Genetic diversity of Grapevine virus A in Washington and California vineyards.
Identifieur interne : 000507 ( Main/Exploration ); précédent : 000506; suivant : 000508Genetic diversity of Grapevine virus A in Washington and California vineyards.
Auteurs : Olufemi J. Alabi ; Maher Al Rwahnih ; Tefera A. Mekuria ; Rayapati A. NaiduSource :
- Phytopathology [ 0031-949X ] ; 2014.
Descripteurs français
- KwdFr :
- ADN complémentaire (composition chimique), ADN complémentaire (génétique), ADN viral (composition chimique), ADN viral (génétique), ARN viral (génétique), Analyse de séquence d'ADN (MeSH), Californie (MeSH), Données de séquences moléculaires (MeSH), Flexiviridae (génétique), Flexiviridae (isolement et purification), Génome viral (génétique), Génotype (MeSH), Génétique des populations (MeSH), Haplotypes (MeSH), Maladies des plantes (virologie), Phylogenèse (MeSH), Protéines de capside (génétique), Protéines virales (génétique), RNA replicase (génétique), Recombinaison génétique (MeSH), Séquence nucléotidique (MeSH), Variation génétique (MeSH), Vitis (virologie), Washington (MeSH).
- MESH :
- composition chimique : ADN complémentaire, ADN viral.
- génétique : ADN complémentaire, ADN viral, ARN viral, Flexiviridae, Génome viral, Protéines de capside, Protéines virales, RNA replicase.
- isolement et purification : Flexiviridae.
- virologie : Maladies des plantes, Vitis.
- Analyse de séquence d'ADN, Californie, Données de séquences moléculaires, Génotype, Génétique des populations, Haplotypes, Phylogenèse, Recombinaison génétique, Séquence nucléotidique, Variation génétique, Washington.
English descriptors
- KwdEn :
- Base Sequence (MeSH), California (MeSH), Capsid Proteins (genetics), DNA, Complementary (chemistry), DNA, Complementary (genetics), DNA, Viral (chemistry), DNA, Viral (genetics), Flexiviridae (genetics), Flexiviridae (isolation & purification), Genetic Variation (MeSH), Genetics, Population (MeSH), Genome, Viral (genetics), Genotype (MeSH), Haplotypes (MeSH), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Plant Diseases (virology), RNA Replicase (genetics), RNA, Viral (genetics), Recombination, Genetic (MeSH), Sequence Analysis, DNA (MeSH), Viral Proteins (genetics), Vitis (virology), Washington (MeSH).
- MESH :
- chemical , chemistry : DNA, Complementary, DNA, Viral.
- chemical , genetics : Capsid Proteins, DNA, Complementary, DNA, Viral, RNA Replicase, RNA, Viral, Viral Proteins.
- geographic : California, Washington.
- genetics : Flexiviridae, Genome, Viral.
- isolation & purification : Flexiviridae.
- virology : Plant Diseases, Vitis.
- Base Sequence, Genetic Variation, Genetics, Population, Genotype, Haplotypes, Molecular Sequence Data, Phylogeny, Recombination, Genetic, Sequence Analysis, DNA.
Abstract
Grapevine virus A (GVA; genus Vitivirus, family Betaflexiviridae) has been implicated with the Kober stem grooving disorder of the rugose wood disease complex. In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.
DOI: 10.1094/PHYTO-06-13-0179-R
PubMed: 24168043
Affiliations:
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Le document en format XML
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In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24168043</PMID><DateCompleted><Year>2014</Year><Month>07</Month><Day>10</Day></DateCompleted><DateRevised><Year>2014</Year><Month>04</Month><Day>14</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0031-949X</ISSN><JournalIssue CitedMedium="Print"><Volume>104</Volume><Issue>5</Issue><PubDate><Year>2014</Year><Month>May</Month></PubDate></JournalIssue><Title>Phytopathology</Title><ISOAbbreviation>Phytopathology</ISOAbbreviation></Journal><ArticleTitle>Genetic diversity of Grapevine virus A in Washington and California vineyards.</ArticleTitle><Pagination><MedlinePgn>548-60</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1094/PHYTO-06-13-0179-R</ELocationID><Abstract><AbstractText>Grapevine virus A (GVA; genus Vitivirus, family Betaflexiviridae) has been implicated with the Kober stem grooving disorder of the rugose wood disease complex. In this study, 26 isolates of GVA recovered from wine grape (Vitis vinifera) cultivars from California and Washington were analyzed for their genetic diversity. An analysis of a portion of the RNA-dependent RNA polymerase (RdRp) and complete coat protein (CP) sequences revealed intra- and inter-isolate sequence diversity. Our results indicated that both RdRp and CP are under strong negative selection based on the normalized values for the ratio of nonsynonymous substitutions per nonsynonymous site to synonymous substitutions per synonymous site. A global phylogenetic analysis of CP sequences revealed segregation of virus isolates into four major clades with no geographic clustering. In contrast, the RdRp-based phylogenetic tree indicated segregation of GVA isolates from California and Washington into six clades, independent of geographic origin or cultivar. Phylogenetic network coupled with recombination analyses showed putative recombination events in both RdRp and CP sequence data sets, with more of these events located in the CP sequence. The preponderance of divergent variants of GVA co-replicating within individual grapevines could increase viral genotypic complexity with implications for phylogenetic analysis and evolutionary history of the virus. The knowledge of genetic diversity of GVA generated in this study will provide a foundation for elucidating the epidemiological characteristics of virus populations at different scales and implementing appropriate management strategies for minimizing the spread of genetic variants of the virus by vectors and via planting materials supplied to nurseries and grape growers.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Alabi</LastName><ForeName>Olufemi J</ForeName><Initials>OJ</Initials></Author><Author ValidYN="Y"><LastName>Al Rwahnih</LastName><ForeName>Maher</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Mekuria</LastName><ForeName>Tefera A</ForeName><Initials>TA</Initials></Author><Author ValidYN="Y"><LastName>Naidu</LastName><ForeName>Rayapati A</ForeName><Initials>RA</Initials></Author></AuthorList><Language>eng</Language><DataBankList 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Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012324" MajorTopicYN="N">RNA Replicase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011995" MajorTopicYN="N">Recombination, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014764" MajorTopicYN="N">Viral Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D027843" MajorTopicYN="N">Vitis</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014861" MajorTopicYN="N" Type="Geographic">Washington</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>10</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>10</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>7</Month><Day>11</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24168043</ArticleId><ArticleId IdType="doi">10.1094/PHYTO-06-13-0179-R</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list></list><tree><noCountry><name sortKey="Al Rwahnih, Maher" sort="Al Rwahnih, Maher" uniqKey="Al Rwahnih M" first="Maher" last="Al Rwahnih">Maher Al Rwahnih</name><name sortKey="Alabi, Olufemi J" sort="Alabi, Olufemi J" uniqKey="Alabi O" first="Olufemi J" last="Alabi">Olufemi J. Alabi</name><name sortKey="Mekuria, Tefera A" sort="Mekuria, Tefera A" uniqKey="Mekuria T" first="Tefera A" last="Mekuria">Tefera A. Mekuria</name><name sortKey="Naidu, Rayapati A" sort="Naidu, Rayapati A" uniqKey="Naidu R" first="Rayapati A" last="Naidu">Rayapati A. Naidu</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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{{Explor lien
|wiki= Bois
|area= GrapevineDiseaseV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:24168043
|texte= Genetic diversity of Grapevine virus A in Washington and California vineyards.
}}
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