Genome phylogeny based on gene content

Species phylogenies derived from comparisons of single genes are rarely con sistent with each other, due to horizontal gene transfer(1), unrecognized p aralogy and highly variable rates of evolution(2). The advent of completely sequenced genomes allows the construction of a phylogeny that is less sens itive to such inconsistencies and more representative of whole-genomes than are single-gene trees. Here, we present a distance-based phytogeny(3) cons tructed on the basis of gene content, rather than on sequence identity, of 13 completely sequenced genomes of unicellular species. The similarity betw een two species is defined as the number of genes that they have in common divided by their total number of genes, Tn this type of phylogenetic analys is, evolutionary distance can be interpreted in terms of evolutionary event s such as the acquisition and loss of genes, whereas the underlying propert ies (the gene content) can be interpreted in terms of function. As such, it takes a position intermediate to phylogenies based on single genes and phy logenies based on phenotypic characteristics. Although our comprehensive ge nome phylogeny is independent of phylogenies based on the level of sequence identity of individual genes, it correlates with the standard reference of prokarytic phylogeny based on sequence similarity of 16s rRNA (ref, 4). Th us, shared gene content between genomes is quantitatively determined by phy logeny, rather than by phenotype, and horizontal gene transfer has only a l imited role in determining the gene content of genomes.