Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)

Detalhes bibliográficos
Autor(a) principal: Sande, Osvaldo Francisco Lino
Data de Publicação: 2014
Tipo de documento: Dissertação
Idioma: por
Título da fonte: LOCUS Repositório Institucional da UFV
Texto Completo: http://locus.ufv.br/handle/123456789/4438
Resumo: The incidence of begomoviruses in Brazil has increased since 1990 with the introduction of the invasive Bemisia tabaci Middle East Asia Minor 1 (MEAM1, previously known as biotype B). The objective of this work was to evaluate the spatio- temporal dynamics of populations of Tomato severe rugose virus infecting tomato crops. Foliar samples with begomovirus-like symptoms such as dwarfing, yellow mosaic and leaf curl were collected in tomato fields located in rural areas of the municipalities of Coimbra in 2013 and 2014 and Florestal in 2014. Total DNA was extracted and used as a template for the amplification of viral genomes using the phi29 DNA polymerase. Viral genomes were cloned in plasmid vectors and fully sequenced. A total of 76 full-length DNA-A clones were obtained. The isolates obtained from tomato samples indicate an almost absolute predominance of Tomato severe rugose virus (ToSRV) in Florestal and Coimbra (replacing Tomato common mosaic virus, ToCmMV, as the dominant begomovirus in Coimbra). Phylogenetic analysis, including additional ToSRV sequences from a number of cultivated and non-cultivated hosts available in GenBank, divided ToSRV isolates into four major clades: (i) Florestal/2008, (ii) São Paulo, Goiás and the Federal District, (iii) Florestal/2014 and (iv) Viçosa, Coimbra, Carandaí and Jaíba. Isolates from Florestal/2008 represent the most divergent group, with a time of divergence from the most recent common ancestor of 15-20 years. However, isolates obtained from Florestal in 2008 and 2014 form distinct clades, suggesting a time-based structuring. The inferred phylogenetic network showed evidence of intraspecific recombination, with the previously described isolates BR:Ube1:2000 and BR:Vic20:10 identified as potential recombinants. The genetic variability of the ToSRV population is not equally distributed among subpopulations, with subpopulations from Viçosa and Florestal/2008 providing a greater contribution to the variability. Neutrality tests were applied to assess evidence of selection on coding regions. The results indicate the occurrence of purifying selection on the CP gene of the subpopulations from Viçosa, Carandaí and Florestal/2014 and on the Rep gene from the subpopulations from Viçosa and Carandaí. Coalescence analysis mapped the mutations occurring along the viral genome. All mutations observed in peppers and in non-cultivated hosts are common to tomatoes and show the same relative age, suggesting that ToSRV is well adapted to tomatoes, with occasional transfer to other hosts by the insect vector.
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spelling Sande, Osvaldo Francisco Linohttp://lattes.cnpq.br/2251576148284405Zerbini Júnior, Francisco Murilohttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783743U5Mizubuti, Eduardo Seiti Gomidehttp://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4785633J8Navas-castilho, Jesús2015-03-26T13:37:55Z2015-03-202015-03-26T13:37:55Z2014-10-03SANDE, Osvaldo Francisco Lino. Genetic structure of populations of the begomovirus Tomato severe rugose virus (ToSRV). 2014. 55 f. Dissertação (Mestrado em Etiologia; Epidemiologia; Controle) - Universidade Federal de Viçosa, Viçosa, 2014.http://locus.ufv.br/handle/123456789/4438The incidence of begomoviruses in Brazil has increased since 1990 with the introduction of the invasive Bemisia tabaci Middle East Asia Minor 1 (MEAM1, previously known as biotype B). The objective of this work was to evaluate the spatio- temporal dynamics of populations of Tomato severe rugose virus infecting tomato crops. Foliar samples with begomovirus-like symptoms such as dwarfing, yellow mosaic and leaf curl were collected in tomato fields located in rural areas of the