Trippe, Elizabeth Uddenberg, Daniel Yakovlev, Igor Yeaman, Sam P42 P43 P44 P45 29
Poster Abstracts Poster <strong>abstract</strong>s are ordered alphabetically by presenting author (underlined). P1 Oak genome sequencing project: genomic data and bioinformatic resources to study oak tree adaptation J. AMSELEM 1 , J.M. AURY 2 , N. FRANCILLONNE 1 , T. ALAEITABAR 1 , C. DA SILVA 2 , S. DUPLESSIS 3 , F. EHRENMANN 4 , C. KLOPP 5 , K. LABADIE 2 , T. LEROY 4 , I. LESUR 4 , T. LETELLIER 1 , I. LUYTEN 1 , C. MICHOTEY 1 , C. BODENES 4 , G. Le PROVOST 4 , F. MURAT 7 , P. FAIVRE RAMPANT 6 , A. KREMER 4 , F. MARTIN 3 , J. SALSE 7 , H. QUESNEVILLE 1 and C. PLOMION 4 1 INRA, UR1164, URGI, Unité de Recherche Génomique Info, route de Saint-Cyr – RD 10, 78026 Versailles, France; 2 CEA, Institut de Génomique (IG), Genoscope, 2 rue Gaston Crémieux, 91057 Evry, France; 3 INRA-Université́ de Lorraine, UMR1136, Interactions Arbres/Micro-organismes, 54280 Champenoux, France; 4 INRA, UMR1202, BIOGECO, 69 route d’Arcachon, 33610 Cestas, France; 5 INRA, MIAT, Plateforme bioinformatique Toulouse Midi-Pyrénées, 24 chemin de Borde-Rouge, 31326 Auzeville Castanet-Tolosan, France; 6 INRA, URGV, Plant Genomics Research, 2 rue Gaston Crémieux, 91057 Evry, France; 7 INRA/UBP UMR1095, Laboratoire Génétique, Diversité́ et Ecophysiologie des Céréales, Site de Crouël 5 Chemin de Beaulieu, 63039 Clermont-Ferrand, France The large, complex and highly heterozygous genome of pedunculate oak (Quercus robur) was sequenced using a whole-genome shotgun approach. Roche 454 GS-FLX sequence reads were assembled into contigs and combined with Illumina reads from paired-end and mate-pair libraries to build a total of 17,910 scaffolds (> 2 kb; 1.34 Gb total size; N50=260 kb). Half of the genome was aligned to a high-density linkage map. We will present the results of the structural (Transposable Elements (TEs), genes) and functional annotations of automatically predicted genes. These data were obtained using robust pipelines (i) REPET to de novo detect, classify and annotate TEs (ii) Eugene to integrate ab initio and similarity gene finding softwares (iii) A functional annotation pipeline, based on Interproscan to search for patterns/motifs and Blast based comparative genomics. We also set up a dedicated integrated genome annotation system based on GMOD based web interfaces (WebApollo/JBrowse and Intermine) to make these data available under a user-friendly environment. This system allows experts of different gene families to curate/validate automatically predicted genes. 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. 30
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