Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes.
Identifieur interne : 000106 ( Main/Corpus ); précédent : 000105; suivant : 000107Detection of Multiple Variants of Grapevine Fanleaf Virus in Single Xiphinema index Nematodes.
Auteurs : Shahinez Garcia ; Jean-Michel Hily ; Véronique Komar ; Claude Gertz ; Gérard Demangeat ; Olivier Lemaire ; Emmanuelle VigneSource :
- Viruses [ 1999-4915 ] ; 2019.
English descriptors
- KwdEn :
- MESH :
- chemical : RNA, Viral.
- genetics : Nepovirus.
- methods : Computational Biology.
- parasitology : Vitis.
- virology : Nematoda, Plant Diseases, Vitis.
- Animals, Disease Vectors, Genetic Variation, High-Throughput Nucleotide Sequencing, Phylogeny.
Abstract
Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode Xiphinema index. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in X. index following nematodes feeding on roots. In this work, aviruliferous X. index were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 X. index tested positive for GFLV. Additionally, either pooled or single X. index carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of X. index as reservoirs of virus diversity.
DOI: 10.3390/v11121139
PubMed: 31835488
PubMed Central: PMC6950412
Links to Exploration step
pubmed:31835488Le document en format XML
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France.</nlm:affiliation></affiliation></author><author><name sortKey="Hily, Jean Michel" sort="Hily, Jean Michel" uniqKey="Hily J" first="Jean-Michel" last="Hily">Jean-Michel Hily</name><affiliation><nlm:affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>Institut Français de la Vigne et du Vin (IFV), 30240 Le Grau-Du-Roi, France.</nlm:affiliation></affiliation></author><author><name sortKey="Komar, Veronique" sort="Komar, Veronique" uniqKey="Komar V" first="Véronique" last="Komar">Véronique Komar</name><affiliation><nlm:affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</nlm:affiliation></affiliation></author><author><name sortKey="Gertz, Claude" sort="Gertz, Claude" uniqKey="Gertz C" first="Claude" last="Gertz">Claude Gertz</name><affiliation><nlm:affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</nlm:affiliation></affiliation></author><author><name sortKey="Demangeat, Gerard" sort="Demangeat, Gerard" uniqKey="Demangeat G" first="Gérard" last="Demangeat">Gérard Demangeat</name><affiliation><nlm:affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</nlm:affiliation></affiliation></author><author><name sortKey="Lemaire, Olivier" sort="Lemaire, Olivier" uniqKey="Lemaire O" first="Olivier" last="Lemaire">Olivier Lemaire</name><affiliation><nlm:affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</nlm:affiliation></affiliation></author><author><name sortKey="Vigne, Emmanuelle" sort="Vigne, Emmanuelle" uniqKey="Vigne E" first="Emmanuelle" last="Vigne">Emmanuelle Vigne</name><affiliation><nlm:affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Viruses</title><idno type="eISSN">1999-4915</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term><term>Computational Biology (methods)</term><term>Disease Vectors (MeSH)</term><term>Genetic Variation (MeSH)</term><term>High-Throughput Nucleotide Sequencing (MeSH)</term><term>Nematoda (virology)</term><term>Nepovirus (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Diseases (virology)</term><term>RNA, Viral (MeSH)</term><term>Vitis (parasitology)</term><term>Vitis (virology)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>RNA, Viral</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Nepovirus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="parasitology" xml:lang="en"><term>Vitis</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Nematoda</term><term>Plant Diseases</term><term>Vitis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Disease Vectors</term><term>Genetic Variation</term><term>High-Throughput Nucleotide Sequencing</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode <i>Xiphinema index</i>. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in <i>X. index</i> following nematodes feeding on roots. In this work, aviruliferous <i>X. index</i> were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 <i>X. index</i> tested positive for GFLV. Additionally, either pooled or single <i>X. index</i> carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of <i>X. index</i> as reservoirs of virus diversity.