municipalities of Coimbra in 2013 and 2014 and Florestal in 2014. Total DNA was extracted and used as a template for the amplification of viral genomes using the phi29 DNA polymerase. Viral genomes were cloned in plasmid vectors and fully sequenced. A total of 76 full-length DNA-A clones were obtained. The isolates obtained from tomato samples indicate an almost absolute predominance of Tomato severe rugose virus (ToSRV) in Florestal and Coimbra (replacing Tomato common mosaic virus, ToCmMV, as the dominant begomovirus in Coimbra). Phylogenetic analysis, including additional ToSRV sequences from a number of cultivated and non-cultivated hosts available in GenBank, divided ToSRV isolates into four major clades: (i) Florestal/2008, (ii) São Paulo, Goiás and the Federal District, (iii) Florestal/2014 and (iv) Viçosa, Coimbra, Carandaí and Jaíba. Isolates from Florestal/2008 represent the most divergent group, with a time of divergence from the most recent common ancestor of 15-20 years. However, isolates obtained from Florestal in 2008 and 2014 form distinct clades, suggesting a time-based structuring. The inferred phylogenetic network showed evidence of intraspecific recombination, with the previously described isolates BR:Ube1:2000 and BR:Vic20:10 identified as potential recombinants. The genetic variability of the ToSRV population is not equally distributed among subpopulations, with subpopulations from Viçosa and Florestal/2008 providing a greater contribution to the variability. Neutrality tests were applied to assess evidence of selection on coding regions. The results indicate the occurrence of purifying selection on the CP gene of the subpopulations from Viçosa, Carandaí and Florestal/2014 and on the Rep gene from the subpopulations from Viçosa and Carandaí. Coalescence analysis mapped the mutations occurring along the viral genome. All mutations observed in peppers and in non-cultivated hosts are common to tomatoes and show the same relative age, suggesting that ToSRV is well adapted to tomatoes, with occasional transfer to other hosts by the insect vector.O gênero Begomovirus (família Geminiviridae) inclui vírus com genoma composto por uma ou duas moléculas circulares de DNA fita simples encapsuladas em partículas icosaédricas geminadas. A incidência de begomovírus no Brasil vem aumentando desde 1990 com a introdução do vetor Bemisia tabaci Middle East Asia Minor 1 (MEAM1, antigo Biótipo B). O objetivo deste trabalho foi avaliar a dinâmica espaço-temporal de populações do begomovírus Tomato severe rugose virus, que infecta naturalmente o tomateiro. Um total de 233 amostras de tomateiro e plantas não-cultivadas apresentando sintomas típicos de begomovírus foram coletadas nos municípios de Coimbra em 2013 e 2014 e Florestal em 2014. O DNA total das amostras foi extraído e utilizado como molde para a amplificação de genomas completos de begomovírus com auxílio da DNA polimerase do fago phi29. Os genomas virais foram clonados em plasmídeos e completamente sequenciados. Um total de 76 genomas completos (DNA-A) foram obtidos neste trabalho. Os isolados obtidos a partir de tomateiro revelaram a quase completa predominância do Tomato severe rugose virus (ToSRV) em Florestal e Coimbra (nesta última região substituindo o Tomato common mosaic virus, ToCmMV). A análise filogenética, incluindo outras sequências de ToSRV previamente descritas a partir de diversos hospedeiros cultivados e não-cultivados e disponíveis no GanBank, evidencia a estruturação dos isolados de ToSRV em quatro clados: (i) Florestal/2008, (ii) São Paulo, Goiás e Distrito Federal, (iii) Florestal/2014 e (iv) Viçosa, Coimbra, Carandaí e Jaíba. Os isolados de Florestal/2008 representam o grupo mais divergente, com um tempo médio de divergência do ancestral comum mais recente de 15-20 anos. Contudo, os isolados coletados em Florestal em 2008 divergem em relação aos isolados coletados em 2014, sugerindo uma estruturação baseada no tempo. A rede filogenética inferida revelou evidências de recombinação intraespecífica, e os isolados BR:Ube1:2000 