DOCSLIB.ORG

Research Collection

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Research Collection Research Collection Doctoral Thesis Molecular and transcriptomic characterization of natural resistance to cassava brown streak viruses in cassava Author(s): Anjanappa, Ravi B. Publication Date: 2015 Permanent Link: https://doi.org/10.3929/ethz-a-010572922 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO. 22704 Molecular and transcriptomic characterization of natural resistance to cassava brown streak viruses in cassava (Manihot esculenta, Crantz) A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) Presented by Ravi Bodampalli Anjanappa Master of Science in Plant Biotechnology, University of Agricultural Sciences, Bangalore Born 12th August 1979 Citizen of India Accepted on the recommendation of Prof. Dr. Wilhelm Gruissem, examiner Prof. Dr. Hervé Vanderschuren, co-examiner Dr. Maruthi M. N. Gowda, co-examiner 2015 Table of Contents Abstract 1 Zusammenfassung 3 Abbreviations 5 General Introduction 7 Chapter 1: Natural Resistance to Plant Viruses 13 Chapter 2: Characterization of brown streak virus-resistant cassava 55 Chapter 3: Transcriptome modulation in susceptible and resistant cassava 82 varieties inoculated with cassava brown streak viruses Chapter 4: Identification and characterization of a resistance-breaking 131 Cassava brown streak virus isolate Chapter 5: Discussion and persceptives 159 Acknowledgements 169 Curriculum Vitae 170 Abstract Cassava (Manihot esculenta Crantz) production in eastern and central African countries is adversely impacted by cassava brown streak disease (CBSD), thereby threatening food security. CBSD is caused by two viral species, Cassava brown streak virus (CBSV) and Ugandan Cassava brown streak virus (UCBSV) which are collectively termed as cassava brown streak viruses (CBSVs). Both are (+) single stranded (ss) RNA viruses of the genus Ipomovirus; family Potyviridae. The prevalence of mixed infections of the two ipomoviruses CBSV and UCBSV along with cassava mosaic geminiviruses (CMGs) that cause cassava mosaic disease (CMD) is now well known. In the present study, 14 elite cassava cultivars (selected from the cassava germplasm and breeding programmes) were assayed using top cleft grafting procedures for identifying novel sources of resistance against the multiple CBSV and UCBSV isolates. These infection assays identified cassava varieties with contrasting levels of virus resistance. KBH 2006/18 and KBH 2006/26, two elite breeding lines from the IITA breeding programme were identified as highly resistant as they remained symptom-free and did not support replication for both CBSV and UCBSV isolates. Importantly, challenging with a mixed infection of CBSVs and East African cassava mosaic virus (EACMV-Ug) could not break the virus resistance. Independent grafting experiment using scions resistant KBH 2006/18 and KBH 2006/26, moderately resistant TMS 30001 and susceptible 60444 varieties was performed over a time course (16, 22 and 28 dag) to identify early molecular interactions. As expected, these assays revealed variable CBSV titers across the different time points. Comparative transcriptome analysis of resistant KBH 2006/18 and susceptible 60444 varieties were performed using Illumina Hiseq2000 from both CBSV-infected and virus-free scions collected at 28 dag. The RNA-seq analysis revealed that an average of 83.5% of the total reads mapped to phytozome cassava reference genome v9 and identified 26,206 genome transcripts. A total of 853 (60.3% of them up-regulated) and 334 (35.6% of them up-regulated) differentially expressed genes (DEGs) were identified in susceptible 60444 and resistant KBH 2006/18 varieties, respectively. Further functional