Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step...

Autores
Bejerman, Nicolas Esteban; Zanini, Andrea Alejandra; Rodriguez Pardina, Patricia; Di Feo, Liliana del Valle
Año de publicación
2016
Idioma
inglés
Tipo de recurso
artículo
Estado
versión aceptada
Descripción
454-pyrosequencing was applied as a tool to identify etiological agents involved in the symptoms observed in a sweet potato sample from Argentina. RNA was purified from symptomatic material and sequenced using a Roche 454 GS-FLX+. BLAST analysis of the viral reads identified the presence of Sweet potato feathery mottle virus (SPFMV)-O and SPFMV-RC strains and Sweet potato virus C (SPVC). For SPFMV-O and SPFMV–RC, 10 878 and 10 812 nucleotides, respectively, were sequenced, whereas a sequence of 10 793 nucleotides was obtained for SPVC. Pairwise comparison of polyprotein nucleotide sequences of O and RC Argentinian isolates (Arg) showed 99% and 98.4% sequence identities with SPFMV-O and SPFMV-RC-M2-41, respectively, whereas SPVC-Arg showed 94.2%, 92.9% and 94.6% sequence identities with SPVC-Il, SPVC-C1 and SPVC-Bungo, respectively. These results allowed us to develop a one-step multiplex reverse transcription-polymerase chain reaction assay (mRT-PCR) for the simultaneous detection and differentiation of SPFMV-O-Arg and SPFMV-RC-Arg and SPVC-Arg. Three specific forward primers unique to each virus and one reverse primer based on a region conserved in all three viruses were designed and used in the assay. These primers were further evaluated using field samples collected from four provinces of Argentina. The results showed that SPVC was the most common virus in samples analysed. This study shows the usefulness of deep sequencing not only to rapidly identify mixed infections between SPFMV-O and SPFMV-RC and SPVC, but also to develop a reliable mRT-PCR assay for detection of these sweet potato pathogens, which cannot be discriminated by serological techniques.
Inst. Patología Vegetal
Fil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Zanini, Andrea Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Rodriguez Pardina, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Di Feo, Liliana del Valle. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fuente
Journal of phytophatology 164 (6) : 386–394. (June 2016)
Materia
Virus de las Plantas
Batata
PCR
Genética
Plant Viruses
Sweet Potatoes
Genetics
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/1249
Acceder
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oai_identifier_str oai:localhost:20.500.12123/1249
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network_name_str INTA Digital (INTA)
spelling Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous DetectionBejerman, Nicolas EstebanZanini, Andrea AlejandraRodriguez Pardina, PatriciaDi Feo, Liliana del ValleVirus de las PlantasBatataPCRGenéticaPlant VirusesSweet PotatoesGenetics454-pyrosequencing was applied as a tool to identify etiological agents involved in the symptoms observed in a sweet potato sample from Argentina. RNA was purified from symptomatic material and sequenced using a Roche 454 GS-FLX+. BLAST analysis of the viral reads identified the presence of Sweet potato feathery mottle virus (SPFMV)-O and SPFMV-RC strains and Sweet potato virus C (SPVC). For SPFMV-O and SPFMV–RC, 10 878 and 10 812 nucleotides, respectively, were sequenced, whereas a sequence of 10 793 nucleotides was obtained for SPVC. Pairwise comparison of polyprotein nucleotide sequences of O and RC Argentinian isolates (Arg) showed 99% and 98.4% sequence identities with SPFMV-O and SPFMV-RC-M2-41, respectively, whereas SPVC-Arg showed 94.2%, 92.9% and 94.6% sequence identities with SPVC-Il, SPVC-C1 and SPVC-Bungo, respectively. These results allowed us to develop a one-step multiplex reverse transcription-polymerase chain reaction assay (mRT-PCR) for the simultaneous detection and differentiation of SPFMV-O-Arg and SPFMV-RC-Arg and SPVC-Arg. Three specific forward primers unique to each virus and one reverse primer based on a region conserved in all three viruses were designed and used in the assay. These primers were further evaluated using field samples collected from four provinces of Argentina. The results showed that SPVC was the most common virus in samples analysed. This study shows the usefulness of deep sequencing not only to rapidly identify mixed infections between SPFMV-O and SPFMV-RC and SPVC, but also to develop a reliable mRT-PCR assay for detection of these sweet potato pathogens, which cannot be discriminated by serological techniques.Inst. Patología VegetalFil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Zanini, Andrea Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Rodriguez Pardina, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; ArgentinaFil: Di Feo, Liliana del Valle. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina2017-09-19T12:04:02Z2017-09-19T12:04:02Z2016info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/1249http://onlinelibrary.wiley.com/doi/10.1111/jph.12466/full1439-0434 (Online)DOI: 10.1111/jph.12466Journal of phytophatology 164 (6) : 386–394. (June 2016)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología AgropecuariaengArgentina (nation)info:eu-repo/semantics/restrictedAccess2025-09-11T10:22:10Zoai:localhost:20.500.12123/1249instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-11 10:22:10.989INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
title Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
spellingShingle Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
Bejerman, Nicolas Esteban
