Rapid Characterization of Aquatic Hyphomycetes by Matrix-Assisted
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Development and Evaluation of Rrna Targeted in Situ Probes and Phylogenetic Relationships of Freshwater Fungi
Development and evaluation of rRNA targeted in situ probes and phylogenetic relationships of freshwater fungi vorgelegt von Diplom-Biologin Christiane Baschien aus Berlin Von der Fakultät III - Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat. - genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. sc. techn. Lutz-Günter Fleischer Berichter: Prof. Dr. rer. nat. Ulrich Szewzyk Berichter: Prof. Dr. rer. nat. Felix Bärlocher Berichter: Dr. habil. Werner Manz Tag der wissenschaftlichen Aussprache: 19.05.2003 Berlin 2003 D83 Table of contents INTRODUCTION ..................................................................................................................................... 1 MATERIAL AND METHODS .................................................................................................................. 8 1. Used organisms ............................................................................................................................. 8 2. Media, culture conditions, maintenance of cultures and harvest procedure.................................. 9 2.1. Culture media........................................................................................................................... 9 2.2. Culture conditions .................................................................................................................. 10 2.3. Maintenance of cultures.........................................................................................................10 -
Preliminary Classification of Leotiomycetes
Mycosphere 10(1): 310–489 (2019) www.mycosphere.org ISSN 2077 7019 Article Doi 10.5943/mycosphere/10/1/7 Preliminary classification of Leotiomycetes Ekanayaka AH1,2, Hyde KD1,2, Gentekaki E2,3, McKenzie EHC4, Zhao Q1,*, Bulgakov TS5, Camporesi E6,7 1Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China 2Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand 3School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand 4Landcare Research Manaaki Whenua, Private Bag 92170, Auckland, New Zealand 5Russian Research Institute of Floriculture and Subtropical Crops, 2/28 Yana Fabritsiusa Street, Sochi 354002, Krasnodar region, Russia 6A.M.B. Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forlì, Italy. 7A.M.B. Circolo Micologico “Giovanni Carini”, C.P. 314 Brescia, Italy. Ekanayaka AH, Hyde KD, Gentekaki E, McKenzie EHC, Zhao Q, Bulgakov TS, Camporesi E 2019 – Preliminary classification of Leotiomycetes. Mycosphere 10(1), 310–489, Doi 10.5943/mycosphere/10/1/7 Abstract Leotiomycetes is regarded as the inoperculate class of discomycetes within the phylum Ascomycota. Taxa are mainly characterized by asci with a simple pore blueing in Melzer’s reagent, although some taxa have lost this character. The monophyly of this class has been verified in several recent molecular studies. However, circumscription of the orders, families and generic level delimitation are still unsettled. This paper provides a modified backbone tree for the class Leotiomycetes based on phylogenetic analysis of combined ITS, LSU, SSU, TEF, and RPB2 loci. In the phylogenetic analysis, Leotiomycetes separates into 19 clades, which can be recognized as orders and order-level clades. -
Phylogeny and Taxonomy of Obscure Genera of Microfungi
Persoonia 22, 2009: 139–161 www.persoonia.org RESEARCH ARTICLE doi:10.3767/003158509X461701 Phylogeny and taxonomy of obscure genera of microfungi P.W. Crous1, U. Braun2, M.J. Wingfield3, A.R. Wood4, H.D. Shin5, B.A. Summerell6, A.C. Alfenas7, C.J.R. Cumagun8, J.Z. Groenewald1 Key words Abstract The recently generated molecular phylogeny for the kingdom Fungi, on which a new classification scheme is based, still suffers from an under representation of numerous apparently asexual genera of microfungi. In an Brycekendrickomyces attempt to populate the Fungal Tree of Life, fresh samples of 10 obscure genera of hyphomycetes were collected. Chalastospora These fungi were subsequently established in culture, and subjected to DNA sequence analysis of the ITS and LSU Cyphellophora nrRNA genes to resolve species and generic questions related to these obscure