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Análise Em Larga Escala Das Regiões Intergênicas ITS, ITS1 E ITS2 Para O Filo Basidiomycota (Fungi)

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Análise Em Larga Escala Das Regiões Intergênicas ITS, ITS1 E ITS2 Para O Filo Basidiomycota (Fungi) UNIVERSIDADE FEDERAL DE MINAS GERAIS INSTITUTO DE CIÊNCIAS BIOLÓGICAS PROGRAMA INTERUNIDADES DE PÓS-GRADUAÇÃO EM BIOINFORMÁTICA DISSERTAÇÃO DE MESTRADO FRANCISLON SILVA DE OLIVEIRA Análise em larga escala das regiões intergênicas ITS, ITS1 e ITS2 para o filo Basidiomycota (Fungi) Belo Horizonte 2015 Francislon Silva de Oliveira Análise em larga escala das regiões intergênicas ITS, ITS1 e ITS2 para o filo Basidiomycota (Fungi) Dissertação apresentada ao Programa Interunidades de Pós-Graduação em Bioinformática da UFMG como requisito parcial para a obtenção do grau de Mestre em Bioinformática. ORIENTADOR: Prof. Dr. Guilherme Oliveira Correa CO-ORIENTADOR: Prof. Dr. Aristóteles Góes-Neto Belo Horizonte 2015 AGRADECIMENTOS À minha família e amigos pelo amor e confiança depositadas em mim. Aos meus orientadores Guilherme e Aristóteles por todo o suporte oferecido durante todo o mestrado. À Fernanda Badotti pelas discussões biológicas sobre o tema de DNA barcoding e por estar sempre disposta a ajudar. À toda equipe do Centro de Excelência em Bioinformática pelos maravilhosos momentos que passamos juntos. Muito obrigado por toda paciência nesse momento final de turbulência do mestrado. Aos membros do Center for Tropical and Emerging Global Diseases pela sensacional receptividade durante o meu estágio de quatro meses na University of Georgia. Um agradecimento especial à Dra. Jessica Kissinger pelos conselhos científicos e à Betsy pela atenção e disponibilidade de ajudar a qualquer momento. Aos colegas do programa de pós-graduação em bioinformática da UFMG pelos momentos de descontração e discussão científica na mesa do bar !. Aos membros da secretaria do programa de pós-graduação pela simpatia e vontade de ajudar sempre. Em especial à Sheila que é um anjo. À Vale, NIH e FAPEMIG pelo provimento de minha bolsa e pelo suporte financeiro para participação em eventos científicos. SUMÁRIO 1! INTRODUÇÃO ................................................................................................................ 1! 1.1! CÓDIGO DE BARRAS DE DNA ......................................................................................... 1! 1.2! A REGIÃO ITS ................................................................................................................. 3! 1.3! REINO FUNGI .................................................................................................................. 3! 1.3.1! Filo Basidiomycota .................................................................................................... 4! 2! OBJETIVOS ..................................................................................................................... 6! 2.1! OBJETIVO GERAL ........................................................................................................... 6! 2.2! OBJETIVOS ESPECÍFICOS ............................................................................................... 6! 3! MATERIAL E MÉTODOS ............................................................................................ 6! 3.1! AQUISIÇÃO DOS DADOS .................................................................................................. 6! 3.2! FILTRAGEM DO BANCO DE DADOS .................................................................................. 8! 3.2.1! Filtros de qualidade .................................................................................................. 9! 3.2.2! Filtros lógicos ........................................................................................................... 10! 3.3! ANÁLISE DOS DADOS ..................................................................................................... 11! 3.3.1! Análise de Barcode Gap .......................................................................................... 11! 3.3.2! Probabilidade de identificação correta ................................................................. 12! 3.3.3! Validação cruzada com BLAST ............................................................................ 12! 4! RESULTADOS E DISCUSSÃO ................................................................................... 13! 4.1! GÊNEROS COM BARCODE GAP ....................................................................................... 15! 4.2! GÊNEROS COM BARCODE GAP EXCLUINDO AS DISTÂNCIAS ATÍPICAS .......................... 25! 4.3! GÊNEROS SEM BARCODE GAP ........................................................................................ 34! 5! CONCLUSÕES .............................................................................................................. 