DOCSLIB.ORG

Eukaryotic Plant Pathogen Detection Through High Throughput Dna/Rna Sequencing Data Analysis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Eukaryotic Plant Pathogen Detection Through High Throughput Dna/Rna Sequencing Data Analysis EUKARYOTIC PLANT PATHOGEN DETECTION THROUGH HIGH THROUGHPUT DNA/RNA SEQUENCING DATA ANALYSIS By ANDRES S. ESPINDOLA Bachelor of Science in Biotechnology Engineering Escuela Politécnica del Ejército Quito, Ecuador 2009 Master of Science in Entomology and Plant Pathology Oklahoma State University Stillwater, Oklahoma 2013 Submitted to the Faculty of the Graduate College of the Oklahoma State University in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY December, 2016 EUKARYOTIC PLANT PATHOGEN DETECTION THROUGH HIGH THROUGHPUT DNA/RNA SEQUENCING DATA ANALYSIS Thesis Approved: Dr. Carla Garzon Thesis Adviser Dr. William Schneider Dr. Stephen Marek Dr. Hassan Melouk ii ACKNOWLEDGEMENTS I would like to express my sincere gratitude to all the people who made possible the completion of my thesis research. Most importantly to my advisor Dr. Carla Garzon for her continuous support, guidance and motivation. She was a great support throughout my PhD. research and thesis writing. I would like to express my deepest gratitude to the members of my advisory committee: Dr. William Schneider, Dr. Stephen Maren and Dr. Hassan Melouk, for their guidance, insightful comments and encouragement. I want to thank the Department of Entomology and Plant Pathology at Oklahoma State University for keeping an excellent environment for the students and professors. This is a great advantage that has helped me to succeed on my research and thesis writing. Thanks to my fellow lab-mates for keeping a competitive and at the same time very friendly environment full of enriching discussions and productive working hours. I would like to thank my wife Patricia Acurio, who has been extremely helpful throughout my PhD., her support, patience, love and encouragement were crucial to succeed completing my degree. Last but not least, I would like to thank my parents, Isabel Camacho & Edison Espindola and my sister, Carolina Espindola for their support and encouragement that helped me to stay strong and productive during this important stage of my life. iii Acknowledgements reflect the views of the author and are not endorsed by committee members or Oklahoma State University. Name: ANDRES SEBASTIAN ESPINDOLA CAMACHO Date of Degree: DECEMBER, 2016 Title of Study: EUKARYOTIC PLANT PATHOGEN DETECTION THROUGH HIGH THROUGHPUT DNA/RNA SEQUENCING DATA ANALYSIS Major Field: PLANT PATHOLOGY Abstract: Plant pathogen detection is crucial for developing appropriate management techniques. A variety of tools are available for rapid plant pathogen detection. Most tools rely on unique features of the pathogen to detect its presence. Immunoassays rely on unique proteins while genetic approaches rely on unique DNA signatures. However, most of these tools can detect a limited number of pathogens at once. E-probe Diagnostics Nucleic acid Analysis (EDNA) is a bioinformatic tool originally designed as a theoretical approach to detect multiple plant pathogens at once. EDNA uses metagenomic databases and bioinformatics to infer the presence/absence of plant pathogens in a given sample. Additionally, EDNA relies on a continuous design and curation of unique signatures termed e-probes. EDNA has been successfully validated in viral, bacterial and eukaryotic plant pathogens. However, most of these validations have been performed solely at the species level and only using DNA sequencing. My thesis involved the refinement of EDNA to increase its detection scope to include plant pathogens at the strain/isolate level. Additional refinements included its increasing EDNA’s capacity to use transcriptomic analysis to detect actively infecting plant pathogens and metabolic pathways. Actively infecting/growing plant pathogen detection was performed by using Slerotinia minor as an eukaryotic model system. We sequenced and annotated the genome of S. minor to be able to use its genome for e-probe generation. In vitro detection of actively growing S. minor was successfully achieved using EDNA for RNA sequencing analysis. However, actively infecting S. minor in peanut was non-detectable. EDNA’s capacity to detect the aflatoxin metabolic pathway was also assesed. Actively producing aflatoxin A. flavus strains (AF70) were successfully used to differentially detect the production of aflatoxin when A. flavus grows in an environment conducive for the production of aflatoxin (maize). Finally, EDNA’s detection scope was assesed with eukaryotic strains having very low genetic diversity within its species (Pythium aphanidermatum). We were able to successfully discriminate P. aphanidermatum P16 strain from P. aphanidermatum BR444, concomitantly, these two strains were differentiated from other related species (Globisporangium irregulare and Pythium deliense) in the same detection run trial. iv TABLE OF CONTENTS CHAPTER I ...................................................................................................................... 1 I INTRODUCTION AND OBJECTIVES ................................................................ 1 Objectives .................................................................................................................... 6 Literature cited............................................................................................................ 6 CHAPTER II ................................................................................................................... 