Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination
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-bo...
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| Format: | Artículo |
| Language: | Inglés |
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Springer
2018
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| Online Access: | 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 |
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| author | Celli, Marcos Giovani Perotto, Maria Cecilia Luciani, Cecilia Elizabeth Pozzi, Elizabeth Alicia Conci, Vilma Cecilia |
| author_browse | Celli, Marcos Giovani Conci, Vilma Cecilia Luciani, Cecilia Elizabeth Perotto, Maria Cecilia Pozzi, Elizabeth Alicia |
| author_facet | Celli, Marcos Giovani Perotto, Maria Cecilia Luciani, Cecilia Elizabeth Pozzi, Elizabeth Alicia Conci, Vilma Cecilia |
| author_sort | Celli, Marcos Giovani |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA3644 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | INTA36442022-11-09T11:29:00Z Molecular characterization of the garlic virus B genome and evidence of allexivirus recombination Celli, Marcos Giovani Perotto, Maria Cecilia Luciani, Cecilia Elizabeth Pozzi, Elizabeth Alicia Conci, Vilma Cecilia Ajo Garlic Allium Sativum Virus de las Plantas Plant Viruses Recombination Recombinación Genomes Genomas GarV-B Virus B del ajo Allexivirus 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 2018-10-19T14:01:47Z 2018-10-19T14:01:47Z 2018 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng info:eu-repo/semantics/restrictedAccess application/pdf Springer European journal of plant pathology 153 (1) : 301–310. (January 2019) |
| spellingShingle | Ajo Garlic Allium Sativum Virus de las Plantas Plant Viruses Recombination Recombinación Genomes Genomas GarV-B Virus B del ajo Allexivirus Celli, Marcos Giovani Perotto, Maria Cecilia Luciani, Cecilia Elizabeth Pozzi, Elizabeth Alicia Conci, Vilma Cecilia 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 |
| 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_short | 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 |
| topic | Ajo Garlic Allium Sativum Virus de las Plantas Plant Viruses Recombination Recombinación Genomes Genomas GarV-B Virus B del ajo Allexivirus |
| 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 |
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