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Identificação E Caracterização Genômica Dos Micovírus De Fungos Obtidos Em Amostras De Solo No Pará, Brasil

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Identificação E Caracterização Genômica Dos Micovírus De Fungos Obtidos Em Amostras De Solo No Pará, Brasil INSTITUTO EVANDRO CHAGAS NÚCLEO DE ENSINO E PÓS-GRADUAÇÃO PROGRAMA DE PÓS-GRADUAÇÃO EM VIROLOGIA RAFAEL RIBEIRO BARATA IDENTIFICAÇÃO E CARACTERIZAÇÃO GENÔMICA DOS MICOVÍRUS DE FUNGOS OBTIDOS EM AMOSTRAS DE SOLO NO PARÁ, BRASIL Ananindeua 2019 RAFAEL RIBEIRO BARATA IDENTIFICAÇÃO E CARACTERIZAÇÃO GENÔMICA DOS MICOVÍRUS DE FUNGOS OBTIDOS EM AMOSTRAS DE SOLO NO PARÁ, BRASIL Tese apresentada ao Programa de Pós-Graduação em Virologia do Instituto Evandro Chagas para a obtenção do título de Doutor em virologia Orientador: Dr. Márcio R. Teixeira Nunes Coorientador: Dr. João L. da S. G. Vianez Jr. Ananindeua 2019 Dados Internacionais de Catalogação na Publicação (CIP) Biblioteca do Instituto Evandro Chagas Barata, Rafael Ribeiro. Identificação e caracterização genômica dos micovírus de fungos obtidos em amostras de solo no Pará, Brasil. / Rafael Ribeiro Barata. – Ananindeua, 2019. 76 f.: il.; 30 cm Orientador: Dr. Márcio Roberto Teixeira Nunes Coorientador: Dr. João Lídio da Silva Gonçalves Vianez Júnior Tese (Doutorado em Virologia) – Instituto Evandro Chagas, Programa de Pós-Graduação em Virologia, 2019. 1. Micovírus. 2. Fungos. 3. Filogenia. I. Nunes, Márcio Roberto Teixeira, orient. II. Vianez Júnior, João Lídio da Silva Gonçalves, coorient. II. Instituto Evandro Chagas. III. Título. CDD: 579.2562 RAFAEL RIBEIRO BARATA IDENTIFICAÇÃO E CARACTERIZAÇÃO GENÔMICA DOS MICOVÍRUS DE FUNGOS OBTIDOS EM AMOSTRAS DE SOLO NO PARÁ, BRASIL Tese apresentada ao Programa de Pós-Graduação em Virologia do Instituto Evandro Chagas, como requisito parcial para obtenção de título de Doutor em Virologia Aprovado em: 14/08/2019 BANCA EXAMINADORA Drª Joana D'Arc Pereira Mascarenhas Instituto Evandro Chagas Dr. Sandro Patroca da Silva Instituto Evandro Chagas Drª Valéria Lima Carvalho Instituto Evandro Chagas Dr. Tibério C. T. Burlamaqui Universidade Federal do Pará Drª Silvia Helena Marques da Silva Instituto Evandro Chagas AGRADECIMENTOS Ao Instituto Evandro Chagas. Ao meu orientador, Dr. Márcio Roberto Teixeira Nunes. À toda equipe do Centro de Inovação Tecnológicas, Seção de Arbovirologia e Febres Hemorrágicas. “...to remove all barriers in the way of science.” Alexandra Elba 5 RESUMO Estima-se que existam milhões de espécies de fungos não descobertas no mundo, e grande parte dessa biodiversidade está concentrada em áreas tropicais, como a Amazônia. Nesta região, espécies pouco conhecidas de fungos do solo podem abrigar uma vasta variedade de espécies de vírus, conhecidos como micovírus. Neste estudo, descrevemos três novas espécies de micovírus obtidas do solo da Área de Proteção Ambiental da Ilha do Combu, localizada no estado do Pará, na Amazônia brasileira. Amostras de solo foram coletadas em cinco pontos ao longo de trilhas florestais. Cada amostra foi posteriormente inoculada em placas de Petri contendo ágar batata dextrose para diferenciação entre colônias morfologicamente distintas e isolamento fúngico. O RNA total dos isolados foi extraído e sequenciado usando o Illumina HiSeq 2500. As leituras foram montadas pelo método de novo, e os contigs gerados foram comparados usando Blastx. Os genes ribossomais foram preditos e utilizados para identificação dos fungos usando a região ITS. Os micovírus foram comparados com outros vírus similares disponíveis no banco de dados NCBI através de inferências filogenéticas de máxima verossimilhança baseadas no gene da polimerase. Dos nove fungos isolados, dois continham micovírus. Um micovírus de dsRNA e um de ssRNA positivo, ambos identificados no Simplicillium sympodiophorum, indicando uma coinfecção. Um micovírus de ssRNA negativo também foi detectado em Mucor irregularis. Estes três vírus são espécies novas, e para eles sugerimos os nomes Combu double-strand RNA mycovirus (CDRV), Combu positive-strand RNA mycovirus (CPRV) e Combu negative-strand RNA mycovirus (CNRV). Esses novos vírus são filogeneticamente próximos dos vírus da família Amalgaviridae, no gênero Ourmiavirus e da ordem Bunyavirales, respectivamente. Nossas análises mostram a necessidade urgente de um método expandido de organização taxonômica para esses novos micovírus e outros micovírus ainda não classificados relatados na literatura. Palavras-chave: micovírus; fungos; filogenia. 