characterization of the DEGs using the MapMan software to identify processes and pathways, revealed 27 and 24 bins MapMan bins or functional classes in susceptible and resistant varieties, respectively. In variety 60444, signaling (MapMan bin 30) was modulated with majority of the DEGs (85 %) being up-regulated while in contrast KBH 2006/18 only 27% of the DEGs were modulated in signaling pathway. In KBH 2006/18, 90% of DEGs related to stress (MapMan bin 20) were up-regulated while 70% of DEGs were up-regulated in susceptible variety. In both the varieties DEGs implicated in photosystem were down-regulated (100%). Further, de novo assembly of unmapped reads determined novel cassava (host) genes, in addition to complete genome sequences of CBSV (TAZ:DES:01) (8,975 nt) and partial sequence of TAZ:DES:02 (6,645 nt). Moreover, analysis 1 of host genes using RT-qPCR, revealed that four DEGs (RDRP1, NTL9, NIMIN2 and BG3) where up-regulated in early time points samples (16 and 22 dag) in susceptible 60444 variety. Further, expression analysis of these genes in moderately resistant TMS 30001 variety also confirmed consistent up-regulation in presence of the virus. CBSV-like symptoms were first reported in resistant variety KBH 2006/18 in a field trail in the Chambezi province in Tanzania in 2012. Field-collected material was multiplied in the greenhouse and used to inoculate KBH 2006/18 scions. CBSD was graft-transmissible to healthy KBH 2006/18, which developed typical CBSD symptoms. We used conserved sequences between CBSV and UCBSV genome sequences to develop primers and amplify fragments of the isolates infecting KBH 2006/18. We detected only one CBSV isolate in the field-collected material that we named CBSV TAZ: Cham:14. Comparing the resistant breaking TAZ:Cham:14 isolate to other isolates (TAZ:DES:01, TAZ:DES:02, and UG:Kab4-3:07) revealed specific mutations in the proteins from the TAZ:Cham:14 isolate with the exception of the 6K1 protein which was identical between TAZ:DES:01 and TAZ:Cham:14. As expected, the sequence diversity was greater between the two CBSVs species (~74.5% identical) than within CBSV isolates (88% identical). This is the first report on CBSV isolates differing in virulence and further efforts are being made to develop infectious clones and to identify molecular virulence determinants of TAZ:Cham:14 in the KBH 2006/18 line. 2 Zussamenfassung Die Produktion von Maniok (Manihot esculenta Crantz) wird in Ost- und Zentralafrikanischen Ländern von der Braunstreifen-Krankheit (Cassava Brown Streak Disease, CBSD) bedroht und gefährdet damit die Ernährungssicherheit in dieser Region. CBSD wird von zwei Virusspezies verursacht, Cassava brown streak virus (CBSV) und Ugandan Cassava brown streak virus (UCBSV), die kollektiv als Cassava brown streak viruses (CBSVs) bezeichnet werden. Beides sind Positive Einzelstrang-RNA Viren der Gattung Ipomovirus; Familie Potyviridae. Die beiden Ipomoviren CBSV und UCBSV treten häufig als Mischinfektion mit Cassava-Mosaik Geminiviren (CMGs) auf, welche die Cassava-Mosaik-Krankheit (Cassava Mosaic Disease, CMD) verursachen. Zur Identifizierung von neuen Resistenzquellen gegen die zahlreichen CBSV und UCBSV Isolate wurden in der vorliegenden Arbeit 14 Elite Maniok-Sorten (von der Maniok Keimplasma-Bank und Zuchtprogrammen selektiert) mittels Aufpfropfen auf infizierte Wurzelstöcke untersucht. Durch diese Infektionsassays wurden Maniok-Sorten mit unterschiedlich stark ausgeprägter Virusresistenz identifiziert. KBH 2006/18 und KBH 2006/26, zwei Elite-Zuchtlinien aus dem IITA Zuchtprogramm, blieben symptomfrei und erlaubten keine Replikation der beiden CBSV und UCBSV Isolate. Auch durch Mischinfektionen mit CBSVs und East African cassava mosaic virus (EACMV-Ug) konnten die Virusresistenz nicht gebrochen werden. Zur Identifizierung von frühen molekularen Wechselwirkungen wurden unabhängige Pfropf-Experimente mit den resistenten Sorten KBH 2006/18 und KBH 2006/26, der mässig resistenten Sorte TMS30001 und der anfälligen Sorte 60444 durchgeführt. Dabei wurden in einem Time-Course-Experiment Proben an 16, 22 und 28 Tagen nach der Pfropfung (TNP) entnommen. Wie zu erwarten zeigten diese Versuche variable CBSV Titer zwischen den verschiedenen Zeitpunkten. Des Weiteren wurden vergleichende Transkriptom-Analysen mit der resistenten Sorte KBH 2006/18 und der anfälligen Sorte 60444 durchgeführt. Dazu wurden CBSV infizierte und virusfreie Pflanzen 28 TNP mittels Illumina Hiseq2000 analysiert. Durchschnittlich 83.5% der gelesenen Fragmente (reads) wurden dem Phytozome Maniok Referenzgenom v9 zugeordnet und 26,206 Transkripte identifiziert. Insgesamt wurden 853 (davon 60.3% hochreguliert) und 334 (davon 35.6% hochreguliert) differentiell exprimierte Gene (DEGs) in 60444 resp. KBH 2006/18 identifiziert. Zur Identifikation von physiologischen Prozessen und Stoffwechselwegen wurden diese DEGs mittels MapMan Software analysiert. Die funktionelle Charakterisierung dieser DEGs ergaben 27 MapMan bins oder funktionelle Klassen in anfälligen und 24 in resistenten Sorten. In 60444 waren hauptsächlich Signaltransduktionsvorgänge (MapMan bin 30) moduliert mit mehrheitlich hochregulierten DEGs (85%), im Gegensatz zu KBH 2006/18 27% DEGs in Signalwegen moduliert waren. 90% der DEGs die im Zusammenhang mit Stress (MapMan bin 20) stehen waren in KBH 2006/18 hochreguliert während in 60444 nur 70% der DEGs 3 hochreguliert waren. In beiden Sorten waren die ins Photosystem involvierten DEGs runterreguliert (100%). Des Weiteren konnten durch die de novo Assemblierung von nicht zugeordneten Fragmenten, nebst der kompletten Genomsequenz von CBSV (TAZ:DES:01) (8975 nt) und der partiellen Sequenz von TAZ:DES:02 (6645
Load more

Recommended publications
  • Elisabeth Mendes Martins De Moura Diversidade De Vírus DNA
    Elisabeth Mendes Martins de Moura Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo Tese apresentada ao Programa de Pós- Graduação em Microbiologia do Instituto de Ciências Biomédicas da Universidade de São Paulo, para obtenção do Titulo de Doutor em Ciências. Área de concentração: Microbiologia Orienta: Prof (a). Dr (a). Dolores Ursula Mehnert versão original São Paulo 2017 RESUMO MOURA, E. M. M. Diversidade de vírus DNA autóctones e alóctones de mananciais e de esgoto da região metropolitana de São Paulo. 2017. 134f. Tese (Doutorado em Microbiologia) - Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, 2017. A água doce no Brasil, assim como o seu consumo é extremamente importante para as diversas atividades criadas pelo ser humano. Por esta razão o consumo deste bem é muito grande e consequentemente, provocando o seu impacto. Os mananciais são normalmente usados para abastecimento doméstico, comercial, industrial e outros fins. Os estudos na área de ecologia de micro-organismos nos ecossistemas aquáticos (mananciais) e em esgotos vêm sendo realizados com mais intensidade nos últimos anos. Nas últimas décadas foi introduzido o conceito de virioplâncton com base na abundância e diversidade de partículas virais presentes no ambiente aquático. O virioplâncton influencia muitos processos ecológicos e biogeoquímicos, como ciclagem de nutriente, taxa de sedimentação de partículas, diversidade e distribuição de espécies de algas e bactérias, controle de florações de fitoplâncton e transferência genética horizontal. Os estudos nesta área da virologia molecular ainda estão muito restritos no país, bem como muito pouco se conhece sobre a diversidade viral na água no Brasil.
