Automatic genome-wide reconstruction of phylogenetic gene trees
1Broad Institute of MIT and Harvard,2School of Engineering and Applied Sciences, Harvard University,3FAS Center for Systems Biology,4Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA and5School of Computer Science & Engineering, Hebrew University, Jerusalem, Israel
*To whom correspondence should be addressed.
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Abstract |
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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 applied to any set of sequenced eukaryotic species with a known phylogeny, and opens the way to systematic studies of the evolution of individual genes, molecular systems and whole genomes.
Contact: aregev{at}broad.mit.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
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