10 II LITERATURE REVIEW...................................................................................... 10 The plant microbiome: microbial diversity and interactions ................................... 10 DNA sequencing: past, present and insights into the future ..................................... 12 First generation sequencing .................................................................................. 12 Second generation sequencing .............................................................................. 14 Third generation sequencing ................................................................................. 18 DNA/RNA–omics in plants ........................................................................................ 20 Metagenomics and community composition ........................................................ 20 Metatranscriptomics and community function ..................................................... 21 EDNA in Plant Pathology ..................................................................................... 22 Model organisms in this study .................................................................................. 23 Pythium aphanidermatum ..................................................................................... 23 Sclerotinia minor .................................................................................................. 28 Aspergillus flavus .................................................................................................. 30 Literature cited.......................................................................................................... 33 v CHAPTER III ................................................................................................................. 47 III GENOME SEQUENCING AND COMPARATIVE GENOMICS OF SCLEROTINIA MINOR, THE CAUSAL AGENT OF SCLEROTINIA BLIGHT PROVIDES INSIGHTS INTO ITS EVOLUTION AND INFECTION STRATEGY .. 47 Abstract ..................................................................................................................... 47 Introduction............................................................................................................... 48 Experimental Procedures.......................................................................................... 51 Fungal culture preparation and inoculation .......................................................... 51 Genome sequence and assembly ........................................................................... 52 Genome annotation ............................................................................................... 52 Phylogenetic analysis ............................................................................................ 53 Phylogenomic analysis.......................................................................................... 53 Carbohydrate active enzymes annotation ............................................................. 54 Pectate lyase protein modeling ............................................................................. 54 Results/Discussion .................................................................................................... 55 Genome annotation ............................................................................................... 55 Orthologs............................................................................................................... 56 CAZymes analysis ................................................................................................ 57 Oxalic acid ............................................................................................................ 59 Phylogenomics of the Leotiomycetes ................................................................... 60 Phylogenetic analysis ............................................................................................ 61 Acknowledgements .................................................................................................... 62 Literature cited.........................................................................................................
Load more

Recommended publications
  • Sclerotinia Diseases of Crop Plants: Biology, Ecology and Disease Management G
    Sclerotinia Diseases of Crop Plants: Biology, Ecology and Disease Management G. S. Saharan • Naresh Mehta Sclerotinia Diseases of Crop Plants: Biology, Ecology and Disease Management Dr. G. S. Saharan Dr. Naresh Mehta CCS Haryana Agricultural University CCS Haryana Agricultural University Hisar, Haryana, India Hisar, Haryana, India ISBN 978-1-4020-8407-2 e-ISBN 978-1-4020-8408-9 Library of Congress Control Number: 2008924858 © 2008 Springer Science+Business Media B.V. No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer.com Foreword The fungus Sclerotinia has always been a fancy and interesting subject of research both for the mycologists and pathologists. More than 250 species of the fungus have been reported in different host plants all over the world that cause heavy economic losses. It was a challenge to discover weak links in the disease cycle to manage Sclerotinia diseases of large number of crops. For researchers and stu- dents, it has been a matter of concern, how to access voluminous literature on Sclerotinia scattered in different journals, reviews, proceedings of symposia, workshops, books, abstracts etc. to get a comprehensive picture. With the publi- cation of book on ‘Sclerotinia’, it has now become quite clear that now only three species of Sclerotinia viz., S.
