Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants.
BACKGROUND
Gene ortholog identification is now a major objective for mining the increasing amount of sequence data generated by complete or partial genome sequencing projects. Comparative and functional genomics urgently need a method for ortholog detection to reduce gene function inference and to aid in the identification of conserved or divergent genetic pathways between several species. As gene functions change during evolution, reconstructing the evolutionary history of genes should be a more accurate way to differentiate orthologs from paralogs. Phylogenomics takes into account phylogenetic information from high-throughput genome annotation and is the most straightforward way to infer orthologs. However, procedures for automatic detection of orthologs are still scarce and suffer from several limitations.


RESULTS
We developed a procedure for ortholog prediction between Oryza sativa and Arabidopsis thaliana. Firstly, we established an efficient method to cluster A. thaliana and O. sativa full proteomes into gene families. Then, we developed an optimized phylogenomics pipeline for ortholog inference. We validated the full procedure using test sets of orthologs and paralogs to demonstrate that our method outperforms pairwise methods for ortholog predictions.


CONCLUSIONS
Our procedure achieved a high level of accuracy in predicting ortholog and paralog relationships. Phylogenomic predictions for all validated gene families in both species were easily achieved and we can conclude that our methodology outperforms similarly based methods.
Conte
Matthieu G
MG
CIRAD, UMR 1096 TA40/03k, Avenue Agropolis, 34398 Montpellier, Cedex 5, France. matthieu.conte@cirad.fr
Gaillard
Sylvain
S
Droc
Gaetan
G
Perin
Christophe
C
D017360:Arabidopsis / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D012275:Oryza / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid