Function prediction in plant genomes from large scale phylogenomics analyses : P0932

Guignon Valentin, Dufayard Jean-François, Briois Sébastien, Conte Matthieu, Rouard Mathieu. 2013. Function prediction in plant genomes from large scale phylogenomics analyses : P0932. In : Plant and Animal Genome XXI conference, San Diego, USA, January 12-16 2013,. s.l. : s.n., Résumé, 1 p. Plant and Animal Genome conference. 21, San Diego, États-Unis, 12 January 2013/16 January 2013.

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Abstract : With the increasing number of plant genomes being sequenced, a major challenge is to accurately transfer annotations from well characterized genomes to newly obtained sequences. GreenPhylDB is a database designed for comparative and functional genomics based on complete genome-derived gene sequences. The database currently includes gene families of protein sequences from 22 plant species, including socio-economically important crops like rice, sorghum, maize, cassava and banana. Genes from all these species are organized in clusters based on sequence similarity. The clusters are manually annotated (i.e. properly named and classified) and sequences included in each cluster are characterized by phylogenetic analysis in order to elucidate evolutionary relationships (e.g. orthologs, super-orthologs, in/out-paralogs) among genes. GreenPhyl provides a reliable and stable catalog of gene families useful for annotation on new genome sequences in plants. With its improved user interface, the new release of GreenPhyl keeps the previous gene clustering quality and introduces additional features such as specific search engines (quick search, deep search, InterPro domain combination and GO family browser). The GreenPhyl's pipeline relies on RapGreen, a new version of the RAP reconciliation tool (Dufayard et al, 2005) that allows us to root gene trees and infer orthology relationships between sequences of a family. GreenPhyl version 3 is available at and is a collaborative resource of SouthGreen (, a bioinformatics platform applied to the genetic and genomic resources analyses of the South and Mediterranean plants. (Résumé d'auteur)

Classification Agris : F30 - Plant genetics and breeding
C30 - Documentation and information

Auteurs et affiliations

  • Guignon Valentin, Bioversity International (FRA)
  • Dufayard Jean-François, CIRAD-BIOS-UMR AGAP (FRA)
  • Briois Sébastien, Syngenta Seeds (FRA)
  • Conte Matthieu, Syngenta Seeds (FRA)
  • Rouard Mathieu, Bioversity International (FRA)

Source : Cirad - Agritrop (

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