The coffee genome hub: a resource for coffee genomes.
Bottom Line: The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released.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.
Affiliation: UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France firstname.lastname@example.org.Show MeSH
Related in: MedlinePlus
Mentions: Overall, the Coffea canephora gene family distribution is consistent compared to the other gene families in plants. Using the InterPro domain distribution tool, 63 transcription factors were studied based the transcription-associated protein (TAP) classification rules (35) leading to the identification of RWP-RK expansion (1). It is interesting to note that there are 211 coffee-specific clusters, ranging from 2 to 18 paralogs and 116 phylum-specific families in the Asterids sharing at least one sequence in common between C. canephora, Solanum tuberosum and Solanum lypercosicum. We identified an over-representation of the NB-ARC superfamily (724 sequences bearing the NB-ARC InterPro signature IPR002182). In addition, a high number of gene copies (47 sequences) were also detected for the Sam Dependent Carboxyl Methyltransferase family that is involved in caffeine synthesis (Figure 1).
Affiliation: UMR Résistance des Plantes aux Bioagresseurs (RPB), Institut de Recherche pour le Développement (IRD), BP 64501, 34394 Montpellier Cedex 5, France email@example.com.