title: Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies.
abstract: The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Plomion
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France.
authors.forename: Joëlle
authors.initials: J
authors.lastname: Amselem
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France.
authors.forename: Tina
authors.initials: T
authors.lastname: Alaeitabar
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Barbe
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Caroline
authors.initials: C
authors.lastname: Belser
authors.affiliation: INRA, CNRGV, Castanet-Tolosan, F-31326, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Bergès
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Bodénès
authors.affiliation: INRA, URGV, Plant Genomics Research, Evry, F-91057, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Boudet
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Boury
authors.affiliation: INRA, URGV, Plant Genomics Research, Evry, F-91057, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Canaguier
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Corinne
authors.initials: C
authors.lastname: Da Silva
authors.affiliation: INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Duplessis
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: François
authors.initials: F
authors.lastname: Ehrenmann
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Barbara
authors.initials: B
authors.lastname: Estrada-Mairey
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Fouteau
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Francillonne
authors.affiliation: Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
authors.affiliation: INRA, URGV, Plant Genomics Research, Evry, F-91057, France.
authors.forename: Cécile
authors.initials: C
authors.lastname: Guichard
authors.affiliation: Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Karine
authors.initials: K
authors.lastname: Labadie
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Céline
authors.initials: C
authors.lastname: Lalanne
authors.affiliation: INRA, URGV, Plant Genomics Research, Evry, F-91057, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Le Clainche
authors.affiliation: INRA, UR0588 Amélioration Génétique et Physiologie Forestières, Orléans, F-45075, France.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Leplé
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Le Provost
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Thibault
authors.initials: T
authors.lastname: Leroy
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Lesur
authors.affiliation: INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France.
authors.forename: Francis
authors.initials: F
authors.lastname: Martin
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Mercier
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France.
authors.forename: Célia
authors.initials: C
authors.lastname: Michotey
authors.affiliation: INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Murat
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Franck
authors.initials: F
authors.lastname: Salin
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France.
authors.forename: Delphine
authors.initials: D
authors.lastname: Steinbach
authors.affiliation: INRA, URGV, Plant Genomics Research, Evry, F-91057, France.
authors.forename: Patricia
authors.initials: P
authors.lastname: Faivre-Rampant
authors.affiliation: Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.|Université d'Evry Val d'Essone, UMR 8030, Evry, CP5706, France.|Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, CP5706, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Wincker
authors.affiliation: INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Salse
authors.affiliation: INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France.
authors.forename: Hadi
authors.initials: H
authors.lastname: Quesneville
authors.affiliation: INRA, UMR1202, BIOGECO, Cestas, F-33610, France.|University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Kremer
mesh_terms: D018745:Genome, Plant; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D029963:Quercus / Q000145:classification / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Quercus robur; genome sequence; genomic resources