revealed thermotolerance profiles, sensitivity to the arabidopsis phytoalexin camalexin, the production of indolic compounds, and the ability to activate auxin responses in planta. These results indicate a rich diversity of yeasts present in the arabidopsis phylloplane and have created culture resources and information useful in the development of model systems for arabidopsis-yeast interactions. Plants constantly interact with a large number of microorganisms, including bacteria, oomycetes, filamentous fungi, and yeasts. Bacteria are the best studied plant-associated microbes and yeasts have received the least atten- tion. These microbes colonize all plant surfaces, where each plant compartment or structure has its own distinct microbiome. -
Using Rdptools Output with Phyloseq John Quensen & Qiong Wang October 23, 2015
Using RDPTools Output with Phyloseq John Quensen & Qiong Wang October 23, 2015 Introduction The purpose of this document is to demonstrate how to generate RDPTools (Cole et al., 2014) output from sequencing data and import it into the R/Bioconductor package phyloseq (McMurdie and Holmes, 2012). Once this is done, the data can be analyzed not only using phyloseq’s wrapper functions, but by any method available in R. For examples see the section Examples of Data Analysis below. You may install R from the Comprehensive R Archive Network (CRAN) repository at http://cran.us. r-project.org/. As an aid to working with R, we suggest that you also install RStudio, an IDE interface for R, available at http://www.rstudio.com/. By loading the Rmd file included with the tutorial files (see below) into RStudio, you can easily recreate the R portions of these tutorials on your own computer. And you can get an explanation of how to use any function in a code block by placing the cursor anywhere in the function name and pressing key F1. RDPTools The Ribosomal Database Project (RDP) at Michigan State University has long provided web-based tools for processing pyrosequencing data. These tools were originally developed for handling data for bacterial and archaeal 16S rRNA genes, but since then their capabilities have been expanded to include functional genes, 28S rRNA and ITS fungal sequences, and Illumina data. To handle the increased demands of analyzing larger data sets, command line versions of the tools have been made available as RDPTools on GitHub (https://github.com/rdpstaff/RDPTools). -
Crittendenia Gen. Nov., a New Lichenicolous Lineage in the Agaricostilbomycetes (Pucciniomycotina), and a Review of the Biology
The Lichenologist (2021), 53, 103–116 doi:10.1017/S002428292000033X Standard Paper Crittendenia gen. nov., a new lichenicolous lineage in the Agaricostilbomycetes (Pucciniomycotina), and a review of the biology, phylogeny and classification of lichenicolous heterobasidiomycetes Ana M. Millanes1, Paul Diederich2, Martin Westberg3 and Mats Wedin4 1Departamento de Biología y Geología, Física y Química Inorgánica, Universidad Rey Juan Carlos, E-28933 Móstoles, Spain; 2Musée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg; 3Museum of Evolution, Norbyvägen 16, SE-75236 Uppsala, Sweden and 4Department of Botany, Swedish Museum of Natural History, P.O. Box 50007, SE-10405 Stockholm, Sweden Abstract The lichenicolous ‘heterobasidiomycetes’ belong in the Tremellomycetes (Agaricomycotina) and in the Pucciniomycotina. In this paper, we provide an introduction and review of these lichenicolous taxa, focusing on recent studies and novelties of their classification, phylogeny and evolution. Lichen-inhabiting fungi in the Pucciniomycotina are represented by only a small number of species included in the genera Chionosphaera, Cyphobasidium and Lichenozyma. The phylogenetic position of the lichenicolous representatives of Chionosphaera has, however, never been investigated by molecular methods. Phylogenetic analyses using the nuclear SSU, ITS, and LSU ribosomal DNA mar- kers reveal that the lichenicolous members of Chionosphaera form a monophyletic group in the Pucciniomycotina, distinct from Chionosphaera and outside the Chionosphaeraceae. The new genus Crittendenia is described to accommodate these lichen-inhabiting spe- cies. Crittendenia is characterized by minute synnemata-like basidiomata, the presence of clamp connections and aseptate tubular basidia from which 4–7 spores discharge passively, often in groups. Crittendenia, Cyphobasidium and Lichenozyma are the only lichenicolous lineages known so far in the Pucciniomycotina, whereas Chionosphaera does not include any lichenicolous taxa. -
Downloaded from by IP: 199.133.24.106 On: Mon, 18 Sep 2017 10:43:32 Spatafora Et Al