    [Show full text]
  • Changes to Virus Taxonomy 2004
    Arch Virol (2005) 150: 189–198 DOI 10.1007/s00705-004-0429-1 Changes to virus taxonomy 2004 M. A. Mayo (ICTV Secretary) Scottish Crop Research Institute, Invergowrie, Dundee, U.K. Received July 30, 2004; accepted September 25, 2004 Published online November 10, 2004 c Springer-Verlag 2004 This note presents a compilation of recent changes to virus taxonomy decided by voting by the ICTV membership following recommendations from the ICTV Executive Committee. The changes are presented in the Table as decisions promoted by the Subcommittees of the EC and are grouped according to the major hosts of the viruses involved. These new taxa will be presented in more detail in the 8th ICTV Report scheduled to be published near the end of 2004 (Fauquet et al., 2004). Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (eds) (2004). Virus Taxonomy, VIIIth Report of the ICTV. Elsevier/Academic Press, London, pp. 1258. Recent changes to virus taxonomy Viruses of vertebrates Family Arenaviridae • Designate Cupixi virus as a species in the genus Arenavirus • Designate Bear Canyon virus as a species in the genus Arenavirus • Designate Allpahuayo virus as a species in the genus Arenavirus Family Birnaviridae • Assign Blotched snakehead virus as an unassigned species in family Birnaviridae Family Circoviridae • Create a new genus (Anellovirus) with Torque teno virus as type species Family Coronaviridae • Recognize a new species Severe acute respiratory syndrome coronavirus in the genus Coro- navirus, family Coronaviridae, order Nidovirales
    [Show full text]
  • Biological and Molecular Characterization of Dahlia Mosaic Caulimovirus Abstract
    BIOLOGICAL AND MOLECULAR CHARACTERIZATION OF DAHLIA MOSAIC CAULIMOVIRUS By VIHANGA PAHALAWATTA A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY WASHINGTON STATE UNIVERSITY Department of Plant Pathology AUGUST 2007 © Copyright by VIHANGA PAHALAWATTA, 2007 All Rights Reserved i To the Faculty of Washington State University: The members of the Committee appointed to examine the dissertation of VIHANGA PAHALAWATTA find it satisfactory and recommend that it be accepted. _____________________________ Chair _____________________________ _____________________________ ____________________________ ii ACKNOWLEDGEMENT I would like to express my sincere gratitude to my major advisor, Dr. Hanu Pappu, for the tremendous support, guidance, encouragement and most of all the numerous opportunities that he made available to me during the time I spent working with him. Dr. Pappu has been an exceptional mentor who has been a constant source of inspiration to me. I would also like to thank Dr. Patricia Okubara, Dr. Ken Eastwell and Dr. Gary Chastagner for their advice, guidance and helpful discussions throughout my tenure. I wish to extend my gratitude to Keri Druffel, who taught me numerous techniques in the laboratory and for all the work she did that made my work so much easier. A special thanks to Robert Brueggeman for technical assistance. I am also grateful to the faculty and staff of the Department of Plant Pathology for all the help and support during my graduate studies at Washington State University. A special thank you to Dr. Tim Murray, for arranging departmental financial support and for giving me the opportunity to serve as a teaching assistant.
    [Show full text]
  • Determinants of Taxonomic Composition of Plant Viruses at the Nature Conservancy’S Tallgrass Prairie Preserve, Oklahoma Vaskar Thapa,1,2 Daniel J
    Virus Evolution, 2015, 1(1): vev007 doi: 10.1093/ve/vev007 Research article Determinants of taxonomic composition of plant viruses at the Nature Conservancy’s Tallgrass Prairie Preserve, Oklahoma Vaskar Thapa,1,2 Daniel J. McGlinn,2,† Ulrich Melcher,3 Michael W. Palmer,2 and Marilyn J. Roossinck1,*,†,‡ 1Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA, 2Department of Botany, Oklahoma State University, Stillwater, OK 74078, USA and 3Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA *Corresponding author: E-mail: [email protected] †Present address: Biology Department, College of Charleston, Charleston, SC, USA. ‡http://orcid.org/0000-0002-1743-0627 Abstract The role of biotic and abiotic factors in shaping the diversity and composition of communities of plant viruses remain understudied, particularly in natural settings. In this study, we test the effects of host identity, location, and sampling year on the taxonomic composition of plant viruses in six native plant species [Ambrosia psilostachya (Asteraceae), Vernonia baldwinii (Asteraceae), Asclepias viridis (Asclepiadaceae), Ruellia humilis (Acanthaceae), Panicum virgatum (Poaceae) and Sorghastrum nutans (Poaceae)] from the Nature Conservancy’s Tallgrass Prairie Preserve in northeastern Oklahoma. We sampled over 400 specimens of the target host plants from twenty sites (plots) in the Tallgrass Prairie Preserve over 4 years and tested them for the presence of plant viruses applying virus-like particle and double-stranded RNA enrichment meth- ods. Many of the viral sequences identified could not be readily assigned to species, either due to their novelty or the short- ness of the sequence.
