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Análise Comparativa E Funcional Do Genoma De Xanthomonas Citri Pv

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Análise Comparativa E Funcional Do Genoma De Xanthomonas Citri Pv UNIVERSIDADE FEDERAL RURAL PROGRAMA DE PÓS-GRADUAÇÃO DE PERNAMBUCO EM FITOPATOLOGIA PRÓ-REITORIA DE PESQUISA E PÓS-GRADUAÇÃO Tese de Doutorado Análise comparativa e funcional do genoma de Xanthomonas citri pv. viticola: aplicação sobre virulência, patogenicidade e posicionamento taxonômico Antonio Roberto Gomes de Farias Recife - PE 2020 ANTONIO ROBERTO GOMES DE FARIAS ANÁLISE COMPARATIVA E FUNCIONAL DO GENOMA DE Xanthomonas citri pv. viticola: APLICAÇÃO SOBRE VIRULÊNCIA, PATOGENICIDADE E POSICIONAMENTO TAXONÔMICO Tese apresentada ao Programa de Pós-Graduação em Fitopatologia da Universidade Federal Rural de Pernambuco, como parte dos requisitos para obtenção do título de Doutor em Fitopatologia. COMITÊ DE ORIENTAÇÃO: Orientadora: Profa. Dra. Elineide Brarbosa de Souza Coorientadores: Prof. Dr. Marco Aurélio Siqueira da Gama Prof. Dr. Valdir de Quiroz Balbino RECIFE-PE Agosto - 2020 Dados Internacionais de Catalogação na Publicação Universidade Federal Rural de Pernambuco Sistema Integrado de Bibliotecas Gerada automaticamente, mediante os dados fornecidos pelo(a) autor(a) F224a Farias, Antonio Roberto Gomes de Análise comparativa e funcional do genoma de Xanthomonas citri pv. viticola: aplicação sobre virulência, patogenicidade e posicionamento taxonômico / Antonio Roberto Gomes de Farias. - 2020. 173 f. : il. Orientadora: Elineide Barbosa de Souza. Inclui referências e anexo(s). Tese (Doutorado) - Universidade Federal Rural de Pernambuco, Programa de Pós-Graduação em Fitopatologia, Recife, 2020. 1. Vitis vinifera. 2. cancro bacteriano. 3. caracterização genômica. 4. filogenômica. 5. sistema de secreção. I. Souza, Elineide Barbosa de, orient. II. Título CDD 632 ANÁLISE COMPARATIVA E FUNCIONAL DO GENOMA DE Xanthomonas citri pv. viticola: APLICAÇÃO SOBRE VIRULÊNCIA, PATOGENICIDADE E POSICIONAMENTO TAXONÔMICO ANTONIO ROBERTO GOMES DE FARIAS Tese defendida e aprovada pela Banca Examinadora em: 24/08/2020 ORIENTADORA: ___________________________________________________________ Profa. Elineide Barbosa de Souza (UFRPE) EXAMINADORES: ___________________________________________________________ Dr. Nelson Bernardi Lima (INTA) ____________________________________________________________ Prof. Adriano Márcio Freire Silva (UFAL) ___________________________________________________________ Dr. Wilson José Silva Junior (UFPE) ___________________________________________________________ Prof. Marcos Paz Saraiva Câmara (UFRPE) RECIFE-PE Agosto - 2020 Aos meus pais Raimundo e Maria do Carmo por todo amor, suporte, permitindo que eu chegasse até aqui e por compreender minha ausência nos últimos anos, Ofereço. À minha família pelo amor, amizade, suporte e incentivo em todos os momentos e a minha namorada Nan pelo amor e suporte, Dedico. AGRADECIMENTOS Aos meus pais, Raimundo Gomes de Farias e Maria do Carmo Gomes de Farias, pelo alicerce formado e suporte, pelo incentivo para nunca desistir e focar em meus objetivos, proporcionando que eu batalhasse pelos meus sonhos e chegasse até esse momento. Aos meus irmãos, Ronaldo, Marineide, Marileide, Ronildo, Marlene, Marilene, Rodrigo e Macilene, pelos momentos de alegrias, pela amizade, amor, apoio, carinho e risadas quando estamos juntos e por entenderem minha ausência. À minha namorada, Nan, por todo o amor e suporte, mesmo estando tão distante. Aos meus orientadores, Profa Dra. Elineide Barbosa de Souza, Prof. Dr. Marco Aurélio Siqueira da Gama e Prof. Dr. Valdir de Queiroz Balbino, pela oportunidade, orientação, ensinamentos, apoio e confiança. Ao Dr. Jong Hyun Ham da Louisiana State University - LSU, pela oportunidade de fazer parte de seu grupo e pela orientação durante meu período na LSU. À Profa Dra Ana Maria Benko Iseppon que através da Rede InterSys possibilitou o sequenciamento dos genomas analisados neste estudo e pelo auxílio no desenvolvimento inicial da pipeline de análise dos dados. Aos colegas do LAFIBAC - UFRPE, LABBE- UFPE e Plant Bacteriology e Department of Plant Pathology and Crop Physiology - LSU, em especial ao Dr. Wilson Júnior (LABBE) e Dr. Tiago Lelis (LSU), por todo apoio, ensinamentos, suporte e aprendizado em conjunto. À UFRPE, que como instituição me proporcionou a oportunidade de realizar o doutorado, em especial ao Programa de Pós-Graduação em Fitopatologia e sua equipe de docentes e demais funcionários pelos ensinamentos e suporte constante. À todas as demais instituições de ensino pelas quais passei até este momento (IFCE, UFRRJ, UFV, UFLA, UFPE e LSU) pelo ensino e suporte. Aos amigos de fora do meio acadêmico, pela torcida e incentivos constantes. À CAPES, pelo auxílio financeiro através da concessão da bolsa de doutorado no Brasil e Doutorado sanduíche no