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The coffee genome hub: a resource for coffee genomes

Dereeper A., Bocs S., Rouard M., Guignon V., Ravel S., Tranchant-Dubreuil C., Poncet V., Garsmeur O., Lashermes P., Droc G.. 2015. Nucleic Acids Research, 43 (D1) : D1028-D1035.

The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In the context of the C. canephora genome sequencing project and to support post-genomics efforts, we developed the Coffee Genome Hub (http://coffee-genome.org/), an integrative genome information system that allows centralized access to genomics and genetics data and analysis tools to facilitate translational and applied research in coffee. We provide the complete genome sequence of C. canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics, syntenic blocks, genetic markers and genetic maps. The hub relies on generic software (e.g. GMOD tools) for easy querying, visualizing and downloading research data. It includes a Genome Browser enhanced by a Community Annotation System, enabling the improvement of automatic gene annotation through an annotation editor. In addition, the hub aims at developing interoperability among other existing South Green tools managing coffee data (phylogenomics resources, SNPs) and/or supporting data analyses with the Galaxy workflow manager. (Résumé d'auteur)

Mots-clés : amélioration des plantes; gène; bioinformatique; génomique; banque de données; système d'information; logiciel; ressource génétique végétale; génome; coffea canephora; coffea; france

Thématique : Génétique et amélioration des plantes; Documentation et information; Méthodes mathématiques et statistiques

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