Poster #RP202
GREENPHYL: A Generic Phylogenomic Pipeline for Ortholog Prediction Between two Model Plant Species Arabidopsis thaliana and Oryza sativa
CONTE Matthieu*, GAILLARD Sylvain*, COURTOIS Brigitte*, RUIZ Manuel*, GUIDERDONI Emmanuel*, PERIN Christophe*
*CIRAD Montpellier FRANCE
Gene ortholog identification is a now major objective for mining the increasing amount of sequence data provided by full or partial genome sequencing projects. Currently, most of the methods available for functional prediction are based on sequence similarity but direct annotation transfer is often misleading. Gene functions change as the result of evolution, and reconstructing the evolutionary history of gene family should be a more accurate way to differentiate orthologs from paralogs. We developed GREENPHYL, an optimized phylogenomic pipeline, following the well established phylogenomic analysis structure: Family clustering, Alignment, Tree construction, Tree analysis. Contrasting to other phylogenomic analysis pipeline, GREENPHYL includes an automatic analysis of the generated tree to detect orthologs, paralogs and also other useful phylogenomic relationships. We evaluated GREENPHYL performances against a set of published genes already functionally characterized in Arabidopsis thaliana and Oryza sativa. GREENPHYL achieved high accuracy level in predicting ortholog/paralog relationships for experimentally characterized proteins. Our pipeline detects interesting new relationships that can be used as a starting point for functional characterisation analysis and comparative genomics. Our results illustrate the power of GREENPHYL for gene function assignment and comparative genomics. Whole phylogenomic analysis of Oryza sativa and Arabidopsis thaliana proteomes is now in progress.