A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)

The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the...

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Autores: Canaguier, Aurélie, Grimplet, Jérôme, Di Gaspero, Gabriele, Scalabrin, Simone, Duchêne, Éric, Choisne, Nathalie, Mohellibi, Nacer, Guichard, Cécile, Rombauts, Stéphane, Le Clainche, Isabelle, Bérard, Aurélie, Chauveau, Aurélie, Bounon, Rémi, Rustenholz, Camille, Morgante, Michele, Le Paslier, Marie Christine, Brunel, Dominique, Adam-Blondon, Anne-Françoise
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2017
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/192898
Acceso en línea:http://hdl.handle.net/10261/192898
Access Level:acceso abierto
Palabra clave:Vitis vinifera
Genome
Chromosomes assembly
Gene annotation
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spelling A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)Canaguier, AurélieGrimplet, JérômeDi Gaspero, GabrieleScalabrin, SimoneDuchêne, ÉricChoisne, NathalieMohellibi, NacerGuichard, CécileRombauts, StéphaneLe Clainche, IsabelleBérard, AurélieChauveau, AurélieBounon, RémiRustenholz, CamilleMorgante, MicheleLe Paslier, Marie ChristineBrunel, DominiqueAdam-Blondon, Anne-FrançoiseVitis viniferaGenomeChromosomes assemblyGene annotationThe grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes).This work was supported by the French National Institute for Agriculture (INRA, France), the University of Udine and the Institute of Applied Genomics (Italy), the Vlaams Institut voor Biotechnologie and the University of Ghent (Belgium), the Istituto de Ciencas de la Vid et del Vino (Logroño, Spain) and several grants: ANR-Plant-KBBE-2008- GrapeReSeq and ANR-2008-Muscares funded by the French National Research Agency (ANR), Valorizzazione dei Principali Vitigni Autoctoni Italiani e dei loro Terroir (Vigneto, no. COSVIR27129) funded by the Italian Ministry of Agriculture and the COST action FA1106 funded under the European FP7 Research ProgramPeer reviewedElsevierInstitut National de la Recherche Agronomique (France)Università degli Studi di UdineInstitute of Applied Genomics (Italy)Flanders Institute for BiotechnologyGhent UniversityEuropean Cooperation in Science and TechnologyAgence Nationale de la Recherche (France)Ministero delle Politiche Agricole Alimentari e ForestaliAdam-Blondon, Anne-Françoise [0000-0002-3412-9086]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]201920192017info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/192898reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Ingléshttp://dx.doi.org/10.1016/j.gdata.2017.09.002Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1928982026-05-22T06:33:51Z
dc.title.none.fl_str_mv A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
title A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
spellingShingle A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
Canaguier, Aurélie
Vitis vinifera
Genome
Chromosomes assembly
Gene annotation
title_short A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
title_full A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
title_fullStr A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
title_full_unstemmed A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
title_sort A new version of the grapevine reference genome assembly (12X.v2) and of its annotation (VCost.v3)
dc.creator.none.fl_str_mv Canaguier, Aurélie
Grimplet, Jérôme
Di Gaspero, Gabriele
Scalabrin, Simone
Duchêne, Éric
Choisne, Nathalie
Mohellibi, Nacer
Guichard, Cécile
Rombauts, Stéphane
Le Clainche, Isabelle
Bérard, Aurélie
Chauveau, Aurélie
Bounon, Rémi
Rustenholz, Camille
Morgante, Michele
Le Paslier, Marie Christine
Brunel, Dominique
Adam-Blondon, Anne-Françoise
author Canaguier, Aurélie
author_facet Canaguier, Aurélie
Grimplet, Jérôme
Di Gaspero, Gabriele
Scalabrin, Simone
Duchêne, Éric
Choisne, Nathalie
Mohellibi, Nacer
Guichard, Cécile
Rombauts, Stéphane
Le Clainche, Isabelle
Bérard, Aurélie
Chauveau, Aurélie
Bounon, Rémi
Rustenholz, Camille
Morgante, Michele
Le Paslier, Marie Christine
Brunel, Dominique
Adam-Blondon, Anne-Françoise
author_role author
author2 Grimplet, Jérôme
Di Gaspero, Gabriele
Scalabrin, Simone
Duchêne, Éric
Choisne, Nathalie
Mohellibi, Nacer
Guichard, Cécile
Rombauts, Stéphane
Le Clainche, Isabelle
Bérard, Aurélie
Chauveau, Aurélie
Bounon, Rémi
Rustenholz, Camille
Morgante, Michele
Le Paslier, Marie Christine
Brunel, Dominique
Adam-Blondon, Anne-Françoise
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.contributor.none.fl_str_mv Institut National de la Recherche Agronomique (France)
Università degli Studi di Udine
Institute of Applied Genomics (Italy)
Flanders Institute for Biotechnology
Ghent University
European Cooperation in Science and Technology
Agence Nationale de la Recherche (France)
Ministero delle Politiche Agricole Alimentari e Forestali
Adam-Blondon, Anne-Françoise [0000-0002-3412-9086]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Vitis vinifera
Genome
Chromosomes assembly
Gene annotation
topic Vitis vinifera
Genome
Chromosomes assembly
Gene annotation
description The grapevine reference genome was published by Jaillon et al. [1]. The sequence for the first version of the genome, called the 8X version, was obtained using a whole genome shotgun strategy and the Sanger sequencing technology and was assembled from reads representing 8X coverage. Soon after, the assembly was improved through the addition of 4X of additional coverage, including more Bacterial Artificial Chromosome end sequences that greatly improved the scaffolding of the sequence contigs [2], [3]. The corresponding scaffolds and raw sequences were deposited in European Molecular Biology Laboratory (EMBL) archives (FN594950-FN597014, 2065 entries, release 102). A new chromosome assembly was also developed, based on an improved version of the maps used for the 8X genome version [2], [3], [4], [5] and was also archived at EMBL (FN597015-FN597047, 33 entries, release 102): it is referenced in the grapevine community as the 12X.v0 version of the grapevine reference genome. The chromosome sequence scaffolding of this version still necessitated improvements as around 9% of the sequence was not anchored to chromosomes (with the corresponding scaffolds stacked in the “Unknown” chromosome) and 3.5% of the sequence could be assigned to a chromosome but without certain placement and orientation within the chromosome (stacked in additional “random” chromosomes).
publishDate 2017
dc.date.none.fl_str_mv 2017
2019
2019
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/192898
url http://hdl.handle.net/10261/192898
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv http://dx.doi.org/10.1016/j.gdata.2017.09.002
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier
publisher.none.fl_str_mv Elsevier
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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