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Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierForestry and Forest Products Research Institute [FFPRI]
dc.contributor.authorUENO, Saneyoshi
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLE PROVOST, Grégoire
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLÉGER, Valérie
hal.structure.identifierSystème d'Information des GENomes des Animaux d'Elevage [SIGENAE]
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorKLOPP, Christophe
hal.structure.identifierUnité de Biométrie et Intelligence Artificielle (ancêtre de MIAT) [UBIA]
dc.contributor.authorNOIROT, Céline
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorFRIGERIO, Jean-Marc
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorSALIN, Franck
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorSALSE, Jérôme
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorABROUK, Michael
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorMURAT, Florent
hal.structure.identifierEcologie et Ecophysiologie Forestières [devient SILVA en 2018] [EEF]
dc.contributor.authorBRENDEL, Oliver
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDERORY, Jérémy
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorABADIE, Pierre
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorLÉGER, Patrick
hal.structure.identifierCentre de Bioinformatique de Bordeaux [CBIB]
dc.contributor.authorCABANE, Cyril
hal.structure.identifierCentre de Bioinformatique de Bordeaux [CBIB]
dc.contributor.authorBARRÉ, Aurélien
hal.structure.identifierCentre de Bioinformatique de Bordeaux [CBIB]
hal.structure.identifierLaboratoire Bordelais de Recherche en Informatique [LaBRI]
dc.contributor.authorDE DARUVAR, Antoine
hal.structure.identifierGenoscope - Centre national de séquençage [Evry] [GENOSCOPE]
dc.contributor.authorCOULOUX, Arnaud
hal.structure.identifierGénomique métabolique [UMR 8030]
dc.contributor.authorWINCKER, Patrick
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorREVIRON, Marie-Pierre
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorKREMER, Antoine
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
dc.date.issued2010
dc.identifier.issn1471-2164
dc.description.abstractEnBACKGROUND: The Fagaceae family comprises about 1,000 woody species worldwide. About half belong to the Quercus family. These oaks are often a source of raw material for biomass wood and fiber. Pedunculate and sessile oaks, are among the most important deciduous forest tree species in Europe. Despite their ecological and economical importance, very few genomic resources have yet been generated for these species. Here, we describe the development of an EST catalogue that will support ecosystem genomics studies, where geneticists, ecophysiologists, molecular biologists and ecologists join their efforts for understanding, monitoring and predicting functional genetic diversity. RESULTS: We generated 145,827 sequence reads from 20 cDNA libraries using the Sanger method. Unexploitable chromatograms and quality checking lead us to eliminate 19,941 sequences. Finally a total of 125,925 ESTs were retained from 111,361 cDNA clones. Pyrosequencing was also conducted for 14 libraries, generating 1,948,579 reads, from which 370,566 sequences (19.0%) were eliminated, resulting in 1,578,192 sequences. Following clustering and assembly using TGICL pipeline, 1,704,117 EST sequences collapsed into 69,154 tentative contigs and 153,517 singletons, providing 222,671 non-redundant sequences (including alternative transcripts). We also assembled the sequences using MIRA and PartiGene software and compared the three unigene sets. Gene ontology annotation was then assigned to 29,303 unigene elements. Blast search against the SWISS-PROT database revealed putative homologs for 32,810 (14.7%) unigene elements, but more extensive search with Pfam, Refseq_protein, Refseq_RNA and eight gene indices revealed homology for 67.4% of them. The EST catalogue was examined for putative homologs of candidate genes involved in bud phenology, cuticle formation, phenylpropanoids biosynthesis and cell wall formation. Our results suggest a good coverage of genes involved in these traits. Comparative orthologous sequences (COS) with other plant gene models were identified and allow to unravel the oak paleo-history. Simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) were searched, resulting in 52,834 SSRs and 36,411 SNPs. All of these are available through the Oak Contig Browser http://genotoul-contigbrowser.toulouse.inra.fr:9092/Quercus_robur/index.html. CONCLUSIONS: This genomic resource provides a unique tool to discover genes of interest, study the oak transcriptome, and develop new markers to investigate functional diversity in natural populations.
dc.language.isoen
dc.publisherBioMed Central
dc.subjectPOLYMORPHISME NUCLÉOTIDIQUE SIMPLE
dc.subjectRESSOURCE GÉNOMIQUE
dc.subject.enCHENE
dc.subject.enOUTIL D'ANALYSE
dc.subject.meshBase Sequence
dc.subject.meshCluster Analysis
dc.subject.meshQuercus
dc.subject.meshRNA, Messenger
dc.subject.meshSequence Analysis, DNA
dc.subject.meshSequence Homology, Nucleic Acid
dc.subject.meshSoftware
dc.subject.meshSpecies Specificity
dc.subject.meshTemperature
dc.subject.meshTrees
dc.subject.meshComputational Biology
dc.subject.meshContig Mapping
dc.subject.meshExpressed Sequence Tags
dc.subject.meshGene Library
dc.subject.meshGenes, Plant
dc.subject.meshMicrosatellite Repeats
dc.subject.meshPeptides
dc.subject.meshPolymorphism, Single Nucleotide
dc.title.enBioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak.
dc.typeArticle de revue
dc.identifier.doi10.1186/1471-2164-11-650
dc.subject.halSciences du Vivant [q-bio]/Bio-Informatique, Biologie Systémique [q-bio.QM]
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
bordeaux.journalBMC Genomics
bordeaux.page650
bordeaux.volume11
bordeaux.peerReviewedoui
hal.identifierhal-00645933
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00645933v1
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