45! REFERÊNCIAS ..................................................................................................................... 46! APÊNDICE I – LINHAS DE COMANDO DA ETAPA DE FILTRAGEM .................... 49! APÊNDICE II – LINHAS DE COMANDO DA ETAPA DE ANÁLISE ......................... 50! APÊNDICE III – ESPÉCIMES UTILIZADOS NAS ANÁLISES .................................... 52! LISTA DE ILUSTRAÇÕES Figura 1: Diagrama de aquisição dos dados do Genbank ........................................................... 7! Figura 2: Exemplo de um cabeçalho FASTA proveniente do UNITE ....................................... 8! Figura 3: Linhas de comando para aquisição dos dados ............................................................. 8! Figura 4: Etapas de Filtragem ..................................................................................................... 9! Figura 5: Países com espécimes na base de análise estudada ................................................... 14! Figura 6: Gráficos de barcode gap para os gêneros Agaricus (A), Antherospora (B), Ceriporiopsis (C), Clavaria (D), Cystodermella (E) e Descolea (F) ....................... 18! Figura 7: Gráficos de barcode gap para os gêneros Endoraecium (A), Entyloma (B), Exobasidium (C), Favolus (D), Fibroporia (E) e Flammulina (F) .......................... 19! Figura 8: Gráficos de barcode gap para os gêneros Fuscoporia (A), Gloeophyllum (B), Gymnopilus (C), Helicobasidium (D), Hyphodermella (E) e Lepista (F) ................ 20! Figura 9: Gráficos de barcode gap para os gêneros Leucopaxillus (A), Lycoperdon (B), Lyomyces (C), Lyophyllum (D), Neofavolus (E) e Octaviania (F) ........................... 21! Figura 10: Gráficos de barcode gap para os gêneros Oligoporus (A), Phellinus (B), Porodaedalea (C), Psathyrella (D), Psilocybe (E) e Pycnoporellus (F) ................. 22! Figura 11: Gráficos de barcode gap para os gêneros Resinicium (A), Rhodocollybia (B), Rigidoporus (C), Thecaphora (D), Tilletia (E) e Tricholomopsis (F) ..................... 23! Figura 12: Gráficos de barcode gap para os gêneros Tylopilus (A), Xerocomus (B) e Xeromphalina (C) .................................................................................................... 24! Figura 13: Gráficos de barcode gap para os gêneros Amanita (A), Amyloporia (B), Antrodia (C), Antrodiella (D), Auricularia (E) e Calvatia (F) ............................................... 28! Figura 14: Gráficos de barcode gap para os gêneros Chlorophyllum (A), Chroogomphus (B), Coprinopsis (C), Datronia (D), Entoloma (E) e Ganoderma (F) ............................ 29! Figura 15: Gráficos de barcode gap para os gêneros Geastrum (A), Gymnopus (B), Hygrocybe (C), Hygrophorus (D), Hymenopellis (E) e Lactifluus (F) .................... 30! Figura 16: Gráficos de barcode gap para os gêneros Lentinellus (A), Lepiota (B), Leucoagaricus (C), Macrolepiota (D), Megacollybia (E) e Melampsora (F) ......... 31! Figura 17: Gráficos de barcode gap para os gêneros Microbotryum (A), Parasola (B), Phanerochaete (C), Phellodon (D), Piloderma (E) e Polyporus (F) ....................... 32! Figura 18: Gráficos de barcode gap para os gêneros Postia (A), Puccinia (B), Russula (C), Sarcodon (D), Suillus (E) e Thelephora (F) ............................................................. 33! Figura 19: Gráficos de barcode gap para os gêneros Tricholoma (A) e Tuberculina (B) ........ 34! Figura 20: Gráfico de barcode gap dos gêneros: Alnicola (A), Armillaria (B), Boletus (C), Butyriboletus (D), Clavulina (E) e Collybia (F) ...................................................... 37! Figura 21: Gráficos de barcode gap para os gêneros Cortinarius (A), Crepidotus (B), Cystoderma (C), Fomitopsis (D), Hebeloma (E) e Hohenbuehelia (F) ................... 38! Figura 22: Gráficos de barcode gap dos gêneros Hydnellum (A), Hydnum (B), Hyphoderma (C), Hypholoma (D), Inocybe (E) e Laccaria (F) .................................................... 39! Figura 23: Gráficos de barcode gap para os gêneros Lactarius (A), Lentinus (B), Melanoleuca (C), Mucidula (D), Mycena (E) e Paxillus (F) ......................................................... 40! Figura 24: Gráficos de barcode gap dos gêneros Rhizopogon (A), Scleroderma (B), Sebacina (C), Stephanospora (D), Strobilurus (E) e Tomentella (F) ...................................... 41! Figura 25: Gráficos de barcode gap dos gêneros Peniophorella (A), Phaeocollybia (B), Pisolithus (C), Pleurotus (D), Pluteus (E) e Ramaria (F) ....................................... 42! Figura 26: Gráficos de barcode gap dos gêneros Trametes (A) e Vuilleminia (B) .................. 43! Figura 27: Gráfico de cordas do gênero Russula ...................................................................... 45! LISTA DE TABELAS Tabela 1: Gêneros com barcode gap ........................................................................................ 16! Tabela 2: Gêneros sem
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