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Diversity of Bemisia Tabaci, the Bacterial Endosymbionts It Harbours and Geminiviruses It Acquires Across Pakistan

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Diversity of Bemisia Tabaci, the Bacterial Endosymbionts It Harbours and Geminiviruses It Acquires Across Pakistan Diversity of Bemisia tabaci, the Bacterial Endosymbionts it Harbours and Geminiviruses it Acquires Across Pakistan Mariyam Masood 2019 Department of Biotechnology Pakistan Institute of Engineering and Applied Sciences Nilore, Islamabad, Pakistan This page intentionally left blank. Diversity of Bemisia tabaci, the Bacterial Endosymbionts it Harbours and Geminiviruses it Acquires Across Pakistan Mariyam Masood Submitted in partial fulfillment of the requirements for the degree of Ph.D. 2019 Department of Biotechnology Pakistan Institute of Engineering and Applied Sciences Nilore, Islamabad, Pakistan Dedications To my Parents And My Husband ii Acknowledgements Saying of the Holy Prophet Muhammad (SAW) is, “A person who is not thankful to his benefactor is not thankful to Allah”. All acclamations, appreciations, and praises go to ALLAH ALMIGHTY, The Supreme, Self-existing, The Compassionate, The Creator of the universe and the day of repayment, Who blessed me with the ability to observe, the mind to thoughts, health and opportunity to add a drop to the already existing ocean of knowledge. I offer my humblest thanks and countless salutations to the Holy Prophet Muhammad (SAW), the bacon of light, the city of eternal knowledge, the messenger of peace, the biggest benefactor of the mankind and forever torch of guidance for humanity. I have no words to thanks my supervisor Dr. Rob W. Briddon. When he left NIBGE he never let me feel at any stage that he is away, always does every possible effort to resolve the problems. I feel lucky to have him as my supervisor, he told me what the actual science and scientific attitude is. I really appreciate his valuable comments, advice, and support in overcoming the numerous obstacles I have been facing through my research and during write up. I feel special being your last Ph.D student in NIBGE. I would like to express my utmost gratitude to Co-supervisor and Director NIBGE, Dr. Shahid Mansoor (SI), for providing me the opportunity to do Ph.D. in a prestigious research institute NIBGE. I am very thankful to him for providing me the not only infrastructure and scientific platform to conduct this research work but also the valuable suggestions he gave throughout my research. I express my utmost appreciation to Dr. Zahid Mukhtar (DCS), Head of Agricultural Biotechnology Division (ABD), NIBGE, for facilitating a pleasant and working environment. A special mention is required for Dr. Imran Amin, a soft-hearted person with scientific attitude. I appreciate him for his valuable feedback, cooperation, and suggestions regarding research. I a am thankful to Dr. Muhammad Saeed for his cooperation. I would also like to thank the Higher Education Commission of Pakistan for funding my six-month stay in the USA. I have no words to say thanks to all my iii senior lab fellows for their being cooperative, Dr. Zafar Iqbal, Qamar Abbas, Dr. Muhammad Shafiq, Dr. M. Nouman Tahir, Dr. Amir Raza, Dr. Amir Hameed, Dr. Ishtiaq Hasan, Dr. Shaista Javaid, Dr. Huma Mumtaz and junior Ali Tahir and Ali Raza. I am very much thankful to my class fellows for providing me best company, Shan-e-Ali Zaidi, Muhammad Umar, Hassan Jamil Malik, Rubab Zehra Naqvi. Nevertheless, I truly blessed to have a gang of friends Muhammad Hamza Rana, Hira Kamal, Roma Mustafa, Iqra Sohail, Hazrat Ismail. I am very much thankful to them for only providing me the moral and emotional support but for being supportive during up and down. Regarding the provision of chemicals and availability of lab equipment, the best technical assistance was provided by Mr. Atiq-ur-Rehman. I want to convey special acknowledgment to the lab supporting staff, Mrs. Yasmeen, Rizwan Ahmad, Amir Iqbal and Ghulam Mustafa for their cooperation in lab work. I am also pleased to acknowledge Dr. Angela.E. Douglas, Cornell University, the USA for her extensive cooperation, guidance, and encouragement during my stay at her lab. I am also very thankful to Dr. Judith K. Brown for giving valuable suggestion in manuscript writing. I also want to appreciate Muhammad Iqbal, Mr. Asif and Mr. Ali Imran of University Cell. They always facilitated and never wasted my time in official hurdles. Last but not least I would like to thank my family; my parents, My Father Masood-ul-Hassan and Mother Mrs. Azra Masood, they deserve special mention for their inseparable support and prayers. My Father-in-Law, Mr. Mujahid Hussain, especially my Mother-in-Law Mrs. Rubina Mujahid for being cooperative all the time. I have no words to express my feelings for my husband, Umair Hussain. I am thankful for his never-ending support, unconditional love and for