Caracterização molecular de dois isolados de Rice stripe necrosis virus
Autor(a) principal: | |
---|---|
Data de Publicação: | 2021 |
Tipo de documento: | Dissertação |
Idioma: | por |
Título da fonte: | Repositório Institucional da UFG |
Texto Completo: | http://repositorio.bc.ufg.br/tede/handle/tede/11327 |
Resumo: | Rice stripe necrosis virus (RSNV) is a benyvirus transmitted by the plasmodioforomycete Polymyxa graminis Ledingham that causes the disease known as rice crinkling. RSNV genome is composed of two single-stranded, polyadenylated, and positive-sense RNA segments that are individually encapsulated in rod-shaped particles. The reemergence of the virus in Africa and South America as well its recent spread beyond the southern region of Brazil indicates the need to understand its genetic variability in order to generate information to assist in the diagnosis and control of the virus. Thus, the objectives of this work were to molecularly characterize two isolates of RSNV obtained from rice in the state of Goiás and to analyze the genetic variability of this virus. For this purpose, samples of two symptomatic plants, collected in experiments at Embrapa Arroz e Feijão in Goianira and Santo Antônio de Goiás, GO, were subjected to total RNA extraction, enrichment of dsRNA, and high-performance sequencing (HTS), resulting in 27 and 66 million reads for each sample. After assembling with Tadpole software, ten contigs were obtained, corresponding to two viral genomes, each composed of two RNA segments (RNA1 and RNA2). The genomic organization and genome size of the studied isolates were similar to those of the other six previously characterized RSNV isolates. The amino acid sequences of the capsid protein of the two isolates showed an identity greater than 95% with other RSNV sequences, and the general identity of the nucleotide sequences of RNA1 and RNA2 was equal to or greater than 95%. Analyzes performed with the RDP4 software program did not detect recombination events in the studied isolates. Phylogenetic trees based on the complete sequences of RNA1 and RNA2 and the coding region of the helicase motif revealed a close phylogenetic relationship between RSNV isolates characterized in this work and those previously characterized and indicated a cluster pattern according to the geographic origin of the isolates. These results collaborate to broaden the understanding of the molecular diversity of RSNV isolates and, thus, contribute to their control. |
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Dianese, Érico de Camposhttp://lattes.cnpq.br/2503998782869167Mello, Raquel Neves dehttp://lattes.cnpq.br/6216296192318059Lau, DouglasMello, Raquel Neves deMelo, Fernando LucasDianese, Érico de Campos http://lattes.cnpq.br/1104571203657046Souza, Daniela Domingos de2021-05-04T14:00:32Z2021-05-04T14:00:32Z2021-02-26SOUZA, D. D. Caracterização molecular de dois isolados de Rice stripe necrosis virus. 2021. 52 f. Dissertação (Mestrado em Agronomia) - Universidade Federal de Goiás, Goiânia, 2021.http://repositorio.bc.ufg.br/tede/handle/tede/11327Rice stripe necrosis virus (RSNV) is a benyvirus transmitted by the plasmodioforomycete Polymyxa graminis Ledingham that causes the disease known as rice crinkling. RSNV genome is composed of two single-stranded, polyadenylated, and positive-sense RNA segments that are individually encapsulated in rod-shaped particles. The reemergence of the virus in Africa and South America as well its recent spread beyond the southern region of Brazil indicates the need to understand its genetic variability in order to generate information to assist in the diagnosis and control of the virus. Thus, the objectives of this work were to molecularly characterize two isolates of RSNV obtained from rice in the state of Goiás and to analyze the genetic variability of this virus. For this purpose, samples of two symptomatic plants, collected in experiments at Embrapa Arroz e Feijão in Goianira and Santo Antônio de Goiás, GO, were subjected to total RNA extraction, enrichment of dsRNA, and