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Identification of New Sub-Saharan African Begomoviruses and Bemisia Tabaci Species Boundaries

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Identification of New Sub-Saharan African Begomoviruses and Bemisia Tabaci Species Boundaries Identification of new Sub-Saharan African begomoviruses and Bemisia tabaci species boundaries Happyness Gabriel Mollel Tesis Doctoral Málaga 2019 AUTOR: Happyness Gabriel Mollel http://orcid.org/0000-0003-4745-8628 EDITA: Publicaciones y Divulgación Científica. Universidad de Málaga Esta obra está bajo una licencia de Creative Commons Reconocimiento-NoComercial- SinObraDerivada 4.0 Internacional: http://creativecommons.org/licenses/by-nc-nd/4.0/legalcode Cualquier parte de esta obra se puede reproducir sin autorización pero con el reconocimiento y atribución de los autores. No se puede hacer uso comercial de la obra y no se puede alterar, transformar o hacer obras derivadas. Esta Tesis Doctoral está depositada en el Repositorio Institucional de la Universidad de Málaga (RIUMA): riuma.uma.es Departamento de Biología Celular, Genética y Fisiología Facultad de Ciencias Programa de Doctorado de Biotecnología Avanzada Identification of new Sub-Saharan African begomoviruses and Bemisia tabaci species boundaries Memoria de TESIS DOCTORAL presentada por la Licenciada en Biotecnología Happyness Gabriel Mollel para optar al grado de Doctora por la Universidad de Málaga Directores Dr. Jesús Navas Castillo Dr. Elvira Fiallo Olivé Dr. John Colvin Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC) Málaga, octubre 2019 Jesús Navas Castillo, Doctor en Ciencias Biológicas, Investigador Científico del Consejo Superior de Investigaciones Científicas y Profesor Asociado del Departamento de Biología Celular, Genética y Fisiología de la Universidad de Málaga, INFORMA que la licenciada Happyness Gabriel Mollel ha realizado en el Laboratorio de Virología del Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), bajo su dirección y tutoría, el trabajo que con el título “Identification of new Sub-Saharan African begomoviruses and Bemisia tabaci species boundaries” constituye su Tesis Doctoral para aspirar al grado de Doctor en Biología y AUTORIZA su lectura en la Universidad de Málaga, haciendo constar que las publicaciones que avalan esta tesis no han sido utilizadas en tesis defendidas con anterioridad. Y para que así conste y tenga los efectos que correspondan en cumplimiento de la legislación vigente, firma el presente informe en Algarrobo-Costa (Málaga) el 1 de octubre de 2019. Elvira Fiallo Olivé, Doctora en Ciencias Biológicas, Investigadora Contratada del Consejo Superior de Investigaciones Científicas, INFORMA que la licenciada Happyness Gabriel Mollel ha realizado en el Laboratorio de Virología del Instituto de Hortofruticultura Subtropical y Mediterránea “La Mayora” (IHSM-UMA-CSIC), bajo su co-dirección, el trabajo que con el título “Identification of new Sub-Saharan African begomoviruses and Bemisia tabaci species boundaries” constituye su Tesis Doctoral para aspirar al grado de Doctor en Biología y AUTORIZA su lectura en la Universidad de Málaga, haciendo constar que las publicaciones que avalan esta tesis no han sido utilizadas en tesis defendidas con anterioridad. Y para que así conste y tenga los efectos que correspondan en cumplimiento de la legislación vigente, firma el presente informe en Algarrobo-Costa (Málaga) el 1 de octubre de 2019. This work was carried out in the Plant Virology Laboratory at Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) (Algarrobo-Costa, Málaga, Spain) and stays at the Natural Research Institute (NRI), University of Greenwich (Chatham Maritime, United Kingdom). It was funded by the Bill & Melinda Gates Foundation (Head Grant Agreement OPP1058938) through a sub-contract (B0436x12) from the NRI and by the Ministerio de Economía y Competitividad (MINECO, Spain) (project AGL2013-48913-C2-1-R co-financed by the European Regional Development Fund). Part of the results of this Doctoral Thesis have been published in JCR journals: Mollel HG, Ndunguru J, Sseruwagi P, Alicai T, Colvin J, Navas-Castillo J, Fiallo-Olivé E (2017) A novel East African monopartite begomovirus-betasatellite complex that infects Vernonia amygdalina. Archives of Virology 162: 1079-1082 [CHAPTER 1] Mollel HG, Sseruwagi P, Ndunguru J, Alicai T, Colvin J, Navas-Castillo J, Fiallo-Olivé E (2017) Desmodium mottle virus, the first legumovirus (genus Begomovirus) from East Africa. Archives of Virology 162: 1799-1803 [CHAPTER 2] Mollel HG, Ndunguru J, Sseruwagi P, Alicai T, Colvin J, Navas-Castillo J, Fiallo-Olivé E (2019) African basil (Ocimum gratissimum) is a reservoir of divergent begomoviruses in East Africa. Plant Disease (in press) DOI: 10.1094/PDIS-08-19-1675-RE [CHAPTER 3] And presented at the scientific conferences: XIV Congreso Nacional de Virología. Cádiz, 2017. XIX