Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy)
The complete nucleotide sequence and genome organization of a new Badnavirus isolated from the autochthonous grapevine variety “Bombino nero” from Apulia (Italy) was determined. The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encode...
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| Veröffentlicht in: | Virus genes 2016-06, Vol.52 (3), p.428-431 |
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| creator | Chiumenti, Michela Giampetruzzi, Annalisa Morelli, Massimiliano Savino, Vito Nicola Martelli, Giovanni Paolo La Notte, Pierfederico Palmisano, Francesco Saldarelli, Pasquale |
| description | The complete nucleotide sequence and genome organization of a new Badnavirus isolated from the autochthonous grapevine variety “Bombino nero” from Apulia (Italy) was determined. The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encoded by each ORF revealed greatest sequence similarity to Grapevine Roditis leaf discoloration-associated virus w4 (GRLDaV; NC_027131). In a pairwise alignment with GLRDaV w4 genome sequence, the “Bombino Nero” sequence was 109 nt longer with a major 57 nt insertion between positions 2405 and 2413. Furthermore, its putative ORF4 is located after the ORF3, while in the GLRDaV w4 sequence, the putative ORF4 completely overlapped ORF3. Nucleotide analysis classifies this new Badnavirus as a GLRDaV strain, which was named GRLDaV-BN. Multi-year field observations showed that the GLRDaV-BN-infected vine was symptomless. |
| doi_str_mv | 10.1007/s11262-016-1305-2 |
| format | Article |
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The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encoded by each ORF revealed greatest sequence similarity to Grapevine Roditis leaf discoloration-associated virus w4 (GRLDaV; NC_027131). In a pairwise alignment with GLRDaV w4 genome sequence, the “Bombino Nero” sequence was 109 nt longer with a major 57 nt insertion between positions 2405 and 2413. Furthermore, its putative ORF4 is located after the ORF3, while in the GLRDaV w4 sequence, the putative ORF4 completely overlapped ORF3. Nucleotide analysis classifies this new Badnavirus as a GLRDaV strain, which was named GRLDaV-BN. Multi-year field observations showed that the GLRDaV-BN-infected vine was symptomless.</description><identifier>ISSN: 0920-8569</identifier><identifier>EISSN: 1572-994X</identifier><identifier>DOI: 10.1007/s11262-016-1305-2</identifier><identifier>PMID: 26924587</identifier><language>eng</language><publisher>New York: Springer US</publisher><subject>Amino Acid Sequence ; Badnavirus - chemistry ; Badnavirus - genetics ; Badnavirus - isolation & purification ; Base Sequence ; Biomedical and Life Sciences ; Biomedicine ; DNA, Viral - genetics ; Genome, Viral ; Italy ; Medical Microbiology ; Open Reading Frames ; Phylogeny ; Plant Diseases - virology ; Plant Leaves - virology ; Plant Sciences ; Sequence Analysis, DNA ; Virology ; Vitis - virology</subject><ispartof>Virus genes, 2016-06, Vol.52 (3), p.428-431</ispartof><rights>Springer Science+Business Media New York 2016</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c372t-12a2ab845d115cc01f4302132056ddf94945c67189492bbec031a2ab93e047343</citedby><cites>FETCH-LOGICAL-c372t-12a2ab845d115cc01f4302132056ddf94945c67189492bbec031a2ab93e047343</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11262-016-1305-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11262-016-1305-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26924587$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Chiumenti, Michela</creatorcontrib><creatorcontrib>Giampetruzzi, Annalisa</creatorcontrib><creatorcontrib>Morelli, Massimiliano</creatorcontrib><creatorcontrib>Savino, Vito Nicola</creatorcontrib><creatorcontrib>Martelli, Giovanni Paolo</creatorcontrib><creatorcontrib>La Notte, Pierfederico</creatorcontrib><creatorcontrib>Palmisano, Francesco</creatorcontrib><creatorcontrib>Saldarelli, Pasquale</creatorcontrib><title>Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy)</title><title>Virus genes</title><addtitle>Virus Genes</addtitle><addtitle>Virus Genes</addtitle><description>The complete nucleotide sequence and genome organization of a new Badnavirus isolated from the autochthonous grapevine variety “Bombino nero” from Apulia (Italy) was determined. The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encoded by each ORF revealed greatest sequence similarity to Grapevine Roditis leaf discoloration-associated virus w4 (GRLDaV; NC_027131). In a pairwise alignment with GLRDaV w4 genome sequence, the “Bombino Nero” sequence was 109 nt longer with a major 57 nt insertion between positions 2405 and 2413. Furthermore, its putative ORF4 is located after the ORF3, while in the GLRDaV w4 sequence, the putative ORF4 completely overlapped ORF3. Nucleotide analysis classifies this new Badnavirus as a GLRDaV strain, which was named GRLDaV-BN. Multi-year field observations showed that the GLRDaV-BN-infected vine was symptomless.