CSAIL Event Calendar: Previous Series

Automatic genome-wide reconstruction of phylogenetic gene trees

Speaker: Aviv Regev , Broad Institute of MIT and Harvard
Date: November 27 2007
Time: 4:15PM to 5:15PM
Location: 32-155
Host: Piotr Indyk, MIT, CSAIL

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 seventeen fully sequenced fungal genomes
spanning 300 million years, generating a genomewide 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.

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