genera. Brycekendrickomyces Dictyosporium (Herpotrichiellaceae) is introduced as a new genus similar to, but distinct from Haplographium and Lauriomyces. Edenia Chalastospora is shown to be a genus in the Pleosporales, with two new species, C. ellipsoidea and C. obclavata, phylogeny to which Alternaria malorum is added as an additional taxon under its oldest epithet, C. gossypii. Cyphellophora taxonomy eugeniae is newly described in Cyphellophora (Herpotrichiellaceae), and distinguished from other taxa in the genus. Thedgonia Dictyosporium is placed in the Pleosporales, with one new species, D. streliziae. The genus Edenia, which was Trochophora recently introduced for a sterile endophytic fungus isolated in Mexico, is shown to be a hyphomycete (Pleospo Verrucisporota rales) forming a pyronellea-like synanamorph in culture. Thedgonia is shown not to represent an anamorph of Vonarxia Mycosphaerella, but to belong to the Helotiales. -
Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two
(topsheet) Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113. Fieldiana, Botany H. Thorsten Lumbsch Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7881 fax: 312-665-7158 e-mail: [email protected] Sabine M. Huhndorf Dept. of Botany Field Museum 1400 S. Lake Shore Dr. Chicago, IL 60605 (312) 665-7855 fax: 312-665-7158 e-mail: [email protected] 1 (cover page) FIELDIANA Botany NEW SERIES NO 00 Myconet Volume 14 Part One. Outine of Ascomycota – 2009 Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 H. Thorsten Lumbsch Sabine M. Huhndorf [Date] Publication 0000 PUBLISHED BY THE FIELD MUSEUM OF NATURAL HISTORY 2 Table of Contents Abstract Part One. Outline of Ascomycota - 2009 Introduction Literature Cited Index to Ascomycota Subphylum Taphrinomycotina Class Neolectomycetes Class Pneumocystidomycetes Class Schizosaccharomycetes Class Taphrinomycetes Subphylum Saccharomycotina Class Saccharomycetes Subphylum Pezizomycotina Class Arthoniomycetes Class Dothideomycetes Subclass Dothideomycetidae Subclass Pleosporomycetidae Dothideomycetes incertae sedis: orders, families, genera Class Eurotiomycetes Subclass Chaetothyriomycetidae Subclass Eurotiomycetidae Subclass Mycocaliciomycetidae Class Geoglossomycetes Class Laboulbeniomycetes Class Lecanoromycetes Subclass Acarosporomycetidae Subclass Lecanoromycetidae Subclass Ostropomycetidae 3 Lecanoromycetes incertae sedis: orders, genera Class Leotiomycetes Leotiomycetes incertae sedis: families, genera Class Lichinomycetes Class Orbiliomycetes Class Pezizomycetes Class Sordariomycetes Subclass Hypocreomycetidae Subclass Sordariomycetidae Subclass Xylariomycetidae Sordariomycetes incertae sedis: orders, families, genera Pezizomycotina incertae sedis: orders, families Part Two. Notes on ascomycete systematics. Nos. 4751 – 5113 Introduction Literature Cited 4 Abstract Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota. -
Lichenicolous Species of Hainesia Belong to Phacidiales (Leotiomycetes) and Are Included in an Extended Concept of Epithamnolia
Mycologia ISSN: 0027-5514 (Print) 1557-2536 (Online) Journal homepage: http://www.tandfonline.com/loi/umyc20 Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia Ave Suija, Pieter van den Boom, Erich Zimmermann, Mikhail P. Zhurbenko & Paul Diederich To cite this article: Ave Suija, Pieter van den Boom, Erich Zimmermann, Mikhail P. Zhurbenko & Paul Diederich (2017): Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia, Mycologia, DOI: 10.1080/00275514.2017.1413891 To link to this article: https://doi.org/10.1080/00275514.2017.1413891 View supplementary material Accepted author version posted online: 13 Dec 2017. Published online: 08 Mar 2018. Submit your article to this journal Article views: 72 View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=umyc20 MYCOLOGIA https://doi.org/10.1080/00275514.2017.1413891 Lichenicolous species of Hainesia belong to Phacidiales (Leotiomycetes) and are included in an extended concept of Epithamnolia Ave Suija a, Pieter van den Boomb, Erich Zimmermannc, Mikhail P. Zhurbenko d, and Paul Diederiche aInstitute of Ecology and Earth Sciences, University of Tartu, 40 Lai Street, 51005 Tartu, Estonia; bArafura 16, NL-5691 JA Son, The Netherlands; cScheunenberg 46, CH-3251 Wengi, Switzerland; dKomarov Botanical Institute, Professor Popov 2, St. Petersburg, 197376, Russia; eMusée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg ABSTRACT ARTICLE HISTORY The lichenicolous taxa currently included in the genus Hainesia were studied based on the nuclear Received 4 April 2017 rDNA (18S, 28S, and internal transcribed spacer [ITS]) genes. -