    [Show full text]
  • Sequences and Phylogenies of Plant Pararetroviruses, Viruses and Transposable Elements
    Hansen and Heslop-Harrison. 2004. Adv.Bot.Res. 41: 165-193. Page 1 of 34. FROM: 231. Hansen CN, Heslop-Harrison JS. 2004 . Sequences and phylogenies of plant pararetroviruses, viruses and transposable elements. Advances in Botanical Research 41 : 165-193. Sequences and Phylogenies of 5 Plant Pararetroviruses, Viruses and Transposable Elements CELIA HANSEN AND JS HESLOP-HARRISON* DEPARTMENT OF BIOLOGY 10 UNIVERSITY OF LEICESTER LEICESTER LE1 7RH, UK *AUTHOR FOR CORRESPONDENCE E-MAIL: [email protected] 15 WEBSITE: WWW.MOLCYT.COM I. Introduction ............................................................................................................2 A. Plant genome organization................................................................................2 20 B. Retroelements in the genome ............................................................................3 C. Reverse transcriptase.........................................................................................4 D. Viruses ..............................................................................................................5 II. Retroelements........................................................................................................5 A. Viral retroelements – Retrovirales....................................................................6 25 B. Non-viral retroelements – Retrales ...................................................................7 III. Viral and non-viral elements................................................................................7
    [Show full text]
  • ICTV Code Assigned: 2011.001Ag Officers)
    This form should be used for all taxonomic proposals. Please complete all those modules that are applicable (and then delete the unwanted sections). For guidance, see the notes written in blue and the separate document “Help with completing a taxonomic proposal” Please try to keep related proposals within a single document; you can copy the modules to create more than one genus within a new family, for example. MODULE 1: TITLE, AUTHORS, etc (to be completed by ICTV Code assigned: 2011.001aG officers) Short title: Change existing virus species names to non-Latinized binomials (e.g. 6 new species in the genus Zetavirus) Modules attached 1 2 3 4 5 (modules 1 and 9 are required) 6 7 8 9 Author(s) with e-mail address(es) of the proposer: Van Regenmortel Marc, [email protected] Burke Donald, [email protected] Calisher Charles, [email protected] Dietzgen Ralf, [email protected] Fauquet Claude, [email protected] Ghabrial Said, [email protected] Jahrling Peter, [email protected] Johnson Karl, [email protected] Holbrook Michael, [email protected] Horzinek Marian, [email protected] Keil Guenther, [email protected] Kuhn Jens, [email protected] Mahy Brian, [email protected] Martelli Giovanni, [email protected] Pringle Craig, [email protected] Rybicki Ed, [email protected] Skern Tim, [email protected] Tesh Robert, [email protected] Wahl-Jensen Victoria, [email protected] Walker Peter, [email protected] Weaver Scott, [email protected] List the ICTV study group(s) that have seen this proposal: A list of study groups and contacts is provided at http://www.ictvonline.org/subcommittees.asp .
    [Show full text]
  • Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond Mikhail M
    Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond Mikhail M. Pooggin, Lyuba Ryabova To cite this version: Mikhail M. Pooggin, Lyuba Ryabova. Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond. Frontiers in Microbiology, Frontiers Media, 2018, 9, pp.644. 10.3389/fmicb.2018.00644. hal-02289592 HAL Id: hal-02289592 https://hal.archives-ouvertes.fr/hal-02289592 Submitted on 16 Sep 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License fmicb-09-00644 April 9, 2018 Time: 16:25 # 1 REVIEW published: 10 April 2018 doi: 10.3389/fmicb.2018.00644 Ribosome Shunting, Polycistronic Translation, and Evasion of Antiviral Defenses in Plant Pararetroviruses and Beyond Mikhail M. Pooggin1* and Lyubov A. Ryabova2* 1 INRA, UMR Biologie et Génétique des Interactions Plante-Parasite, Montpellier, France, 2 Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, UPR 2357, Université de Strasbourg, Strasbourg, France Viruses have compact genomes and usually translate more than one protein from polycistronic RNAs using leaky scanning, frameshifting, stop codon suppression or reinitiation mechanisms.
