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Genomic Characterization of the Cacao Swollen Shoot Virus Complex and Other Theobroma Cacao-Infecting Badnaviruses

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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. I hereby certify that I have read this dissertation prepared under my direction and recommend that it be accepted as fulfilling the dissertation requirement. _______________________________________________________ Date: 7.27.2016 Dissertation Director: Dr. Judith K. Brown 2 STATEMENT BY AUTHOR This dissertation has been submitted in partial fulfillment of the 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 dissertation 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. In all other instances, however, permission must be obtained from the author. SIGNED: Nomatter Chingandu 3 ACKNOWLEDGEMENTS I would like to thank God, the giver of life, for without Him, this would not have been possible. I am also grateful to my dissertation advisor, Dr. J.K. Brown, for the exceptional guidance and support I received under her supervision. Lastly, to my family who were not able to be with me here, thank you very much for loving and encouraging me. My dear sister Heather Johnson, life would not have been the same without you. May God richly bless you all. 4 DEDICATION This dissertation is dedicated to my lovely daughter, Nikita, who encouraged and supported me incessantly. 5 TABLE OF CONTENTS LIST OF TABLES ...............................................................................................................8 LIST OF FIGURES .............................................................................................................9 ABSTRACT .......................................................................................................................11 CHAPTER 1: INTRODUCTION ......................................................................................13 Literature Review...................................................................................................13 CHAPTER 2: UNEXPECTED GENOMIC VARIABILITY OF CACAO SWOLLEN SHOOT VIRUS AT MULTIPLE LOCI PROVIDES PRELIMINARY EVIDENCE FOR MULTIPLE VIRAL SPECIES ...............................................................................................................28 Abstract ...............................................................................................................28 Introduction ............................................................................................................29 Materials and Methods ...........................................................................................33 Results ...............................................................................................................36 Discussion ..............................................................................................................41 CHAPTER 3: THE CACAO SWOLLEN SHOOT VIRUS COMPLEX IN WEST AFRICA COMPRISES FOUR DIVERGENT SPECIES THAT VARY BY GENOME ARRANGEMENT AND CONSERVED PROTEIN DOMAINS ....................................................................56 Abstract ...............................................................................................................56 Introduction ............................................................................................................57 Materials and Methods ...........................................................................................60 Results ...............................................................................................................65 Discussion ..............................................................................................................71 6 CHAPTER 4: IDENTIFICATION AND CHARACTERIZATION OF PREVIOUSLY ELUSIVE BADNAVIRUS SPECIES ASSOCIATED WITH SYMPTOMATIC THEOBROMA CACAO IN TRINIDAD .....................................................................................................91 Abstract ...............................................................................................................91 Introduction ............................................................................................................91 Materials and Methods ...........................................................................................95 Results ...............................................................................................................99 Discussion ............................................................................................................106 REFERENCES .............................................................................................................118 FUTURE DIRECTIONS .................................................................................................130 7 LIST OF TABLES Table 2.1. Primer pairs used for PCR-amplification of eight Cacao swollen shoot virus regions ............................................................................................................................................47 Table 2.2. Frequency of polymerase chain reaction amplification of a fragment of the Cacao swollen shoot virus (CSSV) genome using the eight primer pairs ....................................47 Table 3.1. Six primer pairs used for PCR-amplification of full-length Cacao swollen shoot virus genomes .............................................................................................................................80 Table 3.2. Analyses of predicted open reading frames identified on the plus-strand of Cacao swollen shoot virus genomes .............................................................................................81 Table 3.3. Functional conserved domains predicted from the ORFs of the sequenced CSSV genomes .............................................................................................................................84 Table 3.4. Percentage pairwise nucleotide identity for the RT-RNase H region of Cacao swollen shoot virus ..........................................................................................................................85 Table 3.5. Percentage pairwise nucleotide identity for the complete genomic sequences of Cacao swollen shoot virus .............................................................................................................86 Table 4.1. Analyses of predicted open reading frames identified on the plus-strand of Cacao mild mosaic virus and Cacao yellow vein-banding virus genome ...........................................112 Table 4.2. Percentage pairwise nucleotide identity for the RT-RNase H locus of Cacao mild mosaic virus and Cacao yellow vein-banding virus ........................................................113 Table 4.3. Percentage pairwise nucleotide identity for Cacao mild mosaic virus and Cacao yellow vein-banding virus complete genome sequences .................................................114 8 LIST OF FIGURES Fig. 1.1. Various symptoms exhibited by CSSV-infected plants ......................................27 Fig. 2.1. Map of Cote d’Ivoire showing the cacao growing regions and specific sites from where the plant samples were collected........................................................................................48
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