Evolution of Helotialean Fungi (Leotiomycetes, Pezizomycotina): a Nuclear Rdna Phylogeny
Molecular Phylogenetics and Evolution 41 (2006) 295–312 www.elsevier.com/locate/ympev Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny Zheng Wang a,¤, Manfred Binder a, Conrad L. Schoch b, Peter R. Johnston c, Joseph W. Spatafora b, David S. Hibbett a a Department of Biology, Clark University, 950 Main Street, Worcester, MA 01610, USA b Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA c Herbarium PDD, Landcare Research, Private bag 92170, Auckland, New Zealand Received 5 December 2005; revised 21 April 2006; accepted 24 May 2006 Available online 3 June 2006 Abstract The highly divergent characters of morphology, ecology, and biology in the Helotiales make it one of the most problematic groups in traditional classiWcation and molecular phylogeny. Sequences of three rDNA regions, SSU, LSU, and 5.8S rDNA, were generated for 50 helotialean fungi, representing 11 out of 13 families in the current classiWcation. Data sets with diVerent compositions were assembled, and parsimony and Bayesian analyses were performed. The phylogenetic distribution of lifestyle and ecological factors was assessed. Plant endophytism is distributed across multiple clades in the Leotiomycetes. Our results suggest that (1) the inclusion of LSU rDNA and a wider taxon sampling greatly improves resolution of the Helotiales phylogeny, however, the usefulness of rDNA in resolving the deep relationships within the Leotiomycetes is limited; (2) a new class Geoglossomycetes, including Geoglossum, Trichoglossum, and Sarcoleo- tia, is the basal lineage of the Leotiomyceta; (3) the Leotiomycetes, including the Helotiales, Erysiphales, Cyttariales, Rhytismatales, and Myxotrichaceae, is monophyletic; and (4) nine clades can be recognized within the Helotiales. -
Ricardo De Nardi Fonoff
Universidade de São Paulo Escola Superior de Agricultura “Luiz de Queiroz” Diversidade de fungos do solo da Mata Atlântica Vívian Gonçalves Carvalho Tese apresentada para obtenção do título de Doutor em Ciências. Área de concentração: Microbiologia Agrícola Piracicaba 2012 2 Vívian Gonçalves Carvalho Bacharel e Licenciada em Ciências Biológicas Diversidade de fungos do solo da Mata Atlântica versão revisada de acordo com a resolução CoPGr 6018 de 2011 Orientador: Prof. Dr. MARCIO RODRIGUES LAMBAIS Tese apresentada para obtenção do título de Doutor em Ciências. Área de concentração: Microbiologia Agrícola Piracicaba 2012 Dados Internacionais de Catalogação na Publicação DIVISÃO DE BIBLIOTECA - ESALQ/USP Carvalho, Vívian Gonçalves Diversidade de fungos do solo da Mata Atlântica / Vívian Gonçalves Carvalho. - - versão revisada de acordo com a resolução CoPGr 6018 de 2011. - - Piracicaba, 2012. 203 p. : il. Tese (Doutorado) - - Escola Superior de Agricultura “Luiz de Queiroz”, 2012. 1. Biodiversidade 2. Fungos - Mata Atlântica 3. Filogenia 4. Matéria orgânica do solo 5. Microbiologia do solo 6. Reação em cadeia por polimerase 7. Redes neurais I. Título CDD 631.46 C331d “Permitida a cópia total ou parcial deste documento, desde que citada a fonte – O autor” 3 Dedico este trabalho aos meus pais, Célia e Afrânio , por me ajudarem a realizar meus sonhos, pelo apoio incessante aos meus estudos, pelo amor que sempre deram. Aos meus irmãos, Ana Cláudia, Vinícius e Afrânio, pelo apoio, amor e por entenderem minha ausência. Aos meus sobrinhos, Isabella, Felipe e Samira, minhas alegrias. À vó Ana (in memorian), pelas orações, carinho, e força sempre. Vocês foram essenciais para que eu chegasse até aqui. -
Dominated Forest Plot in Southern Ontario and the Phylogenetic Placement of a New Ascomycota Subphylum
