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Automatic genome-wide reconstruction of phylogenetic gene trees.
| Publication Type | Journal Article |
| Authors | Wapinski, I., Pfeffer A., Friedman N., and Regev A. |
| 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. Supplementary information: Supplementary data are available at Bioinformatics online. |
| Year of Publication | 2007 |
| Journal | Bioinformatics (Oxford, England) |
| Volume | 23 |
| Issue | 13 |
| Pages | i549-58 |
| Date Published (YYYY/MM/DD) | 2007/07/01 |
| ISSN Number | 1367-4803 |
| DOI | 10.1093/bioinformatics/btm193 |
| PubMed | http://www.ncbi.nlm.nih.gov/pubmed/17646342?dopt=Abstract |
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