high-performance sequencing (HTS), resulting in 27 and 66 million reads for each sample. After assembling with Tadpole software, ten contigs were obtained, corresponding to two viral genomes, each composed of two RNA segments (RNA1 and RNA2). The genomic organization and genome size of the studied isolates were similar to those of the other six previously characterized RSNV isolates. The amino acid sequences of the capsid protein of the two isolates showed an identity greater than 95% with other RSNV sequences, and the general identity of the nucleotide sequences of RNA1 and RNA2 was equal to or greater than 95%. Analyzes performed with the RDP4 software program did not detect recombination events in the studied isolates. Phylogenetic trees based on the complete sequences of RNA1 and RNA2 and the coding region of the helicase motif revealed a close phylogenetic relationship between RSNV isolates characterized in this work and those previously characterized and indicated a cluster pattern according to the geographic origin of the isolates. These results collaborate to broaden the understanding of the molecular diversity of RSNV isolates and, thus, contribute to their control.Rice stripe necrosis virus (RSNV) é um benyvirus transmitido pelo plasmodioforomiceto Polymyxa graminis Ledingham e que causa a doença conhecida como encarquilhamento do arroz. O genoma do RSNV é composto por dois segmentos de RNA de fita simples, poliadenilados e de sentido positivo que são encapsidados individualmente em partículas em formato de bastonete. A reemergência do vírus na África e na América do Sul e sua recente disseminação para além da região Sul do Brasil indicam a necessidade de entender sua variabilidade genética a fim de gerar informações que auxiliem na diagnose e controle da virose. Assim, os objetivos deste trabalho foram caracterizar molecularmente dois isolados de RSNV obtidos de arroz no estado de Goiás e analisar a variabilidade genética deste vírus. Para tanto, amostras de duas plantas sintomáticas, coletadas em experimentos da Embrapa Arroz e Feijão em Goianira e Santo Antônio de Goiás, GO, foram submetidas a extração de RNA total, enriquecimento de dsRNA e sequenciamento de alto desempenho (HTS), resultando em 27 e 66 milhões de leituras de cada amostra. Após montagem com o programa Tadpole, dez contigs foram obtidos, correspondendo a dois genomas virais, cada um composto por dois segmentos de RNA (RNA1 e RNA2). A organização genômica e tamanho do genoma dos isolados estudados foram similares àqueles de outros seis isolados de RSNV previamente caracterizados. As sequências de aminoácidos das proteínas do capsídeo dos dois isolados apresentaram identidade superior a 95% com outras sequências de RSNV e a identidade geral das sequências de nucleotídeos dos RNA1 e RNA2 foi igual ou superior a 95%. Análises executadas com o programa RDP4 não detectaram eventos de recombinação nos isolados estudados. Árvores filogenéticas baseadas nas sequências completas dos RNA1 e RNA2 e da região codificadora do motivo helicase revelaram estreita relação filogenética entre os isolados de RSNV caracterizados neste trabalho e aqueles previamente caracterizados e indicaram um padrão de agrupamento de acordo com a origem geográfica dos isolados. Estes resultados colaboram para ampliar o entendimento da diversidade molecular de isolados de RSNV e, assim, contribuir para o seu controle.Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2021-05-04T11:39:41Z No. of bitstreams: 2 license_rdf: 805 bytes, checksum: 4460e5956bc1d1639be9ae6146a50347 (MD5) Dissertação - Daniela Domingos de Souza - 2021.pdf: 1560961 bytes, checksum: 3ace45907a5539b47f7b160f06403616 (MD5)Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2021-05-04T14:00:32Z (GMT) No. of bitstreams: 2 license_rdf: 805 bytes, checksum: 4460e5956bc1d1639be9ae6146a50347 (MD5) Dissertação - Daniela Domingos de Souza - 2021.pdf: 1560961 bytes, checksum: 3ace45907a5539b47f7b160f06403616 (MD5)Made available in DSpace on 2021-05-04T14:00:32Z (GMT). No. of bitstreams: 