e BR:Vic20:10, previamente descritos, foram identificados como possíveis recombinantes. A variabilidade genética da população de ToSRV não se encontra igualmente distribuída entre as subpopulações, com as subpopulações de Viçosa e Florestal/2008 apresentando maior contribuição para a variabilidade. Os resultados de testes de seleção indicam a ocorrência de seleção purificadora atuando no gene CP das subpopulações de Viçosa, Carandaí e Florestal/2014 e no gene Rep das subpopulações de Viçosa e Carandaí. A análise baseada em coalescência mapeou as mutações ao longo do genoma do ToSRV. Todas as mutações observadas em pimentão e plantas não-cultivadas são comuns para tomateiro e apresentam a mesma idade relativa, sugerindo que o ToSRV é uma espécie viral bem adaptada ao tomateiro, com transferência eventual para outros hospedeiros por meio do inseto vetor.Conselho Nacional de Desenvolvimento Científico e Tecnológicoapplication/pdfporUniversidade Federal de ViçosaMestrado em FitopatologiaUFVBREtiologia; Epidemiologia; ControleTomate - Doenças e pragasBegomovírus - GenéticaBegomovírus - VariabilidadeFilogeniaTomato - Diseases and pestsBegomovirus - GeneticsBegomovirus - variabilityPhylogenyCNPQ::CIENCIAS AGRARIAS::AGRONOMIA::FITOSSANIDADE::FITOPATOLOGIAEstrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)Genetic structure of populations of the begomovirus Tomato severe rugose virus (ToSRV)info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/openAccessreponame:LOCUS Repositório Institucional da UFVinstname:Universidade Federal de Viçosa (UFV)instacron:UFVORIGINALtexto completo.pdfapplication/pdf2669997https://locus.ufv.br//bitstream/123456789/4438/1/texto%20completo.pdf01d55c101e33f8b746044d277adb2173MD51TEXTtexto completo.pdf.txttexto completo.pdf.txtExtracted texttext/plain91606https://locus.ufv.br//bitstream/123456789/4438/2/texto%20completo.pdf.txtd8caca5647f27706d7ff98d0ed056446MD52THUMBNAILtexto completo.pdf.jpgtexto completo.pdf.jpgIM Thumbnailimage/jpeg3533https://locus.ufv.br//bitstream/123456789/4438/3/texto%20completo.pdf.jpga1e5c065edf94c8b3b9aa14690fbf6d9MD53123456789/44382016-04-10 23:09:59.83oai:locus.ufv.br:123456789/4438Repositório InstitucionalPUBhttps://www.locus.ufv.br/oai/requestfabiojreis@ufv.bropendoar:21452016-04-11T02:09:59LOCUS Repositório Institucional da UFV - Universidade Federal de Viçosa (UFV)false
dc.title.por.fl_str_mv Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
dc.title.alternative.eng.fl_str_mv Genetic structure of populations of the begomovirus Tomato severe rugose virus (ToSRV)
title Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
spellingShingle Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
Sande, Osvaldo Francisco Lino
Tomate - Doenças e pragas
Begomovírus - Genética
Begomovírus - Variabilidade
Filogenia
Tomato - Diseases and pests
Begomovirus - Genetics
Begomovirus - variability
Phylogeny
CNPQ::CIENCIAS AGRARIAS::AGRONOMIA::FITOSSANIDADE::FITOPATOLOGIA
title_short Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
title_full Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
title_fullStr Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
title_full_unstemmed Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
title_sort Estrutura genética de populações do begomovírus Tomato severe rugose virus (ToSRV)
author Sande, Osvaldo Francisco Lino
author_facet Sande, Osvaldo Francisco Lino
author_role author
dc.contributor.authorLattes.por.fl_str_mv http://lattes.cnpq.br/2251576148284405
dc.contributor.author.fl_str_mv Sande, Osvaldo Francisco Lino
dc.contributor.advisor1.fl_str_mv Zerbini Júnior, Francisco Murilo
dc.contributor.advisor1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4783743U5
dc.contributor.referee1.fl_str_mv Mizubuti, Eduardo Seiti Gomide
dc.contributor.referee1Lattes.fl_str_mv http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4785633J8
dc.contributor.referee2.fl_str_mv Navas-castilho, Jesús
contributor_str_mv Zerbini Júnior, Francisco Murilo
Mizubuti, Eduardo Seiti Gomide
Navas-castilho, Jesús
