Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination

Autores
Celli, Marcos Giovani; Perotto, Maria Cecilia; Luciani, Cecilia Elizabeth; Pozzi, Elizabeth Alicia; Conci, Vilma Cecilia
Año de publicación
2018
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Molecular characterization is important for differentiating allexiviruses species, since detection by serological methods may be uncertain. Eight different species have been reported as infecting garlic: Garlic virus A, B, C, D, E, X (GarV-A, B, C, D, E, X), Shallot virus X (ShVX) and Garlic mite-borne filamentous virus (GarMbFV), and the complete genome is known for six of these. This work reports for the first time the complete sequence of GarV-B and makes a phylogenetic and recombination analysis between the different allexivirus species. Total RNA was obtained of a GarV-B positive garlic plant by ISEM-D using anti-GarV-B antiserum and this was sent for mass sequencing. Deep sequencing revealed the first complete GarV-B genome, consisting of 8327 nucleotides (nt). The genome contained six open reading frames (ORFs) with the typical genome organization which encodes putative proteins of 168 kDa (ORF1), 27 kDa (ORF2), 12 kDa (ORF3), 39 kDa (ORF4), 27 kDa (ORF5) and 14 kDa (ORF6). The comparison of the gene coding for the coat protein of the virus showed a greater identity of nt with other isolates of GarV-B (88.4 to 99.7%) and of GarV-X (75.4 to 78.3%) published in GenBank. The GarV-B replicase gene has not been previously reported in GenBank, so the sequence was compared with GarV-A, -C, −D, −E, −X and ShVX. The highest nt identity values were detected with isolates of GarV-X (73.5 to 74.1%) and GarV-C (71.9 to 72.8%). These results suggest that GarV-X and GarV-B may be different strains of the same virus. A genetic recombination analysis was also performed between the complete sequences of allexiviruses published and obtained in this work and it was detected that the species GarV-D and GarV-E may have arisen from the recombination of the N-terminal portion of GarV-B with the C-terminal portion of GarV-A.
Instituto de Patología Vegetal
Fil: Celli, Marcos Giovani. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Perotto, Maria Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Luciani, Cecilia E. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pozzi, Elizabeth Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Conci, Vilma Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
European journal of plant pathology 153 (1) : 301–310. (January 2019)
Materia
Ajo
Garlic
Allium Sativum
Virus de las Plantas
Plant Viruses
Recombination
Recombinación
Genomes
Genomas
GarV-B
Virus B del ajo
Allexivirus
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/3644
Acceder
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oai_identifier_str oai:localhost:20.500.12123/3644
network_acronym_str INTADig
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network_name_str INTA Digital (INTA)
spelling Molecular characterization of the garlic virus B genome and evidence of allexivirus recombinationCelli, Marcos GiovaniPerotto, Maria CeciliaLuciani, Cecilia ElizabethPozzi, Elizabeth AliciaConci, Vilma CeciliaAjoGarlicAllium SativumVirus de las PlantasPlant VirusesRecombinationRecombinaciónGenomesGenomasGarV-BVirus B del ajoAllexivirusMolecular characterization is important for differentiating allexiviruses species, since detection by serological methods may be uncertain. Eight different species have been reported as infecting garlic: Garlic virus A, B, C, D, E, X (GarV-A, B, C, D, E, X), Shallot virus X (ShVX) and Garlic mite-borne filamentous virus (GarMbFV), and the complete genome is known for six of these. This work reports for the first time the complete sequence of GarV-B and makes a phylogenetic and recombination analysis between the different allexivirus species. Total RNA was obtained of a GarV-B positive garlic plant by ISEM-D using anti-GarV-B antiserum and this was sent for mass sequencing. Deep sequencing revealed the first complete GarV-B genome, consisting of 8327 nucleotides (nt). The genome contained six open reading frames (ORFs) with the typical genome organization which encodes putative proteins of 168 kDa (ORF1), 27 kDa (ORF2), 12 kDa (ORF3), 39 kDa (ORF4), 27 kDa (ORF5) and 14 kDa (ORF6). The comparison of the gene coding for the coat protein of the virus showed a greater identity of nt with other isolates of GarV-B (88.4 to 99.7%) and of GarV-X (75.4 to 78.3%) published in GenBank. The GarV-B replicase gene has not been previously reported in GenBank, so the sequence was compared with GarV-A, -C, −D, −E, −X and ShVX. The highest nt identity values were detected with isolates of GarV-X (73.5 to 74.1%) and GarV-C (71.9 to 72.8%). These results suggest that GarV-X and GarV-B may be different strains of the same virus. A genetic recombination analysis was also performed between the complete sequences of allexiviruses published and obtained in this work and it was detected that the species GarV-D and GarV-E may have arisen from the recombination of the N-terminal portion of GarV-B with the C-terminal portion of GarV-A.Instituto de Patología VegetalFil: Celli, Marcos Giovani. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Perotto, Maria Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Luciani, Cecilia E. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Pozzi, Elizabeth Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Conci, Vilma Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaSpringer2018-10-19T14:01:47Z2018-10-19T14:01:47Z2018info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/3644https://link.springer.com/article/10.1007%2Fs10658-018-1534-4#citeas0929-18731573-8469 (Online)https://doi.org/10.1007/s10658-018-1534-4European journal of plant pathology 153 (1) : 301–310. (January 2019)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-10-16T09:29:20Zoai:localhost:20.500.12123/3644instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-16 09:29:20.772INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
title Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
spellingShingle Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
