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Carvalho Db Dr Arafcf.Pdf (5.863Mb) Universidade Estadual Paulista “Júlio de Mesquita Filho” UNESP Faculdade de Ciências Farmacêuticas Campus de Araraquara “Estudo de transcriptomas por RNAseq em tecidos de cabeça e glândula salivar de Rhodnius montenegrensis e Rhodnius robustus (Hemiptera, Reduviidade, Triatominae). ” Danila Blanco de Carvalho Tese apresentada ao Programa de Pós-Graduação em Biociências e Biotecnologia aplicadas à Farmácia, da Faculdade de Ciências Farmacêuticas, UNESP, como parte dos requisitos para obtenção do Título de Doutor em Biociências e Biotecnologia Aplicadas à Farmácia. Orientador: Prof. Dr. João Aristeu da Rosa Co-orientador: Prof. Dr. Reinaldo Alves de Brito Araraquara – SP 2016 Ficha Catalográfica Elaborada Pelo Serviço Técnico de Biblioteca e Documentação Faculdade de Ciências Farmacêuticas UNESP – Campus de Araraquara Carvalho, Danila Blanco de C331e Estudo de transcriptomas por RNAseq em tecidos de cabeça e glândula salivar de Rhodnius montenegrensis e Rhodnius robustus (Hemiptera, Reduviidade, Triatominae) / Danila Blanco de Carvalho – Araraquara, 2016 81 f. Tese (Doutorado) – Universidade Estadual Paulista. “Júlio de Mesquita Filho”. Faculdade de Ciências Farmacêuticas. Programa de Pós Graduação em Biociências e Biotecnologia aplicadas à Farmácia Orientador: João Aristeu da Rosa Co-orientador: Reinaldo Alves de Brito 1. Doença de Chagas. 2. Triatominae. 3. Rhodnius. 4. Diferenciação específica. 5. Diferenciação molecular. I. Rosa, João Aristeu da, orient. II. Brito, Reinaldo Alves de, coorient. III. Título. CAPES: 40300005 Esse trabalho foi desenvolvido no Laboratório de Parasitologia da Faculdade de Ciências Farmacêuticas da Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Campus de Araraquara-SP, com apoio da CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior), por meio da concessão de bolsa de Doutorado vinculada ao projeto "Estudo Biológico e taxionômico de vetores Trypanosomatidae" - AUXPE - Parasitologia - 1528/2011 processo nº 23038.005285/2011-12 (Processo 2009/52236-2). Dedicatória Ao meu filho, Dante, que chegou alegrando e completando nossas vidas; ao meu marido, Rafael, pelo apoio, companheirismo, compreensão e paciência; aos meus pais, Jerônymo e Maria Eugênia, pelo carinho e confiança e à minha avó Maria da Conceição que sempre acreditou nos meus sonhos! AGRADECIMENTOS Ao Prof. Dr. João Aristeu da Rosa, meu orientador, por todo apoio, amizade incentivo e confiança, desde a graduação, fundamentais para meu crescimento científico, profissional e pessoal! Obrigada! Ao Prof. Dr. Reinaldo Alves de Brito, pela co-orientação, parceria e por gentilmente ter me recebido em seu Laboratório e cedido seu tempo, estrutura e pessoal para o desenvolvimento deste estudo! Ao programa de Pós Graduação em Biociências e Biotecnologia Aplicadas à Farmácia, que possibilitou a execução deste estudo! À CAPES, pela bolsa e auxilio projeto "Estudo Biológico e taxionômico de vetores Trypanosomatidae" - AUXPE - Parasitologia - 1528/2011 processo nº 23038.005285/2011-12 (Processo 2009/52236-2). Ao Prof. Dr. Daniel Frías Lasserre, pela recepção, gentileza e trabalho em seu laboratório durante meu estágio sanduíche na Universid Metropolitana de la Ciencia de la Educacíon em SantiaGO, Chile! Aos colegas do Laboratório de Parasitologia da FCF e do laboratório de Genética de Populações da UFSCAr, pela amizade, apoio, incentivo e convivência, que foram fundamentais para o desenvolvimento desse trabalho! À Dra. Samira Chahad Ehlers pelas aulas de dissecação, auxílio, sugestões, confiança e amizade que foram importantes em todas as etapas para que este trabalho fosse desenvolvido! Ao Dr. Carlos Congrains, pela amizade e por prontamente ter me auxiliado nas etapas de bioinformática fundamentais deste trabalho! À amiga Heloísa Pinotti, pelo auxilio em muitas etapas do trabalho, inclusive como motorista no final da gestação do Dante! Ao amiGO Jader de Oliveira, pela amizade e auxilio na identificação morfológica das espécies do trabalho e também com os diversos tipos de inseto! Às funcionárias Cláudia Lúcia Molina, Daniela Altieri Tita Lockermann Oliveira, Joyce Conceição G. Romero e Flavia Sousa De Jesus da Seção de Pós-Graduação, pela amizade, gentileza e pronto atendimento! A todos os funcionários da FCF que direta, ou indiretamente contribuíram para minha estadia. Aos meus pais pelo apoio e confiança sempre depositados! Ao meu marido, Rafael, pela força e paciência durante todos esses anos! Ao meu filho, Dante, que veio alegrar nossas vidas. Aos meus amiGOs e demais familiares pela paciência, compreensão! E, principalmente a Deus, pela saúde e força durante todos os momentos da minha vida! A todos, muito obrigada! “Só entende o que encontra, quem sabe o que