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The coffee genome hub: a resource for coffee genomes

Dereeper Alexis, Bocs Stéphanie, Rouard Mathieu, Guignon Valentin, Ravel Sébastien, Tranchant-Dubreuil Christine, Poncet Valérie, Garsmeur Olivier, Lashermes Philippe, Droc Gaëtan. 2015. The coffee genome hub: a resource for coffee genomes. Nucleic Acids Research, 43 (D1), D1028-D1035

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Url - jeu de données : http://coffee-genome.org/

Quartile : Outlier, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

Abstract : 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 Agrovoc : Coffea, Coffea canephora, Génome, Ressource génétique végétale, Logiciel, Système d'information, Banque de données, génomique, Bioinformatique, Gène, Amélioration des plantes

Mots-clés géographiques Agrovoc : France

Classification Agris : F30 - Plant genetics and breeding
C30 - Documentation and information
U10 - Mathematical and statistical methods

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Dereeper Alexis, IRD (FRA)
  • Bocs Stéphanie, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7850-4426
  • Rouard Mathieu, Bioversity International (FRA)
  • Guignon Valentin, Bioversity International (FRA)
  • Ravel Sébastien, IRD (FRA)
  • Tranchant-Dubreuil Christine, IRD (FRA)
  • Poncet Valérie, IRD (FRA)
  • Garsmeur Olivier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-8869-3689
  • Lashermes Philippe, IRD (FRA)
  • Droc Gaëtan, CIRAD-BIOS-UMR AGAP (FRA)

Source : Cirad - Agritrop (https://agritrop.cirad.fr/575094/)

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