The coffee genome hub: a resource for coffee genomes.
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.
UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France alexis.dereeper@ird.fr.
Alexis
A
Dereeper
UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
Stéphanie
S
Bocs
Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
Mathieu
M
Rouard
Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
Valentin
V
Guignon
UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France.
Sébastien
S
Ravel
UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France.
Christine
C
Tranchant-Dubreuil
UMR Diversité Adaptation et DEveloppement des plantes (DIADE), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France.
Valérie
V
Poncet
UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France.
Olivier
O
Garsmeur
UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France.
Philippe
P
Lashermes
UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), CIRAD, F-34398 Montpellier, France alexis.dereeper@ird.fr.
Gaëtan
G
Droc
D040503:Coffea / Q000235:genetics* / Q000378:metabolism; D030561:Databases, Nucleic Acid; D020869:Gene Expression Profiling; D018745:Genome, Plant; D023281:Genomics; D053858:Metabolic Networks and Pathways / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012984:Software; D026801:Synteny