    [Show full text]
  • Plant Virus Evolution
    Marilyn J. Roossinck Editor Plant Virus Evolution Plant Virus Evolution Marilyn J. Roossinck Editor Plant Virus Evolution Dr. Marilyn J. Roossinck The Samuel Roberts Noble Foundation Plant Biology Division P.O. Box 2180 Ardmore, OK 73402 USA Cover Photo: Integrated sequences of Petunia vein cleaning virus (in red) are seen in a chromosome spread of Petunia hybrida (see Chapter 4). ISBN: 978-3-540-75762-7 e-ISBN: 978-3-540-75763-4 Library of Congress Control Number: 2007940847 © 2008 Springer-Verlag Berlin Heidelberg This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permission for use must always be obtained from Springer. Violations are liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: WMXDesign GmbH, Heidelberg, Germany Printed on acid-free paper 9 8 7 6 5 4 3 2 1 springer.com Preface The evolution of viruses has been a topic of intense investigation and theoretical development over the past several decades. Numerous workshops, review articles, and books have been devoted to the subject.
    [Show full text]
  • An Abstract of the Dissertation Of
    AN ABSTRACT OF THE DISSERTATION OF Alfredo Diaz Lara for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on December 16, 2016. Title: Identification of Endogenous and Exogenous Pararetroviruses in Red Raspberry (Rubus idaeus L.) and Blueberry (Vaccinium corymbosum L.). Abstract approved: ______________________________________________________ Robert R. Martin The Pacific Northwest (Oregon and Washington in the United States and British Columbia in Canada) is one of the major producers of red raspberry (Rubus idaeus L.) and blueberry (Vaccinium corymbosum L.) in the world. The expansion of growing area with these crops has resulted in the emergence of new virus diseases that cause serious economic losses. The majority of viruses affecting plants (including blueberry and red raspberry) contain RNA genomes. In contrast, plant viruses with DNA genomes are relatively rare and most of the time ignored in virus surveys. The family Caulimoviridae is a group of plant pararetroviruses (reverse-transcribing viruses) with the ability to integrate their DNA into the host genome, resulting in complex molecular interactions that lead to inconsistencies in terms of detection and disease symptoms. Albeit, few studies have been conducted to determine the nature of plant pararetroviruses and their relationships with the associated host. To investigate the presence of pararetroviruses in blueberry and red raspberry, and their possible integration events, different plant material suspected to be infected with viruses was collected in nurseries, commercial fields and clonal germplasm repositories for a period of four years. For blueberry, using rolling circle amplification (RCA) a new virus was identified and named Blueberry fruit drop-associated virus (BFDaV) because of its association with fruit-drop disorder.