    [Show full text]
  • Psychrophilic Fungi from the World's Roof
    Persoonia 34, 2015: 100–112 www.ingentaconnect.com/content/nhn/pimj RESEARCH ARTICLE http://dx.doi.org/10.3767/003158515X685878 Psychrophilic fungi from the world’s roof M. Wang1,2, X. Jiang3, W. Wu3, Y. Hao1, Y. Su1, L. Cai1, M. Xiang1, X. Liu1 Key words Abstract During a survey of cold-adapted fungi in alpine glaciers on the Qinghai-Tibet Plateau, 1 428 fungal isolates were obtained of which 150 species were preliminary identified. Phoma sclerotioides and Pseudogymnoascus pan- glaciers norum were the most dominant species. Psychrotolerant species in Helotiales (Leotiomycetes, Ascomycota) were Phoma sclerotioides studied in more detail as they represented the most commonly encountered group during this investigation. Two Pseudogymnoascus pannorum phylogenetic trees were constructed based on the partial large subunit nrDNA (LSU) to infer the taxonomic place- Psychrophila ments of these strains. Our strains nested in two well-supported major clades, which represented Tetracladium and psychrotolerant a previously unknown lineage. The unknown lineage is distant to any other currently known genera in Helotiales. Tetracladium Psychrophila gen. nov. was therefore established to accommodate these strains which are characterised by globose or subglobose conidia formed from phialides on short or reduced conidiophores. Our analysis also showed that an LSU-based phylogeny is insufficient in differentiating strains at species level. Additional analyses using combined sequences of ITS+TEF1+TUB regions were employed to further investigate the phylogenetic relationships of these strains. Together with the recognisable morphological distinctions, six new species (i.e. P. antarctica, P. lutea, P. oli- vacea, T. ellipsoideum, T. globosum and T. psychrophilum) were described. Our preliminary investigation indicates a high diversity of cold-adapted species in nature, and many of them may represent unknown species.
    [Show full text]
  • The Phylogenetic Relationships of Torrendiella and Hymenotorrendiella Gen
    Phytotaxa 177 (1): 001–025 ISSN 1179-3155 (print edition) www.mapress.com/phytotaxa/ PHYTOTAXA Copyright © 2014 Magnolia Press Article ISSN 1179-3163 (online edition) http://dx.doi.org/10.11646/phytotaxa.177.1.1 The phylogenetic relationships of Torrendiella and Hymenotorrendiella gen. nov. within the Leotiomycetes PETER R. JOHNSTON1, DUCKCHUL PARK1, HANS-OTTO BARAL2, RICARDO GALÁN3, GONZALO PLATAS4 & RAÚL TENA5 1Landcare Research, Private Bag 92170, Auckland, New Zealand. 2Blaihofstraße 42, D-72074 Tübingen, Germany. 3Dpto. de Ciencias de la Vida, Facultad de Biología, Universidad de Alcalá, P.O.B. 20, 28805 Alcalá de Henares, Madrid, Spain. 4Fundación MEDINA, Microbiología, Parque Tecnológico de Ciencias de la Salud, 18016 Armilla, Granada, Spain. 5C/– Arreñales del Portillo B, 21, 1º D, 44003, Teruel, Spain. Corresponding author: [email protected] Abstract Morphological and phylogenetic data are used to revise the genus Torrendiella. The type species, described from Europe, is retained within the Rutstroemiaceae. However, Torrendiella species reported from Australasia, southern South America and China were found to be phylogenetically distinct and have been recombined in the newly proposed genus Hymenotorrendiel- la. The Hymenotorrendiella species are distinguished morphologically from Rutstroemia in having a Hymenoscyphus-type rather than Sclerotinia-type ascus apex. Zoellneria, linked taxonomically to Torrendiella in the past, is genetically distinct and a synonym of Chaetomella. Keywords: ascus apex, phylogeny, taxonomy, Hymenoscyphus, Rutstroemiaceae, Sclerotiniaceae, Zoellneria, Chaetomella Introduction Torrendiella was described by Boudier and Torrend (1911), based on T. ciliata Boudier in Boudier and Torrend (1911: 133), a species reported from leaves, and more rarely twigs, of Rubus, Quercus and Laurus from Spain, Portugal and the United Kingdom (Graddon 1979; Spooner 1987; Galán et al.
