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.
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dig-cirad-fr-5750942024-04-30T09:05:12Z http://agritrop.cirad.fr/575094/ http://agritrop.cirad.fr/575094/ 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. Nucleic Acids Research, 43 (D1), D1028-D1035https://doi.org/10.1093/nar/gku1108 <https://doi.org/10.1093/nar/gku1108> 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 eng 2015 Nucleic Acids Research F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Coffea Coffea canephora génome ressource génétique végétale logiciel système d'information banque de données génomique bioinformatique gène amélioration des plantes http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_11769 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5956 France http://aims.fao.org/aos/agrovoc/c_3081 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/575094/1/document_575094.pdf application/pdf Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1093/nar/gku1108 10.1093/nar/gku1108 info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gku1108 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1093/nar/gku1108 info:eu-repo/semantics/dataset/purl/http://coffee-genome.org/ |
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Europa del Oeste |
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Biblioteca del CIRAD Francia |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Coffea Coffea canephora génome ressource génétique végétale logiciel système d'information banque de données génomique bioinformatique gène amélioration des plantes http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_11769 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_3081 F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Coffea Coffea canephora génome ressource génétique végétale logiciel système d'information banque de données génomique bioinformatique gène amélioration des plantes http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_11769 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_3081 |
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F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Coffea Coffea canephora génome ressource génétique végétale logiciel système d'information banque de données génomique bioinformatique gène amélioration des plantes http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_11769 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_3081 F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Coffea Coffea canephora génome ressource génétique végétale logiciel système d'information banque de données génomique bioinformatique gène amélioration des plantes http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_11769 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_3081 Dereeper, Alexis Bocs, Stéphanie Rouard, Mathieu Guignon, Valentin Ravel, Sébastien Tranchant-Dubreuil, Christine Poncet, Valérie Garsmeur, Olivier Lashermes, Philippe Droc, Gaëtan The coffee genome hub: a resource for coffee genomes |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes C30 - Documentation et information U10 - Informatique, mathématiques et statistiques Coffea Coffea canephora génome ressource génétique végétale logiciel système d'information banque de données génomique bioinformatique gène amélioration des plantes http://aims.fao.org/aos/agrovoc/c_1720 http://aims.fao.org/aos/agrovoc/c_1723 http://aims.fao.org/aos/agrovoc/c_3224 http://aims.fao.org/aos/agrovoc/c_37419 http://aims.fao.org/aos/agrovoc/c_24008 http://aims.fao.org/aos/agrovoc/c_11769 http://aims.fao.org/aos/agrovoc/c_24833 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_37958 http://aims.fao.org/aos/agrovoc/c_3214 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_3081 |
author |
Dereeper, Alexis Bocs, Stéphanie Rouard, Mathieu Guignon, Valentin Ravel, Sébastien Tranchant-Dubreuil, Christine Poncet, Valérie Garsmeur, Olivier Lashermes, Philippe Droc, Gaëtan |
author_facet |
Dereeper, Alexis Bocs, Stéphanie Rouard, Mathieu Guignon, Valentin Ravel, Sébastien Tranchant-Dubreuil, Christine Poncet, Valérie Garsmeur, Olivier Lashermes, Philippe Droc, Gaëtan |
author_sort |
Dereeper, Alexis |
title |
The coffee genome hub: a resource for coffee genomes |
title_short |
The coffee genome hub: a resource for coffee genomes |
title_full |
The coffee genome hub: a resource for coffee genomes |
title_fullStr |
The coffee genome hub: a resource for coffee genomes |
title_full_unstemmed |
The coffee genome hub: a resource for coffee genomes |
title_sort |
coffee genome hub: a resource for coffee genomes |
url |
http://agritrop.cirad.fr/575094/ http://agritrop.cirad.fr/575094/1/document_575094.pdf |
work_keys_str_mv |
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