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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 - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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Overview of the Coffee Genome Hub (A) A gene search is performed with the of SAM dependent carboxyl methyltransferase (IPR005299) InterPro family identifier. The result page returns a list of genes with graphical display on the chromosomes. (B) The gene report summarizes all the data available for a gene and links to additional resources: (C) Gene family—here the distribution of the Sam Dependent Carboxyl Methyltransferase gene family (GP000195) of coffee illustrates its abundance in plants, (D) JBrowse centered on the region of selected gene (±10 kb) and (E) Pathways tools (e.g. biosynthesis of the caffeine).
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Figure 1: Overview of the Coffee Genome Hub (A) A gene search is performed with the of SAM dependent carboxyl methyltransferase (IPR005299) InterPro family identifier. The result page returns a list of genes with graphical display on the chromosomes. (B) The gene report summarizes all the data available for a gene and links to additional resources: (C) Gene family—here the distribution of the Sam Dependent Carboxyl Methyltransferase gene family (GP000195) of coffee illustrates its abundance in plants, (D) JBrowse centered on the region of selected gene (±10 kb) and (E) Pathways tools (e.g. biosynthesis of the caffeine).

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).


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 - Nucleic Acids Res. (2014)

Overview of the Coffee Genome Hub (A) A gene search is performed with the of SAM dependent carboxyl methyltransferase (IPR005299) InterPro family identifier. The result page returns a list of genes with graphical display on the chromosomes. (B) The gene report summarizes all the data available for a gene and links to additional resources: (C) Gene family—here the distribution of the Sam Dependent Carboxyl Methyltransferase gene family (GP000195) of coffee illustrates its abundance in plants, (D) JBrowse centered on the region of selected gene (±10 kb) and (E) Pathways tools (e.g. biosynthesis of the caffeine).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383925&req=5

Figure 1: Overview of the Coffee Genome Hub (A) A gene search is performed with the of SAM dependent carboxyl methyltransferase (IPR005299) InterPro family identifier. The result page returns a list of genes with graphical display on the chromosomes. (B) The gene report summarizes all the data available for a gene and links to additional resources: (C) Gene family—here the distribution of the Sam Dependent Carboxyl Methyltransferase gene family (GP000195) of coffee illustrates its abundance in plants, (D) JBrowse centered on the region of selected gene (±10 kb) and (E) Pathways tools (e.g. biosynthesis of the caffeine).
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).

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.

View Article: PubMed Central - PubMed

Affiliation: 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.

Show MeSH
Related in: MedlinePlus