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Reconstrução Filogenética Do Filo Arthropoda Baseada No Genoma Mitocondrial

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Reconstrução Filogenética Do Filo Arthropoda Baseada No Genoma Mitocondrial Universidade Federal de Pernambuco Centro de Ciências Biológicas Programa de Pós-Graduacão em Genética Marco Antonio de Oliveira dos Santos Reconstrução Filogenética do Filo Arthropoda Baseada no Genoma Mitocondrial Recife 2012 Marco Antonio de Oliveira dos Santos Reconstrução Filogenética do Filo Arthropoda Baseada no Genoma Mitocondrial Tese apresentada ao Programa de Pós-Graduação em Genética da Universidade Federal de Pernambuco como parte dos requisitos exigidos para obtenção do título de Mestre em Genética. Orientador: Valdir de Queiroz Balbino Recife 2012 ii Catalogação na Fonte: Bibliotecário Bruno Márcio Gouveia, CRB-4/1788 S237r Santos, Marco Antonio de Oliveira dos Reconstrução filogenética do filo Arthropoda baseada no genoma mitocondrial / Marco Antonio de Oliveira Santos. – Recife: O Autor, 2012. 90 f. : il., fig., tab. Orientador: Valdir de Queiroz Balbino Tese (doutorado) – Universidade Federal de Pernambuco. Centro de Ciências Biológicas. Pós-graduação em Genética, 2012. Inclui bibliografia e anexos 1. Artrópode 2. Filogenia 3. Genoma I. Balbino, Valdir de Queiroz (orientador) II. Título. 595 CDD (22.ed.) UFPE/CCB-2013-225 Marco Antonio de Oliveira dos Santos Reconstrução Filogenética do Filo Arthropoda Baseada no Genoma Mitocondrial Aprovado em 06/08/2012 Banca Examinadora: ____________________________________________ Dr. Valdir de Queiroz Balbino Universidade Federal de Pernambuco ____________________________________________ Dr. Marcos Antônio de Morais Junior Universidade Federal de Pernambuco ____________________________________________ Dr. Martin Alejandro Montes Universidade Federal Rural de Pernambuco Recife 2012 iii A todos que acreditam em mim. iv Agradecimentos À minha família que me apoiou e incentivou a sempre buscar o melhor de mim. À minha noiva, Clarice, por sempre ficar ao meu lado, mesmo nas horas mais difíceis, e ter se mostrado uma eterna companheira e sempre compreensiva. Ao professor e orientador Valdir Balbino, pela oportunidade, enorme paciência e vontade de indicar os melhores caminhos. Ao pessoal do laboratório pelo companheirismo, troca de conhecimento e bom humor. Principalmente a Carlos, Marcus, Moisés e Tiago que tornaram esse trabalho mais fácil de realizar. Ao CNPQ pela ajuda financeira e ao LABBE pela disponibilidade da infraestrutura. v Resumo Os Arthropoda formam o grupo animal mais abundante e diverso na terra, com mais de um milhão de espécies descritas, apresentando extrema importância econômica, ambiental e médica. Devido a grande diversidade e antiguidade do grupo, inúmeras hipóteses para explicar a história evolutiva dos Arthropoda foram sugeridas ao longo dos anos. No entanto, as relações entre e dentro dos quatro principais grupos do filo (Crustacea, Hexapoda, Myriapoda e Chelicerata) permanecem como uma das grandes questões em aberto na sistemática. Neste contexto, o genoma mitocondrial representa uma importante fonte de informação para a reconstrução filogenética de um grupo taxonômico tão diverso. Assim, esse trabalho teve como objetivo elucidar as relações filogeneticas do filo Arthropoda a partir dos genomas mitocondriais, completamente sequenciados e disponíveis em bancos de dados públicos, utilizando diferentes abordagens computacionais. As análises dos genomas mitocondriais sugerem, com altos valores de suporte, o monofilétismo dos grupos Pancrustacea (Hexapoda + Crustacea) e Mandibulata (Pancrustacea + Myriapoda) indicando que o grupo irmão dos demais Arthropoda é Chelicerata. Além disso, a utilização da entropia de Shannon se mostrou altamente eficiente na seleção de regiões filogeneticamente informativas, sendo mais efetiva que outros métodos utilizados tradicionalmente na análise de genomas mitocondriais. A entropia também se mostrou como ótima fonte de informações para seleção de regiões conservadas destinadas à determinação de iniciadores degenerados para a amplificação de regiões homólogas. Esse trabalho representa um importante passo para a elucidação da história filogenética do filo Arthropoda. Palavras-chave: Arthropoda; Filogenia Molecular; Genoma Mitocondrial; Entropia. vi Abstract Arthropoda are the most abundant and diverse animal group on earth, with over a million described species. They have very important economic and medical, environmental. Given the great diversity and seniority of the group, several hypotheses to explain the evolutionary history of Arthropoda have been suggested over the years. The relationships between and within these four major lineages of the phylum (Crustacea, Hexapoda, Myriapoda and Chelicerata) lineages remain one of the most contentious issues in systematics. The mitochondrial genome represents an