Congreso Nacional de la Sociedad Española de Fitopatología. Toledo, 2018. DEDICATION This thesis is dedicated to my dear husband Juma William Yabeja and lovely son William Juma Yabeja whose their affection, love, encouragement and prayers made me able to get such success and honor, and above all the Almighty God who has led me this far. Every challenging work needs self- effort as well as guidance of elders. I also dedicate this work to my sisters and brothers, and my parents who always loved me unconditionally and taught me to work hard for things I aspire to achieve in life since I was little girl. ACKNOWLEDGEMENTS I would like to express my sincere thanks to my university supervisor, Dr. Jesús Navas-Castillo (IHSM-UMA-CSIC, Spain) and co-supervisors: Dr. Elvira Fiallo-Olivé (IHSM-UMA-CSIC, Spain) and Professor John Colvin (NRI, University of Greenwich, UK), for giving me the opportunity to undertake this study under their supervision, for their constructive criticism and encouragement throughout my study. Special thanks to the Ministerio de Economía y Competitividad (MINECO, Spain) and European Regional Development Fund (AGL2013-48913-C2-1-R), and Bill & Melinda Gates Foundation through a subcontract (B0436x12) from the Natural Resources Institute, University of Greenwich, UK, for funding my tuition fees, research and welfare. I would like to express my sincere appreciations to the team at IHSM-UMA-CSIC especially Ms. Remedios Tovar, Ms. Elisa Navas-Hermosilla, Mr. Miguel López and Mr. Juan Cárdenas García, and team at NRI especially Dr. Sharon van Brunschot, Mr. Stephen Young, Dr. Simon Springate, Dr. Soňa Vyskočilová, Dr. Rekha RA Swamy, Ms. Rebecca Grimsley, Ms. Jackie Atim and Ms. Annet Namuddu for their assistance during my study. I would also like to thank my fellow students and other scientists at IHSM-UMA-CSIC for their support and encouragement during my study. Finally, I would like to thank my parents who nurtured me and sacrificed much of their scarce resources for my education. Their support has enabled me to acquire this higher level of education. TABLE OF CONTENTS ABSTRACT……………………………………………………………………………………………1 RESUMEN EXTENDIDO……………………………………………………………………………5 INTRODUCTION……………………………………………………………………………………17 The genus Begomovirus ............................................................................................................... 19 Genome organization and replication ........................................................................................... 20 Begomovirus ORFs and proteins codified .................................................................................... 21 Phylogeny of begomoviruses ....................................................................................................... 23 Old World and New World begomoviruses .............................................................................. 23 Legumoviruses and sweepoviruses ........................................................................................... 23 DNA satellites associated with begomoviruses ............................................................................. 25 Betasatellites............................................................................................................................ 25 Alphasatellites ......................................................................................................................... 26 Deltasatellites .......................................................................................................................... 26 Taxonomy and nomenclature of begomoviruses and betasatellites................................................ 28 Factors that govern genetic diversity of begomoviruses ................................................................ 28 Mutation .................................................................................................................................. 28 Recombination......................................................................................................................... 29 Pseudo-recombination (reassortment)....................................................................................... 29 Begomoviruses infecting non-cultivated crops ............................................................................. 29 The whitefly Bemisia tabaci ........................................................................................................ 30 Life history .............................................................................................................................. 31 Host range, colonization and population dynamics ................................................................... 33 Systematics .............................................................................................................................
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