    [Show full text]
  • Minireview Snow Molds: a Group of Fungi That Prevail Under Snow
    Microbes Environ. Vol. 24, No. 1, 14–20, 2009 http://wwwsoc.nii.ac.jp/jsme2/ doi:10.1264/jsme2.ME09101 Minireview Snow Molds: A Group of Fungi that Prevail under Snow NAOYUKI MATSUMOTO1* 1Department of Planning and Administration, National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Toyohira-ku, Sapporo 062–8555, Japan (Received January 5, 2009—Accepted January 30, 2009—Published online February 17, 2009) Snow molds are a group of fungi that attack dormant plants under snow. In this paper, their survival strategies are illustrated with regard to adaptation to the unique environment under snow. Snow molds consist of diverse taxonomic groups and are divided into obligate and facultative fungi. Obligate snow molds exclusively prevail during winter with or without snow, whereas facultative snow molds can thrive even in the growing season of plants. Snow molds grow at low temperatures in habitats where antagonists are practically absent, and host plants deteriorate due to inhibited photosynthesis under snow. These features characterize snow molds as opportunistic parasites. The environment under snow represents a habitat where resources available are limited. There are two contrasting strategies for resource utilization, i.e., individualisms and collectivism. Freeze tolerance is also critical for them to survive freezing temper- atures, and several mechanisms are illustrated. Finally, strategies to cope with annual fluctuations in snow cover are discussed in terms of predictability of the habitat. Key words: snow mold, snow cover, low temperature, Typhula spp., Sclerotinia borealis Introduction Typical snow molds have a distinct life cycle, i.e., an active phase under snow and a dormant phase from spring to In northern regions with prolonged snow cover, plants fall.
    [Show full text]
  • 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.
    [Show full text]
  • Draft Genome Sequence of Sclerotinia Borealis, a Psychrophilic Plant Pathogenic Fungus
    Draft Genome Sequence of Sclerotinia borealis, a Psychrophilic Plant Pathogenic Fungus Andrey V. Mardanov, Alexey V. Beletsky, Vitaly V. Kadnikov, Alexander N. Ignatov, Nikolai V. Ravin Centre Bioengineering, Russian Academy of Sciences, Moscow, Russia Sclerotinia borealis is a necrotrophic phytopathogenic fungus notable for its wide host range and environmental persis- tence. It grows at low temperatures, causing snow mold disease of crop plants. To understand the molecular mechanisms of its pathogenesis and adaptation to the psychrophilic lifestyle, we determined the 39.3-Mb draft genome sequence of S. borealis F-4128. Received 9 December 2013 Accepted 10 December 2013 Published 23 January 2014 Citation Mardanov AV, Beletsky AV, Kadnikov VV, Ignatov AN, Ravin NV. 2014. Draft genome sequence of Sclerotinia borealis, a psychrophilic plant pathogenic fungus. Genome Announc. 2(1):e01175-13. doi:10.1128/genomeA.01175-13. Copyright © 2014 Mardanov et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Andrey V. Mardanov, [email protected]. clerotinia species are among the most diverse and widely gene order conservation. The arsenal of genes associated with the Sdistributed phytopathogenic fungi causing many economi- necrotrophic lifestyle is also similar between species, including the cally important diseases of crop plants (1). Sclerotinia borealis genes involved in plant cell wall degradation. However, many ge- Bubák & Vleugel has a broad host range, infecting at least 17 nome regions and genes specific to S. borealis may be responsible plant genera from the families Alliaceae, Asteraceae, Brassi- for its adaptation to particular ecological niches and conditions of caceae, Campanulaceae, Fabaceae, Iridaceae, Pinaceae, and growth.