2 license_rdf: 805 bytes, checksum: 4460e5956bc1d1639be9ae6146a50347 (MD5) Dissertação - Daniela Domingos de Souza - 2021.pdf: 1560961 bytes, checksum: 3ace45907a5539b47f7b160f06403616 (MD5) Previous issue date: 2021-02-26porUniversidade Federal de GoiásPrograma de Pós-graduação em Agronomia (EA)UFGBrasilEscola de Agronomia - EA (RG)Attribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessRSNVPolymyxa graminisOryza sativaHTSArroz tropicalPolymyxa graminisOryza sativaHTSTropical riceRSNVCIENCIAS AGRARIAS::AGRONOMIACaracterização molecular de dois isolados de Rice stripe necrosis virusMolecular characterization of two Rice stripe necrosis virus isolatesinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesis55005005002151reponame:Repositório Institucional da UFGinstname:Universidade Federal de Goiás (UFG)instacron:UFGLICENSElicense.txtlicense.txttext/plain; charset=utf-81748http://repositorio.bc.ufg.br/tede/bitstreams/8b4c58e7-7ae9-4201-ba8f-bd96bfb56d99/download8a4605be74aa9ea9d79846c1fba20a33MD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8805http://repositorio.bc.ufg.br/tede/bitstreams/d3f3b651-6b5d-4408-8099-bbae83113bf9/download4460e5956bc1d1639be9ae6146a50347MD52ORIGINALDissertação - Daniela Domingos de Souza - 2021.pdfDissertação - Daniela Domingos de Souza - 2021.pdfapplication/pdf1560961http://repositorio.bc.ufg.br/tede/bitstreams/cab1bc47-c508-4afe-a9e0-5381dc39572e/download3ace45907a5539b47f7b160f06403616MD53tede/113272021-05-04 11:00:32.931http://creativecommons.org/licenses/by-nc-nd/4.0/Attribution-NonCommercial-NoDerivatives 4.0 Internationalopen.accessoai:repositorio.bc.ufg.br:tede/11327http://repositorio.bc.ufg.br/tedeRepositório InstitucionalPUBhttp://repositorio.bc.ufg.br/oai/requesttasesdissertacoes.bc@ufg.bropendoar:2021-05-04T14:00:32Repositório Institucional da UFG - Universidade Federal de Goiás (UFG)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 |
dc.title.pt_BR.fl_str_mv |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
dc.title.alternative.eng.fl_str_mv |
Molecular characterization of two Rice stripe necrosis virus isolates |
title |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
spellingShingle |
Caracterização molecular de dois isolados de Rice stripe necrosis virus Souza, Daniela Domingos de RSNV Polymyxa graminis Oryza sativa HTS Arroz tropical Polymyxa graminis Oryza sativa HTS Tropical rice RSNV CIENCIAS AGRARIAS::AGRONOMIA |
title_short |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
title_full |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
title_fullStr |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
title_full_unstemmed |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
title_sort |
Caracterização molecular de dois isolados de Rice stripe necrosis virus |
author |
Souza, Daniela Domingos de |
author_facet |
Souza, Daniela Domingos de |
author_role |
author |
dc.contributor.advisor1.fl_str_mv |
Dianese, Érico de Campos |
dc.contributor.advisor1Lattes.fl_str_mv |
http://lattes.cnpq.br/2503998782869167 |
dc.contributor.advisor-co1.fl_str_mv |
Mello, Raquel Neves de |
dc.contributor.advisor-co1Lattes.fl_str_mv |
http://lattes.cnpq.br/6216296192318059 |
dc.contributor.referee1.fl_str_mv |
Lau, Douglas |
dc.contributor.referee2.fl_str_mv |
Mello, Raquel Neves de |
dc.contributor.referee3.fl_str_mv |
Melo, Fernando Lucas |
dc.contributor.referee4.fl_str_mv |
Dianese, Érico de Campos |
dc.contributor.authorLattes.fl_str_mv |
http://lattes.cnpq.br/1104571203657046 |
dc.contributor.author.fl_str_mv |
Souza, Daniela Domingos de |
contributor_str_mv |
Dianese, Érico de Campos Mello, Raquel Neves de Lau, Douglas Mello, Raquel Neves de Melo, Fernando Lucas Dianese, Érico de Campos |
dc.subject.por.fl_str_mv |
RSNV Polymyxa graminis Oryza sativa HTS Arroz tropical |
topic |
RSNV Polymyxa graminis Oryza sativa HTS Arroz tropical Polymyxa graminis Oryza sativa HTS Tropical rice RSNV CIENCIAS AGRARIAS::AGRONOMIA |
dc.subject.eng.fl_str_mv |
Polymyxa graminis Oryza sativa HTS Tropical rice RSNV |
dc.subject.cnpq.fl_str_mv |