Above and Below Ground Fungal Diversity in a Hemlock- Dominated Forest Plot in Southern Ontario and the Phylogenetic Placement of a New Ascomycota Subphylum by Teresita Mae McLenon-Porter A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Ecology and Evolutionary Biology University of Toronto © Copyright by Teresita Mae McLenon-Porter 2008 Above and below ground fungal diversity in a Hemlock- dominated forest plot in southern Ontario and the phylogenetic placement of a new Ascomycota subphylum Teresita Mae McLenon-Porter Doctor of Philosophy Ecology and Evolutionary Biology University of Toronto 2008 General Abstract The objective of this thesis was to assess the diversity and community structure of fungi in a forest plot in Ontario using a variety of field sampling and analytical methods. Three broad questions were addressed: 1) How do different measures affect the resulting view of fungal diversity? 2) Do fruiting bodies and soil rDNA sampling detect the same phylogenetic and ecological groups of Agaricomycotina? 3) Will additional rDNA sampling resolve the phylogenetic position of unclassified fungal sequences recovered from environmental sampling? Generally, richness, abundance, and phylogenetic diversity (PD) correspond and identify the same dominant fungal groups in the study site, although in different proportions. Clades with longer branch lengths tend to comprise a larger proportion of diversity when assessed using PD. Three phylogenetic-based comparisons were found to be variable in their ability to ii detect significant differences. Generally, the Unifrac significance measure (Lozupone et al., 2006) is the most conservative, followed by the P-test (Martin, 2002), and Libshuff library comparison (Singleton et al., 2001) with our dataset. -
BB RR TT 22000066 a Molecular Phylogenetic Study of Selected In
BBB RRR TTT 222000000666 .. Research Reports A Molecular Phylogenetic Study of Selected in Goldian Species Nattawut Boonyuen1,2, Somsak Sivichai2, Jeerapun Worapong1,3 and Nigel Hywel-Jones2 1Department of Biotechnology, Faculty of Science, Mahidol University, Rajdhevee, Bangkok 10400, Thailand, 2BIOTEC, National Center for Genetic Engineering and Biotechnology, Khlong Luang, Pathumthani 12120, Thailand, 3Center for Biotechnology, Institute of Science and Technology for Research and Development, Mahidol University, Bhudthamonthon 4 Rd., Nakornpathom 73170, Thailand Taxonomic studies of Ingoldian fungi are chiefly based on morphological and ontogenetic traits. However, some of them need to be reclassified especially at the genus and species levels. Sivichai et al. (2003) proposed that the anamorph of Hymenoscyphus varicosporoides is a waiting to be described species of Tricladium rather than of the genus Varicosporium sp. as originally delineated by Tubaki (1966). Additionally, the two species, H. varicosporoides and Cudoniella indica, possess almost the same morphological characteristics except for differences in asci staining. Thus, we conducted a molecular phylogenic analysis of complete ITS1-5.8S-ITS2 sequences of 37 selected Ingoldian taxa in Helotiaceae to clarify sexual-asexual links among these two conspecific genera. Significantly, phylogenetic data suggested that 37 selected genera formed a monophyletic group in Helotiaceae, Helotiales. The results indicate that both type species have an anamorph best assigned to T. indicum with a well-supported clade (82%) containing either teleomorph genera of H. varicosporoides, C. indica, or its anamorph. The molecular data suggest that the presence or absence of a staining reaction for the apical ring is not a phylogenetically reliable character. The highly significant identity 98-99.5% of ITS1-2 and 5.8S regions of C. -
Evolution of Reproductive Morphology in Leaf Endophytes
Evolution of Reproductive Morphology in Leaf Endophytes Zheng Wang1*, Peter R. Johnston2, Zhu L. Yang3, Jeffrey P. Townsend1 1 Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America, 2 Herbarium PDD, Landcare Research, Auckland, New Zealand, 3 Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China Abstract The endophytic lifestyle has played an important role in the evolution of the morphology of reproductive structures (body) in one of the most problematic groups in fungal classification, the Leotiomycetes (Ascomycota). Mapping fungal morphologies to two groups in the Leiotiomycetes, the Rhytismatales and Hemiphacidiaceae reveals significant divergence in body size, shape and complexity. Mapping ecological roles to these taxa reveals that the groups include endophytic fungi living on leaves and saprobic fungi living on duff or dead wood. Finally, mapping of the morphologies to ecological roles reveals that leaf endophytes produce small, highly reduced fruiting bodies covered with fungal tissue or dead host tissue, while saprobic species produce large and intricate fruiting bodies. Intriguingly, resemblance between asexual conidiomata and sexual ascomata in some leotiomycetes implicates some common developmental pathways for sexual and asexual development in these fungi. Citation: Wang Z, Johnston PR, Yang ZL, Townsend JP (2009) Evolution of Reproductive Morphology in Leaf Endophytes. PLoS ONE 4(1): e4246. doi:10.1371/ journal.pone.0004246 Editor: Jerome Chave, Centre National de la Recherche Scientifique, France Received September 25, 2008; Accepted December 17, 2008; Published January 22, 2009 Copyright: ß 2009 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. -