Celli, Marcos Giovani
Ajo
Garlic
Allium Sativum
Virus de las Plantas
Plant Viruses
Recombination
Recombinación
Genomes
Genomas
GarV-B
Virus B del ajo
Allexivirus
title_short Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
title_full Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
title_fullStr Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
title_full_unstemmed Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
title_sort Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
dc.creator.none.fl_str_mv Celli, Marcos Giovani
Perotto, Maria Cecilia
Luciani, Cecilia Elizabeth
Pozzi, Elizabeth Alicia
Conci, Vilma Cecilia
author Celli, Marcos Giovani
author_facet Celli, Marcos Giovani
Perotto, Maria Cecilia
Luciani, Cecilia Elizabeth
Pozzi, Elizabeth Alicia
Conci, Vilma Cecilia
author_role author
author2 Perotto, Maria Cecilia
Luciani, Cecilia Elizabeth
Pozzi, Elizabeth Alicia
Conci, Vilma Cecilia
author2_role author
author
author
author
dc.subject.none.fl_str_mv Ajo
Garlic
Allium Sativum
Virus de las Plantas
Plant Viruses
Recombination
Recombinación
Genomes
Genomas
GarV-B
Virus B del ajo
Allexivirus
topic Ajo
Garlic
Allium Sativum
Virus de las Plantas
Plant Viruses
Recombination
Recombinación
Genomes
Genomas
GarV-B
Virus B del ajo
Allexivirus
dc.description.none.fl_txt_mv Molecular characterization is important for differentiating allexiviruses species, since detection by serological methods may be uncertain. Eight different species have been reported as infecting garlic: Garlic virus A, B, C, D, E, X (GarV-A, B, C, D, E, X), Shallot virus X (ShVX) and Garlic mite-borne filamentous virus (GarMbFV), and the complete genome is known for six of these. This work reports for the first time the complete sequence of GarV-B and makes a phylogenetic and recombination analysis between the different allexivirus species. Total RNA was obtained of a GarV-B positive garlic plant by ISEM-D using anti-GarV-B antiserum and this was sent for mass sequencing. Deep sequencing revealed the first complete GarV-B genome, consisting of 8327 nucleotides (nt). The genome contained six open reading frames (ORFs) with the typical genome organization which encodes putative proteins of 168 kDa (ORF1), 27 kDa (ORF2), 12 kDa (ORF3), 39 kDa (ORF4), 27 kDa (ORF5) and 14 kDa (ORF6). The comparison of the gene coding for the coat protein of the virus showed a greater identity of nt with other isolates of GarV-B (88.4 to 99.7%) and of GarV-X (75.4 to 78.3%) published in GenBank. The GarV-B replicase gene has not been previously reported in GenBank, so the sequence was compared with GarV-A, -C, −D, −E, −X and ShVX. The highest nt identity values were detected with isolates of GarV-X (73.5 to 74.1%) and GarV-C (71.9 to 72.8%). These results suggest that GarV-X and GarV-B may be different strains of the same virus. A genetic recombination analysis was also performed between the complete sequences of allexiviruses published and obtained in this work and it was detected that the species GarV-D and GarV-E may have arisen from the recombination of the N-terminal portion of GarV-B with the C-terminal portion of GarV-A.
Instituto de Patología Vegetal
Fil: Celli, Marcos Giovani. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Perotto, Maria Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Luciani, Cecilia E. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Pozzi, Elizabeth Alicia. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Conci, Vilma Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Patología Vegetal; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Molecular characterization is important for differentiating allexiviruses species, since detection by serological methods may be uncertain. Eight different species have been reported as infecting garlic: Garlic virus A, B, C, D, E, X (GarV-A, B, C, D, E, X), Shallot virus X (ShVX) and Garlic mite-borne filamentous virus (GarMbFV), and the complete genome is known for six of these. This work reports for the first time the complete sequence of GarV-B and makes a phylogenetic and recombination analysis between the different allexivirus species. Total RNA was obtained of a GarV-B positive garlic plant by ISEM-D using anti-GarV-B antiserum and this was sent for mass sequencing. Deep sequencing revealed the first complete GarV-B genome, consisting of 8327 nucleotides (nt). The genome contained six open reading frames (ORFs) with the typical genome organization which encodes putative proteins of 168 kDa (ORF1), 27 kDa (ORF2), 12 kDa (ORF3), 39 kDa (ORF4), 27 kDa (ORF5) and 14 kDa (ORF6). The comparison of the gene coding for the coat protein of the virus showed a greater identity of nt with other isolates of GarV-B (88.4 to 99.7%) and of GarV-X (75.4 to 78.3%) published in GenBank. The GarV-B replicase gene has not been previously reported in GenBank, so the sequence was compared with GarV-A, -C, −D, −E, −X and ShVX. The highest nt identity values were detected with isolates of GarV-X (73.5 to 74.1%) and GarV-C (71.9 to 72.8%). These results suggest that GarV-X and GarV-B may be different strains of the same virus. A genetic recombination analysis was also performed between the complete sequences of allexiviruses published and obtained in this work and it was detected that the species GarV-D and GarV-E may have arisen from the recombination of the N-terminal portion of GarV-B with the C-terminal portion of GarV-A.
publishDate 2018
dc.date.none.fl_str_mv 2018-10-19T14:01:47Z
2018-10-19T14:01:47Z
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/3644
https://link.springer.com/article/10.1007%2Fs10658-018-1534-4#citeas
0929-1873
1573-8469 (Online)
https://doi.org/10.1007/s10658-018-1534-4
url http://hdl.handle.net/20.500.12123/3644
https://link.springer.com/article/10.1007%2Fs10658-018-1534-4#citeas
https://doi.org/10.1007/s10658-018-1534-4
identifier_str_mv 0929-1873
1573-8469 (Online)
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.publisher.none.fl_str_mv Springer
publisher.none.fl_str_mv Springer
dc.source.none.fl_str_mv European journal of plant pathology 153 (1) : 301–310. (January 2019)
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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