CIENCIAS AGRARIAS::AGRONOMIA |
description |
Rice stripe necrosis virus (RSNV) is a benyvirus transmitted by the plasmodioforomycete Polymyxa graminis Ledingham that causes the disease known as rice crinkling. RSNV genome is composed of two single-stranded, polyadenylated, and positive-sense RNA segments that are individually encapsulated in rod-shaped particles. The reemergence of the virus in Africa and South America as well its recent spread beyond the southern region of Brazil indicates the need to understand its genetic variability in order to generate information to assist in the diagnosis and control of the virus. Thus, the objectives of this work were to molecularly characterize two isolates of RSNV obtained from rice in the state of Goiás and to analyze the genetic variability of this virus. For this purpose, samples of two symptomatic plants, collected in experiments at Embrapa Arroz e Feijão in Goianira and Santo Antônio de Goiás, GO, were subjected to total RNA extraction, enrichment of dsRNA, and high-performance sequencing (HTS), resulting in 27 and 66 million reads for each sample. After assembling with Tadpole software, ten contigs were obtained, corresponding to two viral genomes, each composed of two RNA segments (RNA1 and RNA2). The genomic organization and genome size of the studied isolates were similar to those of the other six previously characterized RSNV isolates. The amino acid sequences of the capsid protein of the two isolates showed an identity greater than 95% with other RSNV sequences, and the general identity of the nucleotide sequences of RNA1 and RNA2 was equal to or greater than 95%. Analyzes performed with the RDP4 software program did not detect recombination events in the studied isolates. Phylogenetic trees based on the complete sequences of RNA1 and RNA2 and the coding region of the helicase motif revealed a close phylogenetic relationship between RSNV isolates characterized in this work and those previously characterized and indicated a cluster pattern according to the geographic origin of the isolates. These results collaborate to broaden the understanding of the molecular diversity of RSNV isolates and, thus, contribute to their control. |
publishDate |
2021 |
dc.date.accessioned.fl_str_mv |
2021-05-04T14:00:32Z |
dc.date.available.fl_str_mv |
2021-05-04T14:00:32Z |
dc.date.issued.fl_str_mv |
2021-02-26 |
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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masterThesis |
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publishedVersion |
dc.identifier.citation.fl_str_mv |
SOUZA, D. D. Caracterização molecular de dois isolados de Rice stripe necrosis virus. 2021. 52 f. Dissertação (Mestrado em Agronomia) - Universidade Federal de Goiás, Goiânia, 2021. |
dc.identifier.uri.fl_str_mv |
http://repositorio.bc.ufg.br/tede/handle/tede/11327 |
identifier_str_mv |
SOUZA, D. D. Caracterização molecular de dois isolados de Rice stripe necrosis virus. 2021. 52 f. Dissertação (Mestrado em Agronomia) - Universidade Federal de Goiás, Goiânia, 2021. |
url |
http://repositorio.bc.ufg.br/tede/handle/tede/11327 |
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por |
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por |
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Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
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Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
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openAccess |
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Universidade Federal de Goiás |
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Programa de Pós-graduação em Agronomia (EA) |
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UFG |
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Brasil |
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Escola de Agronomia - EA (RG) |
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Universidade Federal de Goiás |
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