Fungal Systematics and Evolution PAGES 169–215
VOLUME 1 JUNE 2018 Fungal Systematics and Evolution PAGES 169–215 doi.org/10.3114/fuse.2018.01.08 New and Interesting Fungi. 1 P.W. Crous1,2,3*, R.K. Schumacher4, M.J. Wingfield5, A. Akulov6, S. Denman7, J. Roux2, U. Braun8, T.I. Burgess9, A.J. Carnegie10, K.Z. Váczy11, E. Guatimosim12, P.B. Schwartsburd13, R.W. Barreto14, M. Hernández-Restrepo1, L. Lombard1, J.Z. Groenewald1 1Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands 2Department of Genetics, Biochemistry and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa 3Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands 4Hölderlinstraße 25, 15517 Fürstenwalde / Spree, Germany 5Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa 6Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine 7Forest Research, Alice Holt Lodge, Farnham, Surrey, UK 8Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik und Botanischer Garten, Herbarium, Neuwerk 21, 06099 Halle (Saale), Germany 9Centre for Phytophthora Science and Management, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia 10Forest Health & Biosecurity, NSW Department of Primary Industries, Level 12, 10 Valentine Ave, Parramatta NSW 2150, Locked Bag 5123, Parramatta NSW 2124, Australia 11Centre for Research and Development, Eszterházy Károly University, H-3300 Eger, Hungary 12Instituto de Ciências Biológicas, Universidade Federal do Rio Grande, CEP: 96170-000, São Lourenço do Sul, Brazil 13Departamento de Biologia Vegetal, Universidade Federal de Viçosa, CEP: 36.570-900, Viçosa, Minas Gerais, Brazil 14Departamento de Fitopatologia, Universidade Federal de Viçosa, CEP: 36.570-900, Viçosa, Minas Gerais, Brazil *Corresponding author: [email protected] Editor-in-Chief KeyProf. -
Helotiales, Ascomycota) Based on Cultural, Morphological, and Molecular Studies1
American Journal of Botany 92(9): 1565–1574. 2005. LIFE HISTORY AND SYSTEMATICS OF THE AQUATIC DISCOMYCETE MITRULA (HELOTIALES, ASCOMYCOTA) BASED ON CULTURAL, MORPHOLOGICAL, AND MOLECULAR STUDIES1 ZHENG WANG,2 MANFRED BINDER, AND DAVID S. HIBBETT Department of Biology, Clark University, 950 Main Street, Worcester, Massachusetts 01610 USA Mitrula species represent a group of aquatic discomycetes with uncertain position in the Helotiales and an unknown life history. Mitrula species were studied using a combination of cultural, morphological, and molecular techniques. Pure colonies were isolated from Mitrula elegans, and conidia were induced in vitro. Herbarium materials from Europe, Asia, and North America were studied. Sequences of rDNA, including partial small subunit rDNA, large subunit DNA and ITS, were used to infer phylogenetic relationships both within Mitrula and between Mitrula and other inoperculate discomycetes, with special attention to fungi that resemble Mitrula in morphology or ecology. Equally weighted parsimony analyses, likelihood analyses, constrained parsimony analyses, and Bayesian analyses were performed. Results suggest that (1) the anamorph of M. elegans produces brown bicellular conidia, (2) a new subalpine species M. brevispora is distinct, (3) more than six lineages and clades can be recognized in Mitrula, (4) the morphological species M. elegans is not monophyletic, (5) a close relationship between Mitrula and either Geoglossaceae or Sclerotiniaceae is not supported, (6) the Helotiaceae is paraphyletic, and (7) Mitrula belongs to a clade within the Helotiales that also includes other aero-aquatic genera, Cudoniella, Hydrocina, Vibrissea, Ombrophila, and Hymenoscyphus. Key words: aquatic fungi; decomposition; ecology; mitosporic fungi; vernal pools. Mitrula Fr. species, the so-called swamp beacons, represent litter in forest ecosystems.