    [Show full text]
  • Common Protein Sequence Signatures Associate with Sclerotinia Borealis Lifestyle and Secretion in Fungal Pathogens of the Sclerotiniaceae
    ORIGINAL RESEARCH published: 24 September 2015 doi: 10.3389/fpls.2015.00776 Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae Thomas Badet 1, 2, Rémi Peyraud 1, 2 and Sylvain Raffaele 1, 2* Edited by: 1 Laboratoire des Interactions Plantes-Microorganismes, Institut National de la Recherche Agronomique, UMR441, Delphine Vincent, Castanet-Tolosan, France, 2 Laboratoire des Interactions Plantes-Microorganismes, Centre National de la Recherche Department of Environment and Scientifique, UMR2594, Castanet-Tolosan, France Primary Industries, Australia Reviewed by: Fungal plant pathogens produce secreted proteins adapted to function outside fungal Jana Sperschneider, Commonwealth Scientific and cells to facilitate colonization of their hosts. In many cases such as for fungi from Industrial Research Organisation, the Sclerotiniaceae family the repertoire and function of secreted proteins remains Australia elusive. In the Sclerotiniaceae, whereas Sclerotinia sclerotiorum and Botrytis cinerea are Kim Marilyn Plummer, La Trobe University, Australia cosmopolitan broad host-range plant pathogens, Sclerotinia borealis has a psychrophilic *Correspondence: lifestyle with a low optimal growth temperature, a narrow host range and geographic Sylvain Raffaele, distribution. To spread successfully, S. borealis must synthesize proteins adapted to Laboratoire des Interactions Plante Micro-organismes, 24 Chemin de function in its specific environment. The search for signatures of adaptation to S. borealis Borde Rouge – Auzeville, 31326 lifestyle may therefore help revealing proteins critical for colonization of the environment Castanet Tolosan, France by Sclerotiniaceae fungi. Here, we analyzed amino acids usage and intrinsic protein [email protected] disorder in alignments of groups of orthologous proteins from the three Sclerotiniaceae Specialty section: species.
    [Show full text]
  • Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan
    Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Agricultural Science (Doctoral Program in Biosphere Resource Science and Technology) Yan-Jie ZHAO Contents Chapter 1 Introduction ............................................................................................................... 1 1–1 The genus Lambertella in Rutstroemiaceae .................................................................... 1 1–2 Taxonomic problems of Lambertella .............................................................................. 5 1–3 Allied genera of Lambertella ........................................................................................... 7 1–4 Objectives of the present research ................................................................................. 12 Chapter 2 Materials and Methods ............................................................................................ 17 2–1 Collection and isolation ................................................................................................. 17 2–2 Morphological examination .......................................................................................... 17 2–3 Observation of cultural characteristics .......................................................................... 18 2–4 DNA extraction
    [Show full text]
  • Microdochium Nivale in Perennial Grasses: Snow Mould Resistance, Pathogenicity and Genetic Diversity
    Philosophiae Doctor (PhD), Thesis 2016:32 (PhD), Doctor Philosophiae ISBN: 978-82-575-1324-5 Norwegian University of Life Sciences ISSN: 1894-6402 Faculty of Veterinary Medicine and Biosciences Department of Plant Sciences Philosophiae Doctor (PhD) Thesis 2016:32 Mohamed Abdelhalim Microdochium nivale in perennial grasses: Snow mould resistance, pathogenicity and genetic diversity Microdochium nivale i flerårig gras: Resistens mot snømugg, patogenitet og genetisk diversitet Postboks 5003 Mohamed Abdelhalim NO-1432 Ås, Norway +47 67 23 00 00 www.nmbu.no Microdochium nivale in perennial grasses: Snow mould resistance, pathogenicity and genetic diversity. Microdochium nivale i flerårig gras: Resistens mot snømugg, patogenitet og genetisk diversitet. Philosophiae Doctor (PhD) Thesis Mohamed Abdelhalim Department of Plant Sciences Faculty of Veterinary Medicine and Biosciences Norwegian University of Life Sciences Ås (2016) Thesis number 2016:32 ISSN 1894-6402 ISBN 978-82-575-1324-5 Supervisors: Professor Anne Marte Tronsmo Department of Plant Sciences, Norwegian University of Life Sciences P.O. Box 5003, 1432 Ås, Norway Professor Odd Arne Rognli Department of Plant Sciences, Norwegian University of Life Sciences P.O. Box 5003, 1432 Ås, Norway Adjunct Professor May Bente Brurberg Department of Plant Sciences, Norwegian University of Life Sciences P.O. Box 5003, 1432 Ås, Norway The Norwegian Institute of Bioeconomy Research (NIBIO) Pb 115, NO-1431 Ås, Norway Researcher Dr. Ingerd Skow Hofgaard The Norwegian Institute of Bioeconomy Research (NIBIO) Pb 115, NO-1431 Ås, Norway Dr. Petter Marum Graminor AS. Bjørke forsøksgård, Hommelstadvegen 60 NO-2344 Ilseng, Norway Associate Professor Åshild Ergon Department of Plant Sciences, Norwegian University of Life Sciences P.O.