UC Riverside UC Riverside Previously Published Works Title The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. Permalink https://escholarship.org/uc/item/4485m01m Journal Microbiology spectrum, 5(5) ISSN 2165-0497 Authors Spatafora, Joseph W Aime, M Catherine Grigoriev, Igor V et al. Publication Date 2017-09-01 DOI 10.1128/microbiolspec.funk-0053-2016 License https://creativecommons.org/licenses/by-nc-nd/4.0/ 4.0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies JOSEPH W. SPATAFORA,1 M. CATHERINE AIME,2 IGOR V. GRIGORIEV,3 FRANCIS MARTIN,4 JASON E. STAJICH,5 and MEREDITH BLACKWELL6 1Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; 2Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907; 3U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; 4Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d’Excellence Recherches Avancés sur la Biologie de l’Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France; 5Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California–Riverside, Riverside, CA 92521; 6Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208 ABSTRACT The kingdom Fungi is one of the more diverse INTRODUCTION clades of eukaryotes in terrestrial ecosystems, where they In 1996 the genome of Saccharomyces cerevisiae was provide numerous ecological services ranging from published and marked the beginning of a new era in decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and fungal biology (1). -
Fungal Allergy and Pathogenicity 20130415 112934.Pdf
Fungal Allergy and Pathogenicity Chemical Immunology Vol. 81 Series Editors Luciano Adorini, Milan Ken-ichi Arai, Tokyo Claudia Berek, Berlin Anne-Marie Schmitt-Verhulst, Marseille Basel · Freiburg · Paris · London · New York · New Delhi · Bangkok · Singapore · Tokyo · Sydney Fungal Allergy and Pathogenicity Volume Editors Michael Breitenbach, Salzburg Reto Crameri, Davos Samuel B. Lehrer, New Orleans, La. 48 figures, 11 in color and 22 tables, 2002 Basel · Freiburg · Paris · London · New York · New Delhi · Bangkok · Singapore · Tokyo · Sydney Chemical Immunology Formerly published as ‘Progress in Allergy’ (Founded 1939) Edited by Paul Kallos 1939–1988, Byron H. Waksman 1962–2002 Michael Breitenbach Professor, Department of Genetics and General Biology, University of Salzburg, Salzburg Reto Crameri Professor, Swiss Institute of Allergy and Asthma Research (SIAF), Davos Samuel B. Lehrer Professor, Clinical Immunology and Allergy, Tulane University School of Medicine, New Orleans, LA Bibliographic Indices. This publication is listed in bibliographic services, including Current Contents® and Index Medicus. Drug Dosage. The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any change in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug. All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means electronic or mechanical, including photocopying, recording, microcopy- ing, or by any information storage and retrieval system, without permission in writing from the publisher. -
Leucosporidium Himalayensis Fungal Planet Description Sheets 423
422 Persoonia – Volume 42, 2019 Leucosporidium himalayensis Fungal Planet description sheets 423 Fungal Planet 927 – 19 July 2019 Leucosporidium himalayensis S.M. Singh, Roh. Sharma & Shouche, sp. nov. Etymology. Name reflects the Himalaya, the place where this fungus was Notes — An initial BLASTn similarity search using the LSU collected. sequence of the ex-type culture with the NCBI nucleotide data- Classification — Leucosporidiaceae, Leucosporidiales, In base showed the highest similarity to Leucosporidium fragarium certae sedis, Microbotryomycetes. CBS 6254 (GenBank NG_058330; 99.5 % identity, 97 % query cover) followed by Sampaiozyma ingeniosa CBS 4240 (Gen- Yeast colonies on SD agar Petri dishes are creamy-white, rais- Bank NG_058398; 96.60 % identity; query coverage 96 %). ed, margin entire. In external appearance, the colonies have a The BLASTn similarity search of the ex-type ITS sequence with glabrous texture. Cells are subglobose to ovoid, 2–5 µm, oc- NCBIs database showed the highest similarity to Leucospori curring singly and budding is mostly polar, occurring frequently dium fragarium CBS 6254 (GenBank NR_073287; 94.45 % and repeatedly from the site of the primary budding scar. Sexual identity, 99 % query coverage) followed by Leucosporidium reproduction was not observed. Pseudohyphae formation ab- drummii CBS 11562 (GenBank NR_137036; 95.02 % identity, sent. Growth occurred at 15 °C which is very similar to the 99 % query coverage). The neighbour-joining (NJ) phyloge- primary habitat of this strain. Optimum growth was observed netic analyses of ITS and LSU rRNA regions was done using after 15 d. The following compounds are assimilated: D-xylose, sequences of other species of Leucosporidium. The combine D-saccharose, L-arabinose, Calcium-2-keto-gluconate.