Poster presented at 2009 Annual Research Meeting of the Generation Challenge Programme. Bamako (Mali), 20-23 September 200

Aluome, C.

Conte, M.G.

Laporte, M-A.

Rouard, M.

English

Laporte, Marie-Angélique

CGSpace (CGIAR)

GreenPhylDB v2.0: An improved database for plant functional GenomicsConte M.G1, Laporte M.A2, Aluome C3 ,Perin C3, Rouard M11  Bioversity International - Commodities for Livelihoods programme Parc Scientifique Agropolis II, 34397Montpellier - Cedex 5, France 2 CEFE - UMR 5175 - 1919 Route de Mende - F34293 Montpellier cedex 5, France 3 CIRAD, Department BIOS, UMR DAP - TA40/03, 34398 Montpellier, FranceGreenPhylDB is a resource of comparative genomic for plant functional genomics. Here, we present the version 2 which contains a catalogue of gene families for 15 full genomes of plants covering a broad taxonomy of green plants. Results of our automatic clustering is first manually annotated and then analyzed by a phylogeny approach to predict orthologs. This ortholog prediction is particularly useful for functional genomics and candidate gene identification. We describe as well our update platform that allows us to integrate and maintain our database up to date with new genome releases. References: (http://greenphyl.cirad.fr) Conte MG, Gaillard S, Droc G, Périn C (2008). Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants. BMC Genomics, 2008, 183Conte MG, Gaillard S, Lanau N, Rouard M, Périn C (2008). GreenPhylDB: a database for plant comparative genomics. Nucleic Acids Research. 2008 January; 36 D991–D998Contacts:Mathieu Rouard (m.rouard@cgiar.org)Matthieu Conte (m.conte@cgiar.org) Data update platformTo backup the database before anymodificationto insert or update genomes in the database to insert or update all information available on genes present in the database:UniProt, KEGG, PIRSF, InterProto follow active jobsRationale: Sequencing and annotation projects generate regularly new or updated releases of genome annotation. Moreover, data associated to each gene (domains, classification, cross references…) is then also susceptible to change.Objective: Provide a regularly updated database totally linked to externaldata.Description: This structure grant database administrator to insert or updatedata in our system. The system allow to track changes in the database.Family annotation platformGene cluster structure ( allow subgroup identification)Cluster informationView cluster domain architectureSummary of manually curated data available on cluster gene members.(PIRSF, UniProt, KEGG, InterPro family signatures)6 steps with automatic control of annotationSummary of non curated data available on cluster gene members.(Interpro domain, Pubmed, gene annotation, GO)Objective: Provide a comprehensive list a plant gene families with manually curation Description: This structure allows granted users to annotate gene clusters that were automatically generated. This platform proposes statistics of the different data available on gene clusters members. Rationale: Identify proper catalogue of homeomorphic plant gene families - genes that evolved from a common ancestor and sharing full-length sequence similarity and common domain architecture - is a valuable resource for evolution studies, future gene annotation, and orthologs inference.From orthologs prediction to functionA sequence of RiceConfidence score in %2 genes of Arabidopsis 1 gene of riceResponse to hydricstress stimulus2 orthologs found in ArabidopsisExpressed in the panicule Expressed in the siliqueSeed developmentResponse to stress Response to stressAlgaeDicotsMonocotsRationale: Fast progress in sequencing and annotation projects has enabled us to work now on 15 full plant genomes including economically and socially important crops like rice, sorghum and maize Objectives: Integrate in our database all genomes fully annotated with relatively good annotation to take benefit of all information available on new speciesDescription: This taxonomy coverage is also useful for accurate orthologs prediction through phylogenetics. These plant genomes should help us to unravel some aspects of green plant evolution. New genomesRationale: The main assumption behind orthologs identification is the conservation of genes functions (at least sharing a similar function) across evolution of closely related species.Objective: Help biologists with functional validation.Description: we crossed references our orthologs to Genevestigator which is a reference expression database allowing studies of gene-regulation in a wide variety of contexts, such as plants under stress .Project–SP4 G4008.21: Large scale phylogenomic analyses to gene function prediction for GCP crops (PI: Mathieu Rouard)

GreenPhylDB v2.0: An improved database for plant functional genomics

https://cgspace.cgiar.org/bitstream/10568/67476/1/Conte_GreenPhylDBv2.0.pdf

GreenPhylDB v2.0: An improved database for plant functional genomics

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