important source of information for phylogenetic reconstructions of a taxonomic group as diverse. Thus, this study aimed to elucidate the phylogenetics relationships of the phylum Arthropoda by use the completely sequenced and available mitochondrial genomes in public databases, using different computational approaches. Analyses of mitochondrial genomes suggest with high values support the monophyly of groups Pancrustacea (Hexapoda + Crustacea) and Mandibulata (Pancrustacea + Myriapoda) indicating that Chelicerata is sister group of other Arthropoda. Furthermore, the use of Shannon's entropy proved highly effective in the selection of phylogenetically informative regions. Shannon's entropy was more effective than other methods traditionally used in the analysis of mitochondrial genomes. The entropy also showed like great source of information for selection of conserved regions to determination of degenerate primers. This work represents an important step to elucidate the phylogenetics history of the phylum Arthropoda. Key words: Arthropoda; Molecular phylogeny; Mitochondrial Genome; Entropy. vii Lista de Ilustrações Figura 1. Diversidade do filo Arthropoda. 3 Figura 2. Esquema genoma mitocondrial. 10 Figura 3. Árvore de UPGMA baseada na ordem gênica do genoma mitocondrial dos Arthropoda. 33 Figura 4. Gráficos mostrando os valores de entropia para os genes ATP6, ATP8, COX1, COX2, COX3, CYTB, ND1 e ND2. 40 Figura 4. Gráficos mostrando os valores de entropia para os genes ND3, ND4, ND4L, ND5 e ND6. 41 Figura 5. Gráficos mostrando a saturação das sequências de DNA iniciais e para os dois métodos de seleção empregados nos genes ATP6, COX1 e COX2. 43 Figura 6. Gráficos mostrando a saturação das sequências de DNA iniciais e para os dois métodos de seleção empregados nos genes COX3, CYTB e ND1. 44 Figura 8. Gráficos mostrando a saturação das sequências de DNA iniciais e para os dois métodos de seleção empregados nos genes ND3, ND4 e ND5. 45 Figura 7. Gráfico mostrando os valores de entropia para os genomas mitocondriais da ordem Diptera. 47 Figura 8. Árvore filogenética da ordem díptera baseada nas regiões amplificadas com iniciadores degenerados. 50 Figura 9. Árvore filogenética do filo Arthropoda baseada nas regiões selecionadas por entropia. 53 Figura 10. Continuação da árvore filogenética do filo Arthropoda baseada nas regiões selecionadas por entropia. 54 Figura 11. Árvore filogenética do filo Arthropoda baseada nos blocos concervados selecionadas. 55 viii Figura 12. Continuação da árvore filogenética do filo Arthropoda baseada nos blocos concervados selecionadas. 56 ix Lista de Tabelas Tabela 1. Variação no viés GC% dos genes mitocondriais 34 Tabela 2. Variabilidade dos genes mitocondriais. 36 Tabela 3. Comparação entre número de sítios identificados como de baixa entropia e pertencentes a blocos conservados. 38 Tabela 4. Iniciadores degenerados definidos para a amplificação dos genomas mitocondriais de dípteros. 48 Tabela 5. Modelos evolutivos aplicados na reconstrução filogenética dos Arthropoda. 51 x Lista de Abreviaturas ATP Adenosina Trifosfato AIC Akaike Information Criterion ATP6 ATP F0 Sintase Subunidade 6 ATP8 ATP F0 Sintase Subunidade 8 COX1 Subunidade 1 da citocromo c oxidase COX2 Subunidade 2 da citocromo c oxidase COX3 Subunidade 3 da citocromo c oxidase CYTB Citocromo B DNA Ácido Desoxirribonucléico EST Etiquetas de Genes Expressos MCMC Cadeia de Markov de Monte Carlo MtDNA DNA Mitocondrial NCBI Centro Nacional para Informação Biotecnológica ND1 Subunidade 1 da NADH Desidrogenase ND2 Subunidade 2 da NADH Desidrogenase ND3 Subunidade 3 da NADH Desidrogenase ND4 Subunidade 4 da NADH Desidrogenase ND4L Subunidade 4L da NADH Desidrogenase ND5 Subunidade 5 da NADH Desidrogenase ND6 Subunidade 6 da NADH Desidrogenase NNI Nearest Neighbor Interchange xi pb Pares de Bases PCR Reação da Polimera em Cadeia RNA Ácido Ribonucléico RNAt Ácido Ribonucléico Transportador UPGMA Método de Agrupamento Pareado Não Ponderado com Média Aritmética xii Sumário Resumo vi Abstract vii Lista de ilustrações viii Lista de tabelas ix Lista de abreviaturas xi 1. Introdução 1 2. Revisão da Literatura 3 2.1. Filo Arthropoda 3 2.1.1 Evolução dos Arthropoda 4 2.1.2. Ordem Diptera 7 2.1.2.1.Gênero Chrysomya (Diptera: Calliphoridae) 9 2.2. Genoma Mitocondrial 9 2.2.1. Genoma Mitocondrial em Estudos Evolutivos 11 2.2.2. Ordem Genética em Mitocôndrias 12 2.3. Filogenia Molecular 13 2.3.1. Métodos para Seleção de Regiões 16 xiii Filogeneticamente Informativas 2.4. Genômica Comparativa 19 3. Objetivos 21 4. Material e Métodos 22 4.1. Criação do Banco de Dados 22 4.1.1. Construção do Banco de Dados Local 22 4.2. Seleção de Genomas 23 4.3. Análise de Sintenia 24 4.4. Alinhamento de Sequências 24 4.5. Análises de Variabilidade 25 4.6. Identificação de Regiões Problemáticas 26 4.7. Definição de Iniciadores Para Amplificação do Genoma Mitocondrial
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