    [Show full text]
  • Biological Control of Sclerotinia Stem Rot of Soybean with Sporidesmium Sclerotivorum Luis Enrique Del Rió Mendoza Iowa State University
    Iowa State University Capstones, Theses and Retrospective Theses and Dissertations Dissertations 1999 Biological control of Sclerotinia stem rot of soybean with Sporidesmium sclerotivorum Luis Enrique del Rió Mendoza Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/rtd Part of the Agricultural Science Commons, Agriculture Commons, Agronomy and Crop Sciences Commons, and the Plant Pathology Commons Recommended Citation del Rió Mendoza, Luis Enrique, "Biological control of Sclerotinia stem rot of soybean with Sporidesmium sclerotivorum " (1999). Retrospective Theses and Dissertations. 12658. https://lib.dr.iastate.edu/rtd/12658 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Retrospective Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion.
    [Show full text]
  • Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan
    Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan 著者 趙 彦傑 内容記述 この博士論文は全文公表に適さないやむを得ない事 由があり要約のみを公表していましたが、解消した ため、2017年8月23日に全文を公表しました。 year 2014 その他のタイトル 日本産Lambertella属および基質性子座を形成する 類縁属の分類学的研究 学位授与大学 筑波大学 (University of Tsukuba) 学位授与年度 2013 報告番号 12102甲第6938号 URL http://hdl.handle.net/2241/00123740 Taxonomic Study of Lambertella (Rutstroemiaceae, Helotiales) and Allied Substratal Stroma Forming Fungi from Japan A Dissertation Submitted to the Graduate School of Life and Environmental Sciences, the University of Tsukuba in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Agricultural Science (Doctoral Program in Biosphere Resource Science and Technology) Yan-Jie ZHAO Contents Chapter 1 Introduction ............................................................................................................... 1 1–1 The genus Lambertella in Rutstroemiaceae .................................................................... 1 1–2 Taxonomic problems of Lambertella .............................................................................. 5 1–3 Allied genera of Lambertella ........................................................................................... 7 1–4 Objectives of the present research ................................................................................. 12 Chapter 2 Materials and Methods ............................................................................................ 17 2–1 Collection and isolation
    [Show full text]
  • Sommerfeltia 31 Innmat 20080203.Indd
    SOMMERFELTIA 31 (2008) 125 SNOW MOLD FUNGUS, TYPHULA ISHIKARIENSIS GROUP III, IN ARC- TIC NORWAY CAN GROW AT A SUB-LETHAL TEMPERATURE AFTER FREEZING STRESS AND DURING FLOODING. T. Hoshino, A.M. Tronsmo & I. Yumoto Hoshino, T., Tronsmo, A.M. & Yumoto, I. 2008. Snow mold fungus, Typhula ishikariensis group III, in Arctic Norway can grow at a sub-lethal temperature after freezing stress and during flooding. – Sommerfeltia 31: 125-131. ISBN 82-7420-045-4. ISSN 0800-6865. Isolates of the snow mold fungus Typhula ishikariensis group III, which is predominant in Finnmark (northern Norway) and Svalbard, are more resistant to freezing stress than group I isolates from the southern part of Norway. Group III isolates showed irregular growth on potato dextrose agar (PDA) plates when subjected to heat stress at 10˚C. However, group III isolates showed relatively good growth on PDA at 10˚C after freezing treatment. The optimal temperatures for mycelial growth were 5˚C on PDA and 10˚C in potato dextrose broth (PDB), and group III isolates showed normal mycelial growth at 10˚C in PDB. Mycelium of group III isolates cultivated in water poured into PDA plates, and normal hyphal extension was observed only in the liquid media. Hyphal growth became irregular when mycelia had extended above the surface of the liquid media. These results suggested that group III isolates can grow at a sub-lethal temperature after freezing stress and during flooding. Soil freezing and thawing occurs regularly in the Arctic, and physiological characteristics of group III isolates are well adapted to climatic conditions in the Arctic.
    [Show full text]