The Coffee Genome Hub

Date: Sunday, January 12, 2014
Time: 4:00 PM
Room: Pacific Salon 4-5 (2nd Floor)
Alexis Dereeper , IRD, UMR RPB, F-34394 Montpellier, France
Gaëtan Droc , CIRAD, UMR AGAP, F-34398 Montpellier, France
Stéphanie Bocs , CIRAD, UMR AGAP, Montpellier, France
Sebastien Ravel , IRD, UMR RPB, Montpellier, France
Valentin Guignon , Bioversity International, Commodity Systems & Genetic Resources, 34397 Montpellier Cedex 5, France
Dominique This , Montpellier SupAgro, UMR AGAP, F-34060 Montpellier, France
Michelle Cotta , CIRAD, UMR AGAP, Montpellier, France
Philippe Lashermes , Institut de Recherche pour le Développement, Montpellier, France
The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently obtained and portends to be published and released in the coming months. In the context of the C.canephora genome sequence project and to support post-genomics efforts, we developed the Coffee Genome Hub, an integrative genome information system accessible through the South Green Bioinformatics Platform, providing centralized access to coffee community to genomics, genetics and breeding data and analysis tools to facilitate basic, translational and applied research in coffee.

Available data are the complete genome sequence of C.canephora along with gene structure, gene product information, metabolism, gene families, transcriptomics (ESTs, RNA-Seq), syntenic blocs, genetic markers and genetic maps. The hub provides also generic softwares (e.g. GMOD tools) for easy querying, visualizing and downloading research data. Notably, the Coffee Genome Hub includes a Genome Browser for the C.canephora genome sequence, enhanced by a Community Annotation System (CAS) enabling the improvement of automatic gene annotation through an annotation editor and facilitating the study of gene families, and a chromosome viewer displaying the distribution of genomics feature along the chromosomes. In addition, the hub aims at developing interoperability between other existing South Green tools managing Coffee data (phylogenomics resources, SNPs) and/or allowing data analyses (workflow manager).

The Coffee Genome Hub can be accessed at http://coffee-genome.org/.