</description><subject>Amino Acid Sequence</subject><subject>Badnavirus - chemistry</subject><subject>Badnavirus - genetics</subject><subject>Badnavirus - isolation & purification</subject><subject>Base Sequence</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>DNA, Viral - genetics</subject><subject>Genome, Viral</subject><subject>Italy</subject><subject>Medical Microbiology</subject><subject>Open Reading Frames</subject><subject>Phylogeny</subject><subject>Plant Diseases - virology</subject><subject>Plant Leaves - virology</subject><subject>Plant Sciences</subject><subject>Sequence Analysis, DNA</subject><subject>Virology</subject><subject>Vitis - virology</subject><issn>0920-8569</issn><issn>1572-994X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp1kcGKFDEQhoMo7jj6AF4k4GX20JpKJ53u47Kr48KAsKh4a2rS6Z0s6c6YpAd2H8cnNT2zigieqqC-_68qfkJeA3sHjKn3EYBXvGBQFVAyWfAnZAFS8aJpxPenZMEazopaVs0ZeRHjHWOsrrl4Ts541XAha7UgP69MMjpZP1IcOzp4Z_TkMFC9w4A6mWAf8Dj2PUW6Drg3BzsaeuM7m2ykzmBPOxu1dz4cyQJj9NpiMh092DBFulrfbK7w2zk9YLA4JmrnbRSn5PUu7fzoM3Q7W9M--IFe7Cdnka6uE7r785fkWY8umlePdUm-fvzw5fJTsfm8vr682BS6VDwVwJHjthayA5BaM-hFyTiUnMmq6_pGNELqSkGdO77dGs1KmBVNaZhQpSiXZHXy3Qf_YzIxtUN-yziHo8kHtqBqJZSC7Lkkb_9B7_wUxnzdkWKlkjBTcKJ08DEG07f7YAcM9y2wdg6wPQXY5gDbOcCWZ82bR-dpO5juj-J3YhngJyDm0Xhrwl-r_-v6CwyFprs</recordid><startdate>20160601</startdate><enddate>20160601</enddate><creator>Chiumenti, Michela</creator><creator>Giampetruzzi, Annalisa</creator><creator>Morelli, Massimiliano</creator><creator>Savino, Vito Nicola</creator><creator>Martelli, Giovanni Paolo</creator><creator>La Notte, Pierfederico</creator><creator>Palmisano, Francesco</creator><creator>Saldarelli, Pasquale</creator><general>Springer US</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TM</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20160601</creationdate><title>Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy)</title><author>Chiumenti, Michela ; Giampetruzzi, Annalisa ; Morelli, Massimiliano ; Savino, Vito Nicola ; Martelli, Giovanni Paolo ; La Notte, Pierfederico ; Palmisano, Francesco ; Saldarelli, Pasquale</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c372t-12a2ab845d115cc01f4302132056ddf94945c67189492bbec031a2ab93e047343</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Amino Acid Sequence</topic><topic>Badnavirus - chemistry</topic><topic>Badnavirus - genetics</topic><topic>Badnavirus - isolation & purification</topic><topic>Base Sequence</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>DNA, Viral - genetics</topic><topic>Genome, Viral</topic><topic>Italy</topic><topic>Medical Microbiology</topic><topic>Open Reading Frames</topic><topic>Phylogeny</topic><topic>Plant Diseases - virology</topic><topic>Plant Leaves - virology</topic><topic>Plant Sciences</topic><topic>Sequence Analysis, DNA</topic><topic>Virology</topic><topic>Vitis - virology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Chiumenti, Michela</creatorcontrib><creatorcontrib>Giampetruzzi, Annalisa</creatorcontrib><creatorcontrib>Morelli, Massimiliano</creatorcontrib><creatorcontrib>Savino, Vito Nicola</creatorcontrib><creatorcontrib>Martelli, Giovanni Paolo</creatorcontrib><creatorcontrib>La Notte, Pierfederico</creatorcontrib><creatorcontrib>Palmisano, Francesco</creatorcontrib><creatorcontrib>Saldarelli, Pasquale</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Public Health Database</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Virus genes</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chiumenti, Michela</au><au>Giampetruzzi, Annalisa</au><au>Morelli, Massimiliano</au><au>Savino, Vito Nicola</au><au>Martelli, Giovanni Paolo</au><au>La Notte, Pierfederico</au><au>Palmisano, Francesco</au><au>Saldarelli, Pasquale</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy)</atitle><jtitle>Virus genes</jtitle><stitle>Virus Genes</stitle><addtitle>Virus Genes</addtitle><date>2016-06-01</date><risdate>2016</risdate><volume>52</volume><issue>3</issue><spage>428</spage><epage>431</epage><pages>428-431</pages><issn>0920-8569</issn><eissn>1572-994X</eissn><abstract>The complete nucleotide sequence and genome organization of a new Badnavirus isolated from the autochthonous grapevine variety “Bombino nero” from Apulia (Italy) was determined. The genome of this virus consists of 7097 nt and has four open reading frames (ORFs). Analysis of putative proteins encoded by each ORF revealed greatest sequence similarity to Grapevine Roditis leaf discoloration-associated virus w4 (GRLDaV; NC_027131). In a pairwise alignment with GLRDaV w4 genome sequence, the “Bombino Nero” sequence was 109 nt longer with a major 57 nt insertion between positions 2405 and 2413. Furthermore, its putative ORF4 is located after the ORF3, while in the GLRDaV w4 sequence, the putative ORF4 completely overlapped ORF3. Nucleotide analysis classifies this new Badnavirus as a GLRDaV strain, which was named GRLDaV-BN. Multi-year field observations showed that the GLRDaV-BN-infected vine was symptomless.</abstract><cop>New York</cop><pub>Springer US</pub><pmid>26924587</pmid><doi>10.1007/s11262-016-1305-2</doi><tpages>4</tpages></addata></record> |
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| ispartof | Virus genes, 2016-06, Vol.52 (3), p.428-431 |
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| source | MEDLINE; SpringerLink Journals |
| subjects | Amino Acid Sequence Badnavirus - chemistry Badnavirus - genetics Badnavirus - isolation & purification Base Sequence Biomedical and Life Sciences Biomedicine DNA, Viral - genetics Genome, Viral Italy Medical Microbiology Open Reading Frames Phylogeny Plant Diseases - virology Plant Leaves - virology Plant Sciences Sequence Analysis, DNA Virology Vitis - virology |
| title | Detection and molecular characterization of a Grapevine Roditis leaf discoloration-associated virus (GRLDaV) variant in an autochthonous grape from Apulia (Italy) |
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