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31835488</PMID><DateCompleted><Year>2020</Year><Month>09</Month><Day>24</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>24</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1999-4915</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>12</Issue><PubDate><Year>2019</Year><Month>12</Month><Day>10</Day></PubDate></JournalIssue><Title>Viruses</Title><ISOAbbreviation>Viruses</ISOAbbreviation></Journal><ArticleTitle>Detection of Multiple Variants of Grapevine Fanleaf Virus in Single <i>Xiphinema index</i> Nematodes.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E1139</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/v11121139</ELocationID><Abstract><AbstractText>Grapevine fanleaf virus (GFLV) is responsible for a widespread disease in vineyards worldwide. Its genome is composed of two single-stranded positive-sense RNAs, which both show a high genetic diversity. The virus is transmitted from grapevine to grapevine by the ectoparasitic nematode <i>Xiphinema index</i>. Grapevines in diseased vineyards are often infected by multiple genetic variants of GFLV but no information is available on the molecular composition of virus variants retained in <i>X. index</i> following nematodes feeding on roots. In this work, aviruliferous <i>X. index</i> were fed on three naturally GFLV-infected grapevines for which the virome was characterized by RNAseq. Six RNA-1 and four RNA-2 molecules were assembled segregating into four and three distinct phylogenetic clades of RNA-1 and RNA-2, respectively. After 19 months of rearing, single and pools of 30 <i>X. index</i> tested positive for GFLV. Additionally, either pooled or single <i>X. index</i> carried multiple variants of the two GFLV genomic RNAs. However, the full viral genetic diversity found in the leaves of infected grapevines was not detected in viruliferous nematodes, indicating a genetic bottleneck. Our results provide new insights into the complexity of GFLV populations and the putative role of <i>X. index</i> as reservoirs of virus diversity.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Garcia</LastName><ForeName>Shahinez</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hily</LastName><ForeName>Jean-Michel</ForeName><Initials>JM</Initials><Identifier Source="ORCID">0000-0001-9141-9701</Identifier><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Institut Français de la Vigne et du Vin (IFV), 30240 Le Grau-Du-Roi, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Komar</LastName><ForeName>Véronique</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gertz</LastName><ForeName>Claude</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Demangeat</LastName><ForeName>Gérard</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lemaire</LastName><ForeName>Olivier</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vigne</LastName><ForeName>Emmanuelle</ForeName><Initials>E</Initials><Identifier Source="ORCID">0000-0002-3287-0786</Identifier><AffiliationInfo><Affiliation>Unité Mixte de Recherche (UMR) Santé de la Vigne et Qualité du Vin, Institut National de la Recherche Agronomique (INRA)-Université de Strasbourg, BP 20507, 68021 Colmar Cedex, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>12</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Viruses</MedlineTA><NlmUniqueID>101509722</NlmUniqueID><ISSNLinking>1999-4915</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012367">RNA, Viral</NameOfSubstance></Chemical></ChemicalList><SupplMeshList><SupplMeshName Type="Organism" UI="C000623901">Grapevine fanleaf virus</SupplMeshName></SupplMeshList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004199" MajorTopicYN="Y">Disease Vectors</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009348" MajorTopicYN="N">Nematoda</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017860" MajorTopicYN="N">Nepovirus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000821" MajorTopicYN="N">virology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012367" MajorTopicYN="N">RNA, Viral</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D027843" MajorTopicYN="N">Vitis</DescriptorName><QualifierName UI="Q000469" MajorTopicYN="Y">parasitology</QualifierName><QualifierName UI="Q000821" MajorTopicYN="Y">virology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">GFLV</Keyword><Keyword MajorTopicYN="Y">High Throughput Sequencing (HTS), detection</Keyword><Keyword MajorTopicYN="Y">Restriction Fragment Length Polymorphism (RFLP)</Keyword><Keyword MajorTopicYN="Y">Vitis vinifera</Keyword><Keyword MajorTopicYN="Y">Xiphinema index</Keyword><Keyword MajorTopicYN="Y">acquisition</Keyword><Keyword MajorTopicYN="Y">bottleneck</Keyword><Keyword MajorTopicYN="Y">genetic diversity</Keyword><Keyword 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