6 ABSTRACT It is estimated that there are millions of undiscovered fungal species in the world, and much of this biodiversity is concentrated in tropical areas, such as the Amazon. In this region, little- known soil fungal species may harbor a vast bounty of virus species, known as mycoviruses. In this study, we describe three new mycovirus species obtained from the soil of the Combu Island Environmental Protection Area, located in the state of Pará in the Brazilian Amazon. Soil samples were collected at five points along forest trails. Each sample was later inoculated into Petri dishes containing potato dextrose agar for differentiation between morphologically distinct colonies and fungal isolation. Total RNA from the isolates was extracted and sequenced using an Illumina HiSeq 2500. The reads were assembled by the de novo method, and the generated contigs were compared using Blastx. Ribosomal genes were predicted and utilized for fungal identification using the ITS region. The mycoviruses were compared to other similar viruses available in the NCBI database through maximum-likelihood phylogenetic inferences based on the polymerase gene. Of the nine isolated fungal samples, two contained mycoviruses. A dsRNA and a positive ssRNA mycovirus was also identified in Simplicillium sympodiophorum, establishing the presence of simultaneous co-infection. A negative ssRNA mycovirus was also detected in Mucor irregularis. These three viruses are new species, and we suggest the names Combu double-strand RNA mycovirus (CDRV), Combu positive-strand RNA mycovirus (CPRV) and Combu negative-strand RNA mycovirus (CNRV). These novel viruses are phylogenetically close related to viruses of the family Amalgaviridae, in the genus Ourmiavirus and the order Bunyavirales. Our analyses show the urgent need for an expanded taxonomic organization method for these new mycoviruses and for future as-yet-unclassified mycoviruses reported in the literature. Keywords: Mycoviruses; Fungi; Phylogeny. 7 SUMÁRIO 1 INTRODUÇÃO ..................................................................................................................... 8 2 REVISÃO DA LITERATURA .......................................................................................... 10 2.1 O SEQUENCIAMENTO E A DESCOBERTA DE NOVOS VÍRUS ............................... 10 2.2 BREVE HISTÓRICO SOBRE OS MICOVÍRUS ............................................................. 11 2.3 A CRIAÇÃO E A ORGANIZAÇÃO DAS FAMÍLIAS COM MICOVÍRUS .................. 12 2.4 CARACTERÍSTICAS DAS FAMÍLIAS COM MICOVÍRUS ......................................... 16 2.5 NÚMERO DE ESPÉCIES DE FUNGOS E DE MICOVÍRUS ......................................... 27 2.6 RELAÇÃO VÍRUS E HOSPEDEIRO ............................................................................... 28 2.6.1 Reprodução dos Fungos e dos Micovírus .................................................................... 31 2.6.2 Utilização de Micovírus no Controle de Pragas Agrícolas ........................................ 32 2.7 RIQUEZA DE ESPÉCIES DE FUNGOS NO SOLO ........................................................ 33 2.8 ESTUDOS COM MICOVÍRUS NO BRASIL ................................................................... 35 3 OBJETIVOS ........................................................................................................................ 37 3.1 GERAL ............................................................................................................................... 37 3.2 ESPECÍFICOS ................................................................................................................... 37 4 MATERIAL E MÉTODOS ................................................................................................ 38 4.1 ÁREA DE ESTUDO E MÉTODO DE COLETA.............................................................. 38 4.2 ISOLAMENTO DOS FUNGOS A PARTIR DO SOLO ................................................... 38 4.3 EXTRAÇÃO DO RNA E SEQUENCIAMENTO ............................................................. 39 4.4 BIOINFORMÁTICA ......................................................................................................... 40 4.4.1 Identificação molecular dos fungos .............................................................................. 40 4.4.2 Identificação dos vírus .................................................................................................. 41 4.4.3 Análises filogenéticas dos vírus .................................................................................... 41 5 RESULTADOS .................................................................................................................... 42 6 DISCUSSÃO ........................................................................................................................ 55 7 CONCLUSÃO ...................................................................................................................... 60 REFERÊNCIAS ..................................................................................................................... 61 APÊNDICES ........................................................................................................................... 74 8 1 INTRODUÇÃO Os vírus, na condição de parasitas intracelulares obrigatórios,
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