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An integrated information system dedicated to oak genomics and genetics

hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorAMSELEM, Joëlle
hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorFRANCILLONNE, Nicolas
hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorMICHOTEY, Célia
hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorLETELLIER, Thomas
hal.structure.identifierLaboratoire de Bioinformatique pour la Génomique et la Biodiversité [LBGB]
dc.contributor.authorAURY, Jean-Marc
hal.structure.identifierLaboratoire de Bioinformatique pour la Génomique et la Biodiversité [LBGB]
dc.contributor.authorDA SILVA, Corinne
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorDUPLESSIS, Sébastien
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorEHRENMANN, François
hal.structure.identifierLaboratoire de Bioinformatique pour la Génomique et la Biodiversité [LBGB]
dc.contributor.authorFAYE, Sébastien
hal.structure.identifierUnité de Mathématiques et Informatique Appliquées de Toulouse [MIAT INRA]
dc.contributor.authorGASPIN, Christine
hal.structure.identifierUnité de Mathématiques et Informatique Appliquées de Toulouse [MIAT INRA]
dc.contributor.authorKLOPP, Christophe
hal.structure.identifierGenoscope - Centre national de séquençage [Evry] [GENOSCOPE]
dc.contributor.authorLABADIE, Karine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLESUR, Isabelle
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLEROY, Thibault
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorMURAT, Florent
hal.structure.identifierMathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] [MaIAGE]
dc.contributor.authorRUÉ, Olivier
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBODENES, Catherine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLEPLÉ, Jean-Charles
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierEtude du Polymorphisme des Génomes Végétaux [EPGV]
dc.contributor.authorFAIVRE RAMPANT, Patricia
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierInteractions Arbres-Microorganismes [IAM]
dc.contributor.authorMARTIN, Francis
hal.structure.identifierUnité de Recherche Génomique Info [URGI]
dc.contributor.authorQUESNEVILLE, Hadi
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorSALSE, Jérôme
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2018
dc.date.conference2018-01-13
dc.description.abstractEnGnpIS is an information system designed to integrate and link genomic, genetic and environmental data into a single environment dedicated to plant (crops and forest trees) and fungi data. GnpIS is regularly improved with new functionalities answering specific needs raised by scientists and released several times a year. We propose to illustrate the integrated genome annotation system we set up with a focus on the interoperability between genomic and genetic data (e.g. Markers, QTL) present in GnpIS-core, through the use case Quercus robur (the pedunculate oak), a large, complex and highly heterozygous genome.This genome annotation system relies on GMOD interfaces such as WebApollo/JBrowse and Intermine to make these data available under a user-friendly environment. All annotations and analysis results (Transposable Elements (TEs), genes, ncRNA ...) and functional annotation (protein-coding genes) were obtained using powerful and robust pipelines: (i) REPET used to detect, classify and annotate TEs representing 50% of the genome; (ii) Eugene which integrates ab initio and similarity gene finding softwares to predict gene models; (iii) ncRNA were annotated using different tools to annotate lncRNA, miRNA, rRNA, tRNA (iv) A functional annotation pipeline mainly based on Interproscan and comparative genomics was performed on the 25,808 highly confident predicted proteins. This system allows experts to analyze their protein families of interest and curate/validate gene structure.All together these resources provide a framework to study the two key evolutionary processes that explain the remarkable diversity found within the Quercus genus: local adaptation and speciation.
dc.language.isoen
dc.subject.enGenomics
dc.subject.enGenetics
dc.subject.enInformation system
dc.subject.enOak
dc.title.enAn integrated information system dedicated to oak genomics and genetics
dc.typeCommunication dans un congrès
dc.subject.halSciences du Vivant [q-bio]
bordeaux.page27 slides
bordeaux.conference.titlePAG XXVI Plant and Animal Genome Conference
bordeaux.countryUS
bordeaux.conference.citySan Diego
bordeaux.peerReviewedoui
hal.identifierhal-01839185
hal.version1
hal.invitednon
hal.proceedingsoui
hal.conference.end2018-01-17
hal.popularnon
hal.audienceNon spécifiée
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01839185v1
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