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Published online on January 3, 2005, 10.1073/pnas.0408810102 OPEN ACCESS ARTICLE


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Evolution
Phylogeny determined by protein domain content

( fold superfamily )

Song Yang *, Russell F. Doolittle *, and Philip E. Bourne {dagger}{ddagger}

Departments of *Chemistry and Biochemistry and {dagger}Pharmacology and San Diego Supercomputer Center, University of California at San Diego, La Jolla, CA 92093

Contributed by Russell F. Doolittle, November 26, 2004

A simple classification scheme that uses only the presence or absence of a protein domain architecture has been used to determine the phylogeny of 174 complete genomes. The method correctly divides the 174 taxa into Archaea, Bacteria, and Eukarya and satisfactorily sorts most of the major groups within these superkingdoms. The most challenging problem involved 119 Bacteria, many of which have reduced genomes. When a weighting factor was used that takes account of difference in genome size (number of considered folds), small-genome taxa were mostly grouped with their full-sized counterparts. Although not every organism appears exactly at its classical phylogenetic position in these trees, the agreement appears comparable with the efforts of others by using sophisticated sequence analysis and/or combinations of gene content and gene order. During the course of the study, it emerged that there is a core set of {approx}50 folds that is found in all 174 genomes and a single fold diagnostic of all Archaea.

Freely available online through the PNAS open access option.

{ddagger}To whom correspondence should be addressed.

Philip E. Bourne, E-mail: pbourne{at}ucsd.edu

www.pnas.org/cgi/doi/10.1073/pnas.0408810102
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