Automatic genome-wide reconstruction of phylogenetic gene trees

Gene duplication and divergence is a major evolutionary force. Despite the growing number of fully sequenced genomes, methods for investigating these events on a genome-wide scale are still in their infancy. Here, we present SYNERGY, a novel and scalable algorithm that uses sequence similarity and a given species phylogeny to reconstruct the underlying evolutionary history of all genes in a large group of species. In doing so, SYNERGY resolves homology relations and accurately distinguishes orthologs from paralogs. We applied our approach to a set of nine fully sequenced fungal genomes spanning 150 million years, generating a genome-wide catalog of orthologous groups and corresponding gene trees. Our results are highly accurate when compared to a manually curated gold standard, and are robust to the quality of input according to a novel jackknife confidence scoring. The reconstructed gene trees provide a comprehensive view of gene evolution on a genomic scale. Our approach can be app...

• Type: Conference
• Year: 2007
• Where: ISMB
• Authors: Ilan Wapinski, Avi Pfeffer, Nir Friedman, Aviv Regev
• Keywords: Computational Biology, Gene Trees, ISMB 2007, Major Evolutionary Force, Sequenced