    [Show full text]
  • Genomic Characterization of the Cacao Swollen Shoot Virus Complex and Other Theobroma Cacao-Infecting Badnaviruses
    Genomic Characterization of the Cacao Swollen Shoot Virus Complex and other Theobroma Cacao-Infecting Badnaviruses Item Type text; Electronic Dissertation Authors Chingandu, Nomatter Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 29/09/2021 07:25:04 Link to Item http://hdl.handle.net/10150/621859 GENOMIC CHARACTERIZATION OF THE CACAO SWOLLEN SHOOT VIRUS COMPLEX AND OTHER THEOBROMA CACAO-INFECTING BADNAVIRUSES by Nomatter Chingandu __________________________ A Dissertation Submitted to the Faculty of the SCHOOL OF PLANT SCIENCES In Partial Fulfillment of the Requirements For the Degree of DOCTOR OF PHILOSOPHY WITH A MAJOR IN PLANT PATHOLOGY In the Graduate College THE UNIVERSITY OF ARIZONA 2016 1 THE UNIVERSITY OF ARIZONA GRADUATE COLLEGE As members of the Dissertation Committee, we certify that we have read the dissertation prepared by Nomatter Chingandu, entitled “Genomic characterization of the Cacao swollen shoot virus complex and other Theobroma cacao-infecting badnaviruses” and recommend that it be accepted as fulfilling the dissertation requirement for the Degree of Doctor of Philosophy. _______________________________________________________ Date: 7.27.2016 Dr. Judith K. Brown _______________________________________________________ Date: 7.27.2016 Dr. Zhongguo Xiong _______________________________________________________ Date: 7.27.2016 Dr. Peter J. Cotty _______________________________________________________ Date: 7.27.2016 Dr. Barry M. Pryor _______________________________________________________ Date: 7.27.2016 Dr. Marc J. Orbach Final approval and acceptance of this dissertation is contingent upon the candidate’s submission of the final copies of the dissertation to the Graduate College.
    [Show full text]
  • Explaining Chemical Reactions
    Single and Mixed Infections of Plant RNA and DNA Viruses are Prevalent in Commercial Sweet Potato in Honduras and Guatemala Item Type text; Electronic Thesis Authors Avelar, Ana Sofia Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 27/09/2021 02:50:51 Link to Item http://hdl.handle.net/10150/578609 SINGLE AND MIXED INFECTIONS OF PLANT RNA AND DNA VIRUSES ARE PREVALENT IN COMMERCIAL SWEET POTATO IN HONDURAS AND GUATEMALA by Ana Sofia Avelar ____________________________ A Thesis Submitted to the Faculty of the SCHOOL OF PLANT SCIENCES In Partial Fulfillment of the Requirements For the Degree of MASTER OF SCIENCE In the Graduate College THE UNIVERSITY OF ARIZONA 2015 2 STATEMENT BY AUTHOR This thesis has been submitted in partial fulfillment of requirements for an advanced degree at the University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this thesis are allowable without special permission, provided that an accurate acknowledgement of the source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department or the Dean of the Graduate College when in his or her judgment the proposed use of the material is in the interests of scholarship.
    [Show full text]
  • University of Oklahoma Graduate College Direct Metagenomic Detection and Analysis of Plant Viruses Using an Unbiased High-Throug
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE DIRECT METAGENOMIC DETECTION AND ANALYSIS OF PLANT VIRUSES USING AN UNBIASED HIGH-THROUGHPUT SEQUENCING APPROACH A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By GRAHAM BURNS WILEY Norman, Oklahoma 2009 DIRECT METAGENOMIC DETECTION AND ANALYSIS OF PLANT VIRUSES USING AN UNBIASED HIGH-THROUGHPUT SEQUENCING APPROACH A DISSERTATION APPROVED FOR THE DEPARTMENT OF CHEMISTRY AND BIOCHEMISTRY BY Dr. Bruce A. Roe, Chair Dr. Ann H. West Dr. Valentin Rybenkov Dr. George Richter-Addo Dr. Tyrell Conway ©Copyright by GRAHAM BURNS WILEY 2009 All Rights Reserved. Acknowledgments I would first like to thank my father, Randall Wiley, for his constant and unwavering support in my academic career. He truly is the “Winston Wolf” of my life. Secondly, I would like to thank my wife, Mandi Wiley, for her support, patience, and encouragement in the completion of this endeavor. I would also like to thank Dr. Fares Najar, Doug White, Jim White, and Steve Kenton for their friendship, insight, humor, programming knowledge, and daily morning coffee sessions. I would like to thank Hongshing Lai and Dr. Jiaxi Quan for their expertise and assistance in developing the TGPweb database. I would like to thank Dr. Marilyn Roossinck and Dr. Guoan Shen, both of the Noble Foundation, for their preparation of the samples for this project and Dr Rick Nelson and Dr. Byoung Min, also both of the Noble Foundation, for teaching me plant virus isolation techniques. I would like to thank Chunmei Qu, Ping Wang, Yanbo Xing, Dr.
    [Show full text]