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Metagenomic Analysis of the Begomovirus Diversity in Tomatoes in Central Brazil and Impact of the Ty-1 Tolerance Gene on Viral Evolutionary Dynamics

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Metagenomic Analysis of the Begomovirus Diversity in Tomatoes in Central Brazil and Impact of the Ty-1 Tolerance Gene on Viral Evolutionary Dynamics Universidade de Brasília Instituto de Ciências Biológicas Departamento de Fitopatologia Programa de Pós-Graduação em Fitopatologia Doctoral Thesis Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics LUCIANE DE NAZARÉ ALMEIDA DOS REIS Brasília - DF 2020 LUCIANE DE NAZARÉ ALMEIDA DOS REIS Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics Thesis presented to the University of Brasília as a partial requirement for obtaining the title of Doctor in Phytopathology by the Post-Graduate Program in Phytopathology. Advisor Dra. Rita de Cássia Pereira Carvalho Co-advisor Dr. Leonardo Silva Boiteux BRASÍLIA, DF– BRASIL 2020 FICHA CATALOGRÁFICA Reis, A. N. L. Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics Luciane de Nazaré Almeida dos Reis. Brasília, 2020. Pages number p.:205 Doctoral Thesis - Programa de Pós-Graduação em Fitopatologia, Universidade de Brasília, Brasília, DF. I- Tomato, NGS, Geminiviridae, Begomovirus, Genomoviridae. II- Universidade de Brasília. PPG/FIT. III- Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics Aos meus pais Eliecê Almeida dos Reis e Lucival Nunes dos Reis. Ao meu irmão Luan Almeida dos Reis. Aos meus avós Deusarina Goes Almeida e Ubiratan Nascimento Almeida (In memorian). Ao meu Amor Gustavo Ribeiro Dedico Agradecimentos A Deus, dono de toda a ciência, sabedoria e poder. Minha gratidão pelo dom da vida e por toda a força para que eu terminasse mais essa etapa da minha vida. Aos meus pais Eliecê Almeida dos Reis e Lucival Nunes dos Reis por todo apoio e amor incondicional. Ao meu irmão amado, Luan Almeida dos Reis. Ao meu amor, meu namorado Gustavo Ribeiro por todo apoio, paciência e carinho durante todo esse tempo. Aos pais do meu namorado Márcia Rodrigues e Carlos Rodrigues por toda a ajuda e por me receberem com todo o carinho na sua casa. A minha orientadora professora Rita de Cássia Pereira Carvalho pela amizade, incentivo e orientação durante todos esses anos de mestrado e doutorado. Ao meu co-orientador Leonardo Silva Boiteux por toda a ajuda, incentivo e orientação durante todos esses anos de doutorado. Ao Dr. Fernando Lucas de Melo pela colaboração e incentivo. A Dra. Maria Esther Noronha Fonseca Boiteux por todo incentivo e colaboração no trabalho. Aos colegas do mestrado e doutorado Flávia, Josiane, Macária, Ikaro e Juliana. Aos colegas de laboratório Felipe, Maria Luísa, Amanda, Jordânia e Vinícius. Em especial agradeço a Josiane e Felipe pela amizade e carinho durante todos esses anos desde o meu mestrado, por terem tornado meus dias mais alegres no laboratório. As minhas amigas a distância Ghaby Berberian e Kamille Vieira pelas conversas e apoio. A minha companheira e amiga de República Fernanda Kitano, pelo apoio e palavras de incentivo. Aos amigos que fiz durante esses anos de UnB: Lucas, Catharine, Jamile, João Lucas, Kamila, Vitória, Elenice, Anna Sofya, Érica, Lincon, Sheila, Jefferson e Bianca agradeço por todo o carinho. Aos professores: Juvenil Enrique Cares, Cleber Furlanetto, Adalberto Côrrea Café Filho, Carlos Hidemi Uesugi, Renato de Oliveira Resende, Fernando Lucas Melo, Maurício Rossato, Alice Kazuko Inoue-Nagata, Robert Neil Gerard Miller, Marisa Álvares da Silva Velloso Ferreira, Helson Mario Martins do Vale, José Carmine Dianese, Luís Eduardo Bassay Blum, Denise Vilela de Rezende e Danilo Batista Pinho. A Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES). Ao Programa de Pós-Graduação em Fitopatologia da Universidade de Brasília (PPG-FIT). Ao Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico (CNPq) pela bolsa de estudos. Work carried out in the Department of Plant Pathology of the Institute of Biological Sciences of the University of Brasília (UnB), under the guidance of Dr. Rita de Cássia Pereira Carvalho. Financial Support by Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Embrapa. Metagenomic analysis of the begomovirus diversity in tomatoes in Central Brazil and impact of the Ty-1 tolerance gene on viral evolutionary dynamics LUCIANE DE NAZARÉ ALMEIDA DOS REIS Thesis approved__/__/___by: ___________________________________________ Dr. Cleber Furlanetto Departament of Plant Pathology (UnB) (Internal Examiner) ___________________________________________ Érico de Campos Dianese Universidade Federal de Goiás (UFG) (External Examiner) ___________________________________________ Dra. Mirtes Freitas Lima Embrapa Vegetable Crops (External Examiner) ___________________________________________ Gabriel Sérgio Costa Alves Departament of Cell Biology (UnB) (External Examiner – Surrogate) ___________________________________________ Dra. Rita de Cássia Pereira Carvalho Departament of Plant Pathology (UnB) (President) BRASÍLIA, DF – BRASIL 2020 SUMMARY LIST OF FIGURES ...................................................................................................... 