tolerating my tantrums. I am thankful to my loving son Sarib Umair for being an inspiration and reason for joy. I am thankful to Mansoor-ul-Hassan, Madiha Masood, Ummara Qureshi, Shahnah Qureshi, Yamina Qureshi for providing me escape from my work. Mariyam Masood iv v Copyrights Statement The entire contents of this thesis entitled Diversity of Bemisia tabaci, the Bacterial Endosymbionts it Harbours and the Geminiviruses it Acquires Across Pakistan by Mariyam Masood are an intellectual property of Pakistan Institute of Engineering & Applied Sciences (PIEAS). No portion of the thesis should be reproduced without obtaining explicit permission from PIEAS. vi Table of Contents Dedications .................................................................................................................... ii Acknowledgments......................................................................................................... iii Declaration of Originality ............................................ Error! Bookmark not defined. Copyrights Statement ..................................................................................................... v Table of contents .......................................................................................................... vii List of Figures ................................................................................................................ x List of Tables ................................................................................................................ xi Abstract ....................................................................................................................... xii List of Publications ..................................................................................................... xiv List of Abbreviations and Symbols.............................................................................. xv 1 Introduction and Review of Literature ................................................................... 1 1.1 Bemisia tabaci ................................................................................................. 1 1.1.1 Morphology.............................................................................................. 1 1.1.2 Geographical Distribution ........................................................................ 2 1.1.3 Host Range ............................................................................................... 2 1.1.4 Life Cycle of Bemisia tabaci ................................................................... 2 1.2 Economic Impact of B. tabaci ......................................................................... 4 1.3 History and Synonymization ........................................................................... 6 1.4 Host Races and the Biotype Concept .............................................................. 7 1.5 Bemisia tabaci, a Cryptic Species Complex ................................................... 8 1.6 Endosymbionts ................................................................................................ 9 1.6.1 Primary Endosymbionts ........................................................................... 9 1.6.2 Secondary Endosymbionts ..................................................................... 10 1.7 Bemisia tabaci Transmitted Viruses ............................................................. 13 1.8 Mechanisms of Virus Transmission by Whiteflies ....................................... 13 1.8.1 Begomovirus Transmission by B. tabaci ............................................... 13 1.9 Geminiviruses................................................................................................ 14 1.9.1 Classification of Geminiviruses ............................................................. 16 1.9.2 The Genus Begomovirus ........................................................................ 16 1.9.3 Satellites Associated with Geminiviruses .............................................. 19 1.10 Objectives of the Study.............................................................................. 24 vii 2 Materials and Methods ......................................................................................... 25 2.1 Insect Collection and Storage ........................................................................ 25 2.2 DNA Extraction............................................................................................. 25 2.3 Quantification of DNA .................................................................................. 25 2.4 Amplification of DNA .................................................................................. 25 2.4.1 Polymerase Chain Reaction (PCR) Amplification ................................ 25 2.4.2 Rolling Circle Amplification (RCA) ..................................................... 26 2.5 Gel Electrophoresis
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