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Bioinformatics 2007 23(13):i549-i558; doi:10.1093/bioinformatics/btm193
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Automatic genome-wide reconstruction of phylogenetic gene trees

Ilan Wapinski 1,2,3, Avi Pfeffer 2, Nir Friedman 5 and Aviv Regev 3,4,*

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.


  Abstract

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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