11 LIST OF TABLES ........................................................................................................ 20 RESUMO GERAL ....................................................................................................... 21 GENERAL ABSTRACT........................................................................................................23 GENERAL INTRODUCTION ................................................................................... 25 HYPOTHESES ............................................................................................................. 27 GENERAL OBJECTIVE ............................................................................................ 27 SPECIFICS OBJECTIVES ......................................................................................... 27 CHAPTER 1. LITERATURE REVIEW ................................................................... 28 1. The tomato ............................................................................................................. 28 2. Main pathogens in tomato crop ............................................................................... 29 2.1. Main fungal pathogens ......................................................................................... 29 2.2. Main bacterial pathogens ..................................................................................... 29 2.3. Main nematode pathogens ................................................................................... 30 2.4. Diseases of viral etiology ..................................................................................... 30 3. Family Geminiviridae ............................................................................................ 32 3.1. Genera of the Geminiviridae family .................................................................. 35 3.1.1. Becurtovirus ..................................................................................................... 35 3.1.2. Capulavirus ...................................................................................................... 35 3.1.3. Curtovirus ......................................................................................................... 36 3.1.4. Eragrovirus ...................................................................................................... 36 3.1.5. Grablovirus ....................................................................................................... 36 3.1.6. Mastrevirus ....................................................................................................... 36 3.1.7. Topocuvirus ...................................................................................................... 37 3.1.8. Turncurtovirus ................................................................................................. 37 3.1.9. Begomovirus ..................................................................................................... 38 4. Transmission of begomovirus species ................................................................. 42 5. Satellite DNAs associated with begomovirus species ......................................... 45 6. Replication of begomovirus in host cells ............................................................. 47 7. Genetic variability in begomovirus ..................................................................... 48 8 7.1. Mutation……………………………………………………………………..…...48 7.2. Recombination…………………………………………………………………...49 7.3. Pseudo-recombination…………………………………………………………....50 8. Begomovirus diversity in tomato in Brazil and the world ................................. 50 9. Resistance genes to begomovirus characterized in tomato ............................... 63 10. Next-generation Sequencing (NGS) applied to Plant Virology....................... 68 11. Family Genomoviridae ........................................................................................ 72 11.1 Gemycircularvirus .............................................................................................. 75 CHAPTER 2. Metagenomics of Neotropical single-stranded DNA (ssDNA) viruses in tomato cultivars with and without the Ty–1 gene.................................................
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