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GnpAnnot

GnpAnnot

A Structural, functional and comparative annotation platform dedicated to plants 'and their bio-aggressors' genomes

GnpAnnot is a ANR project on green genomics which intends to develop a community system of structural and functional annotation supported by comparative genomics and dedicated to plant and bio-aggressor genomes allowing both automatic predictions and manual curations of genomic objects.

Duration: 01/01/2008 to 31/12/2010

Coordinator: Stephanie Sidibe-bocs

Tropical monocots : Stéphanie Sidibe-Bocs

Laboratorie Address Person Contact
UMR Développement & Amélioration des plantes (DAP) 1098 CIRAD INRA IRD SupAgro UM2 INRIA CIRAD-DAP Montpellier Stéphanie Sidibe-Bocs, Valentin Guignon, Gaetan Droc, Franck-Christophe Baurens, Olivier Garsmeur, Jean-François Ramie, Manuel Ruiz stephanie.sidibe-bocs[at]cirad.fr
Bioversity Commodities for livelihood (CfL) Private compagny - Montpellier Mathieu Rouard, Nicolas Roux

 

rouard[at]cgiar.org

Wheat/Grapevine : Michael Alaux

Laboratories Address Person Contact
Unité de Recherche Génomique Info (URGI) INRA DGAP INRA Versailles Michael Alaux, Laertitia Brigitte, Erik Kimmel, Cyril Pommier, Isabelle Luyten, Delphine Steinbach, Hadi Quesneville michael.alaux[at]versailles.inra.fr
UMR Amélioration & Santé des Plantes (ASP) 1095 INRA UBP INRA Clermont-Ferrand Philippe Leroy leroy[at]clermont.inra.fr
UMR Sciences Pour l'oenologie (SPO) 1083 INRA SupAgro UM1 INRA Montpellier Nancy Terrier terrier[at]ensam.inra.fr

Fungus : Joelle Amselem

Laboratories Address Person Contact
UMR BIOlogie et GEstion des Risques en agriculture Champignons Pathogènes des Plantes (BIOGER-CPP) 1290 INRA AgroParisTech INRA Versailles Joelle Amselem, Baptiste Brault, Adeline Simon, Victoria Dominguez Del Angel, Sabine Fillinger, Michel Meyer, Thierry Rouxel, Marc-Henri Lebrun joelle.amselem[at]versailles.inra.fr

Insects : Fabrice Legeai

Laboratories Address Person Contact
UMR Biologie des Organismes et des Populations appliquées à la Protection des Plantes (BIO3P) 1099 INRA Rennes AgroCampus INRA Rennes Fabrice Legeai, Jean-Pierre Gauthier, Denis Tagu fabrice.legeai[at]rennes.inra.fr
UMR Biologie intégrative et virologie des insectes (BIVI) 1231 INRA UM2 et le réseau Génomique Lépidoptère INRA Montpellier Philippe Fournier, François Cousserans, Emmanuelle D'Alençon, Bernard Duvic, Jean-Michel Escoubas, René Feyereisen fourniep[at]ensam.inra.fr

Collaboration with Paramecium : Olivier Arnaiz

Laboratories Address Person Contact
Centre Génétique Moléculaire CNRS Gif-sur-Yvette Olivier Arnaiz, Linda Sperling olivier.arnaiz[at]cgm.cnrs-gif.fr

Links:

GnpAnnot portal

 

Description:

Crops are the major source of food. Up to 30% of crop yield is lost due to pests and pathogens. In the era of high throughput technology, the number of plant and bioaggressor genomes sequenced partially or completely increases exponentially. Gene annotation is a crucial step in nucleic sequence analysis which needs to define gene structure, protein function and homology relationships. While variations exist between eukaryotic species, generally genome annotation is a hard task for many reasons: large genomes, polyploidy, high proportion of non coding DNA and repeats, mosaic gene structure (intron/exon). Gene finder softwares are improving but they cannot replace manual annotation. Systems have been developed to help genomic data curation, but none of them satisfy all following requirements:

  • manual structural, functional and comparative annotation of eukaryotic genes
  • database, analysis pipeline and annotator Web interfaces
  • genericity, modularity, portability, sustainability and compatibility.

CIRAD, INRA and Bioversity uses to work together, and they propose to mutualize theirs efforts to develop and use a platform which allows users to annotate automatically or manually, to browse genomes, and to perform genome comparative analyses. The work will be divided into five work packages:

  • database and flow management
  • annotator interface implementation
  • interoperability with other systems
  • sequence exploitation and platform release
  • manual annotation and platform validation.

This platform will be exploited immediately on well identified sequencing projects studying genome structure and evolution and/or researching genes of agronomical interest. Four platform instances will be released on three sites: monocots (CIRAD Montpellier), insects (INRA Rennes), fungi (URGI Versailles) and wheat-grape (URGI Versailles).

 

Fundings:

Update: 24 Jun 2010
Creation date: 27 Apr 2010
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