procura. ” Prof. Antônio Carlos Pizolitto Lista de Siglas e Abreviaturas DCA: doença de Chagas aguda SINAN: Sistema de Informação de Agravos de Notificação Rm: Rhodnius montenegrensis Rr: Rhodnius robustus SNP: Polimorfismo de Nucleotídeo Único GO: Gene Ontology Lista de Figuras Figura 1 Fêmea de R. montenegrensis. A. dorsal; B. ventral 36 Figura 2 Fêmea de R. robustus. A. dorsal; B. ventral 37 Figura 3 Termos do Gene Ontology encontrados para as regiões codificantes de R. montenegrensis e R. robustus 48 Figura 4 Valor absoluto da diferença de frequências (D) dos alelos em 13.696 SNPs compartilhados entre R. montenegrensis e R. robustus 49 Figura 5 Diferença média de frequência dos alelos dos transcritos (D̅) entre R. montenegrensis e R. robustus 50 Figura 6 Distribuição de SNPs por contig 50 Lista de Tabelas Tabela 1 Resumo estatístico das montagens de tecido de cabeça e glândula salivar de R. montenegrensis (Rm) e R. robustus (Rr) 46 Tabela 2 Anotação pelo programa Blastx dos contigs com 100% de diferença após o enriquecimento com o TopGO 51 Tabela 3 Anotação e função dos 7 contigs sabidamente importantes com Ka/Ks maior que 1 52 Glossário Contig: conjunto de reads formados após a montagem, seriam os “genes”. 퐃̅ : média de D para os SNPs de um determinado transcrito. D: diferença entre as frequências alélicas de um SNP da variante R. montenegrensis e R. robustus. Kmer: fragmentos gerados pelo programa de montagem Trinity para reorganizá-los em contigs. N50: metade da soma dos comprimentos de todos contigs. O número de bases de todas os contigs mais curtos do que o N50 estará perto do número de bases de todos contigs mais lonGOs do que o N50. Pair –end reads: o programa gera sempre um par de read. Read: são as sequências de leitura feitas pelo sequenciador. SNP : Polimorfismo de Nucleotídeo Único. SNP calling: procurar esses polimorfismos entre os alelos, feito pelo programa VarScan 2. SUMÁRIO Lista de Abreviaturas e Siglas 08 Lista de Figuras 09 Lista de Tabelas 10 Glossário 11 Capítulo I 15 1. Resumo 16 2. Abstract 18 3. Introdução 20 3.1. Situação da doença de Chagas no Brasil e no Mundo 21 3.2. Triatomíneos e Distribuição espacial no Brasil 24 3.3. Espécies do gênero Rhodnius 28 3.4. Processo de especiação 29 3.5. Sequenciamento de Próxima geração 32 4. Objetivos 35 4.1. Caracterização de transcriptoma de tecidos de cabeça e 35 glândulas salivares de R. montenegrensis e R. robustus. 4.2. Buscar diferenças que possam auxiliar no entendimento do processo de diferenciação, bem como para a identificação 35 específica de R. montenegrensis e R. robustus. 5. Material e Métodos 35 5.1. Exemplares 35 5.2. Dissecação dos insetos 37 5.3. Extração do RNA total 38 5.4. Purificação do RNA 39 5.5. Sequenciamento em Hi-seq 2500 Illumina 39 5.6. Análise de bioinformática 39 5.6.1. Filtragem e montagem das sequências – SeqyClean e 40 Trinity 5.6.2. Alinhamento das Sequências - Bowtie2 41 5.6.3. Busca de Variantes - VarScan2 42 5.6.4. Predição de regiões codificantes (CDS) 42 5.6.5. Avaliação da qualidade da montagem e anotação do transcriptoma por BUSCO 43 5.6.6. Anotação funcional 43 5.6.7. Teste de seleção Ka/Ks 44 6. Resultados 45 6.1. De novo transcriptome assembly 45 6.2. Regiões codificantes (CDS) e anotação funcional 46 49 6.3. Polimorfismo de Nucleotídeo Único (SNPs) encontrado 51 6.4. Anotação funcional dos contigs D̅ = 100% 51 6.5. Teste de seleção Ka/Ks 7. Discussão 52 8. Conclusão 58 9. Desafios encontrados no decorrer do estudo 58 10. Referências bibliográficas 59 Capítulo II 66 A novel association between Rhodnius neglectus and Livistona australis palm tree in an urban center foreshadowing the risk of Chagas disease transmission by vectorial invasions in Monte Alto City, São Paulo, Brazil. Study of the external female genitalia of 14 Rhodnius species (Hemiptera, Reduviidae, Triatominae) using scanning electron microscopy. CAPÍTULO I 1. Resumo CARVALHO, Danila Blanco. “Estudo de transcriptomas por RNAseq em tecidos de cabeça e glândula salivar de Rhodnius montenegrensis e Rhodnius robustus (Hemiptera, Reduviidade, Triatominae)”. Defesa (Doutorado em Biociências e Biotecnologia aplicadas à Farmácia) – Faculdade de Ciências Farmacêuticas – UNESP, Araraquara, SP. A doença de Chagas é uma das principais parasitoses que ocorrem na América Latina, cujo agente etiológico é o protozoário Trypanosoma cruzi, que é veiculado por triatomíneos. Estima-se que entre oito milhões de pessoas estejam infectadas. Rhodnius é um dos gêneros que pode veicular T. cruzi e inclui espécies estreitamente relacionadas com baixos níveis de diferenciação morfológica. Atualmente, existem 19 espécies conhecidas, entre elas, Rhodnius montenegrensis que é considerada a fim de Rhodnius robustus. Para investigar as diferenças
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