dc.subject.por.fl_str_mv Tomate - Doenças e pragas
Begomovírus - Genética
Begomovírus - Variabilidade
Filogenia
topic Tomate - Doenças e pragas
Begomovírus - Genética
Begomovírus - Variabilidade
Filogenia
Tomato - Diseases and pests
Begomovirus - Genetics
Begomovirus - variability
Phylogeny
CNPQ::CIENCIAS AGRARIAS::AGRONOMIA::FITOSSANIDADE::FITOPATOLOGIA
dc.subject.eng.fl_str_mv Tomato - Diseases and pests
Begomovirus - Genetics
Begomovirus - variability
Phylogeny
dc.subject.cnpq.fl_str_mv CNPQ::CIENCIAS AGRARIAS::AGRONOMIA::FITOSSANIDADE::FITOPATOLOGIA
description The incidence of begomoviruses in Brazil has increased since 1990 with the introduction of the invasive Bemisia tabaci Middle East Asia Minor 1 (MEAM1, previously known as biotype B). The objective of this work was to evaluate the spatio- temporal dynamics of populations of Tomato severe rugose virus infecting tomato crops. Foliar samples with begomovirus-like symptoms such as dwarfing, yellow mosaic and leaf curl were collected in tomato fields located in rural areas of the municipalities of Coimbra in 2013 and 2014 and Florestal in 2014. Total DNA was extracted and used as a template for the amplification of viral genomes using the phi29 DNA polymerase. Viral genomes were cloned in plasmid vectors and fully sequenced. A total of 76 full-length DNA-A clones were obtained. The isolates obtained from tomato samples indicate an almost absolute predominance of Tomato severe rugose virus (ToSRV) in Florestal and Coimbra (replacing Tomato common mosaic virus, ToCmMV, as the dominant begomovirus in Coimbra). Phylogenetic analysis, including additional ToSRV sequences from a number of cultivated and non-cultivated hosts available in GenBank, divided ToSRV isolates into four major clades: (i) Florestal/2008, (ii) São Paulo, Goiás and the Federal District, (iii) Florestal/2014 and (iv) Viçosa, Coimbra, Carandaí and Jaíba. Isolates from Florestal/2008 represent the most divergent group, with a time of divergence from the most recent common ancestor of 15-20 years. However, isolates obtained from Florestal in 2008 and 2014 form distinct clades, suggesting a time-based structuring. The inferred phylogenetic network showed evidence of intraspecific recombination, with the previously described isolates BR:Ube1:2000 and BR:Vic20:10 identified as potential recombinants. The genetic variability of the ToSRV population is not equally distributed among subpopulations, with subpopulations from Viçosa and Florestal/2008 providing a greater contribution to the variability. Neutrality tests were applied to assess evidence of selection on coding regions. The results indicate the occurrence of purifying selection on the CP gene of the subpopulations from Viçosa, Carandaí and Florestal/2014 and on the Rep gene from the subpopulations from Viçosa and Carandaí. Coalescence analysis mapped the mutations occurring along the viral genome. All mutations observed in peppers and in non-cultivated hosts are common to tomatoes and show the same relative age, suggesting that ToSRV is well adapted to tomatoes, with occasional transfer to other hosts by the insect vector.
publishDate 2014
dc.date.issued.fl_str_mv 2014-10-03
dc.date.accessioned.fl_str_mv 2015-03-26T13:37:55Z
dc.date.available.fl_str_mv 2015-03-20
2015-03-26T13:37:55Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
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dc.identifier.citation.fl_str_mv SANDE, Osvaldo Francisco Lino. Genetic structure of populations of the begomovirus Tomato severe rugose virus (ToSRV). 2014. 55 f. Dissertação (Mestrado em Etiologia; Epidemiologia; Controle) - Universidade Federal de Viçosa, Viçosa, 2014.
dc.identifier.uri.fl_str_mv http://locus.ufv.br/handle/123456789/4438
identifier_str_mv SANDE, Osvaldo Francisco Lino. Genetic structure of populations of the begomovirus Tomato severe rugose virus (ToSRV). 2014. 55 f. Dissertação (Mestrado em Etiologia; Epidemiologia; Controle) - Universidade Federal de Viçosa, Viçosa, 2014.
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