exterior. A todos os demais que direta ou indiretamente contribuíram com ações que culminaram para este momento. SUMÁRIO CAPÍTULO I - Introdução Geral.................................................................................11 1. INTRODUÇÃO GERAL.....................................................................................12 1.1. A cultura da videira..............................................................................................12 1.2. O cancro bacteriano da videira.............................................................................13 1.2.1. Xanthomonas citri pv. viticola .............................................................................18 1.3. Interações Xanthomonas x hospedeiro.................................................................22 1.4. Mecanismos de patogenicidade e virulência de espécies de Xanthomonas .........24 1.5. Uso da genômica para taxonomia ........................................................................41 2. REFERÊNCIAS BIBLIOGRÁFICAS .................................................................44 CAPÍTULO II ................................................................................................................66 Comparative Genomics of Xanthomonas citri pv. viticola strains raise doubts about the classification of pathovars in X. citri................................................................................67 Abstract ............................................................................................................................68 Introduction ......................................................................................................................69 Material and methods.......................................................................................................70 Results..............................................................................................................................72 Discussion ........................................................................................................................76 References ........................................................................................................................80 CAPÍTULO III ..............................................................................................................105 Insights into the gene content related to pathogenicity and virulence of Xanthomonas citri pv. viticola in grapevines..........................................................................................106 ABSTRACT.....................................................................................................................107 BACKGROUND .............................................................................................................108 RESULTS ........................................................................................................................110 DISCUSSION ..................................................................................................................114 CONCLUSION ................................................................................................................119 MATERIAL AND METHODS .......................................................................................120 REFERENCES.................................................................................................................124 CONCLUSÕES GERAIS................................................................................................171 RESUMO GERAL A viticultura é uma das frutíferas de maior importância econômica mundial. O Brasil é um grande produtor, com destaque para o Submédio do Vale do São Francisco, Região Nordeste, pelo potencial produtivo econômico local. No entanto, a ocorrência de problemas fitossanitários, principalmente o cancro bacteriano da videira causado pela bactéria Xanthomonas citri pv. viticola, têm dificultado essa expansão. Detectada no Brasil pela primeira vez em 1998, esta bactéria se caracteriza como uma das mais importantes fitobacterioses da videira, pelos danos causados e pelo sério risco potencial ao desenvolvimento da viticultura no Brasil e no mundo. Em diversas espécies de Xanthomonas e outras bactérias fitopatogênicas, estudos genômicos e de genética molecular têm revelado os principais mecanismos de patogênese e virulência, adaptabilidade, além de inferências taxonômicas e filogenômicas desses microrganismos. No entanto, estudos envolvendo X. citri pv. viticola para estes propósitos inexistem. Este trabalho teve como objetivos realizar análises pangenômica e filogenômica de X. citri pv. viticola e espécies relacionadas e utilizar análises de genômica comparativa para obtenção de informações sobre funções de possíveis genes de patogenicidade, virulência e aplicações de técnicas moleculares para investigar
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