Virus de las Plantas
Batata
PCR
Genética
Plant Viruses
Sweet Potatoes
Genetics
title_short Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
title_full Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
title_fullStr Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
title_full_unstemmed Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
title_sort Use of 454-Pyrosequencing for the characterization of Sweet potato virus C and Sweet Potato Feathery Mottle virus Isolates fron Argentina and Development of a Multiplex one - step RT-PCR for Their Simultaneous Detection
dc.creator.none.fl_str_mv Bejerman, Nicolas Esteban
Zanini, Andrea Alejandra
Rodriguez Pardina, Patricia
Di Feo, Liliana del Valle
author Bejerman, Nicolas Esteban
author_facet Bejerman, Nicolas Esteban
Zanini, Andrea Alejandra
Rodriguez Pardina, Patricia
Di Feo, Liliana del Valle
author_role author
author2 Zanini, Andrea Alejandra
Rodriguez Pardina, Patricia
Di Feo, Liliana del Valle
author2_role author
author
author
dc.subject.none.fl_str_mv Virus de las Plantas
Batata
PCR
Genética
Plant Viruses
Sweet Potatoes
Genetics
topic Virus de las Plantas
Batata
PCR
Genética
Plant Viruses
Sweet Potatoes
Genetics
dc.description.none.fl_txt_mv 454-pyrosequencing was applied as a tool to identify etiological agents involved in the symptoms observed in a sweet potato sample from Argentina. RNA was purified from symptomatic material and sequenced using a Roche 454 GS-FLX+. BLAST analysis of the viral reads identified the presence of Sweet potato feathery mottle virus (SPFMV)-O and SPFMV-RC strains and Sweet potato virus C (SPVC). For SPFMV-O and SPFMV–RC, 10 878 and 10 812 nucleotides, respectively, were sequenced, whereas a sequence of 10 793 nucleotides was obtained for SPVC. Pairwise comparison of polyprotein nucleotide sequences of O and RC Argentinian isolates (Arg) showed 99% and 98.4% sequence identities with SPFMV-O and SPFMV-RC-M2-41, respectively, whereas SPVC-Arg showed 94.2%, 92.9% and 94.6% sequence identities with SPVC-Il, SPVC-C1 and SPVC-Bungo, respectively. These results allowed us to develop a one-step multiplex reverse transcription-polymerase chain reaction assay (mRT-PCR) for the simultaneous detection and differentiation of SPFMV-O-Arg and SPFMV-RC-Arg and SPVC-Arg. Three specific forward primers unique to each virus and one reverse primer based on a region conserved in all three viruses were designed and used in the assay. These primers were further evaluated using field samples collected from four provinces of Argentina. The results showed that SPVC was the most common virus in samples analysed. This study shows the usefulness of deep sequencing not only to rapidly identify mixed infections between SPFMV-O and SPFMV-RC and SPVC, but also to develop a reliable mRT-PCR assay for detection of these sweet potato pathogens, which cannot be discriminated by serological techniques.
Inst. Patología Vegetal
Fil: Bejerman, Nicolas Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Zanini, Andrea Alejandra. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Rodriguez Pardina, Patricia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
Fil: Di Feo, Liliana del Valle. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina
description 454-pyrosequencing was applied as a tool to identify etiological agents involved in the symptoms observed in a sweet potato sample from Argentina. RNA was purified from symptomatic material and sequenced using a Roche 454 GS-FLX+. BLAST analysis of the viral reads identified the presence of Sweet potato feathery mottle virus (SPFMV)-O and SPFMV-RC strains and Sweet potato virus C (SPVC). For SPFMV-O and SPFMV–RC, 10 878 and 10 812 nucleotides, respectively, were sequenced, whereas a sequence of 10 793 nucleotides was obtained for SPVC. Pairwise comparison of polyprotein nucleotide sequences of O and RC Argentinian isolates (Arg) showed 99% and 98.4% sequence identities with SPFMV-O and SPFMV-RC-M2-41, respectively, whereas SPVC-Arg showed 94.2%, 92.9% and 94.6% sequence identities with SPVC-Il, SPVC-C1 and SPVC-Bungo, respectively. These results allowed us to develop a one-step multiplex reverse transcription-polymerase chain reaction assay (mRT-PCR) for the simultaneous detection and differentiation of SPFMV-O-Arg and SPFMV-RC-Arg and SPVC-Arg. Three specific forward primers unique to each virus and one reverse primer based on a region conserved in all three viruses were designed and used in the assay. These primers were further evaluated using field samples collected from four provinces of Argentina. The results showed that SPVC was the most common virus in samples analysed. This study shows the usefulness of deep sequencing not only to rapidly identify mixed infections between SPFMV-O and SPFMV-RC and SPVC, but also to develop a reliable mRT-PCR assay for detection of these sweet potato pathogens, which cannot be discriminated by serological techniques.
publishDate 2016
dc.date.none.fl_str_mv 2016
2017-09-19T12:04:02Z
2017-09-19T12:04:02Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/1249
http://onlinelibrary.wiley.com/doi/10.1111/jph.12466/full
1439-0434 (Online)
DOI: 10.1111/jph.12466
url http://hdl.handle.net/20.500.12123/1249
http://onlinelibrary.wiley.com/doi/10.1111/jph.12466/full
identifier_str_mv 1439-0434 (Online)
DOI: 10.1111/jph.12466
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.coverage.none.fl_str_mv Argentina (nation)
dc.source.none.fl_str_mv Journal of phytophatology 164 (6) : 386–394. (June 2016)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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