2015
35th New Phytologist Symposium: The genomes of forest trees: new frontiers of forest biology, Boston, 16-17/06/2015
16 Jun 2015 Oak genome sequencing project: genomic data and bioinformatic resources to study oak tree adaptationJ. Amselem , J.M. Aury, N. Francillonne, T. Alaeitabar, C. Da Silva, S. Duplessis, F. Ehrenmann, C. Klopp, K. Labadie, T. Leroy, I. Lesur, T. Letellier, I. Luyten, C. Michotey, C. Bodenes, G. Le Provost, F. Murat, P. Faivre Rampant, A. Kremer, F. Martin, J. Salse, H. Quesneville, C. Plomion
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 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.
Creation date: 08 Jul 2015
eZ PublishPublication supervisor: A-F. Adam-Blondon
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