Figure 3

Phylogenetic profile of 74 gene families derived from 'promiscuous' sequences. We identified 13,055 sequences from the complete genome datasets as possessing significant sequence similarity to each of the 198 complete genomes. Gene family assignments obtained from the COGENT database were used to group these promiscuous sequences into 74 gene families. Annotations associated with the gene families show the high incidence of tRNA synthetases (blue text) and ABC transporters (red text). Phylogenetic profiles of each gene family were constructed from the presence or absence of promiscuous sequences in each genome. Two dimensional hierarchical clustering was performed on the profiles using average linkage on the basis of their Spearman rank correlation coefficients. Colored boxes indicate: presence of a promiscuous sequence in the genome (yellow); presence of a non-promiscuous sequence in the genome (blue, shaded according to the number of genomes with which it shares a sequence similarity match - in cases of more than one family member in a genome, the member with the highest number of matches was used); or absence of any family member in the genome (black box). Although the first nine gene families (indicated by the orange bar) contain representatives from the majority of genomes, the remaining gene families demonstrate various levels of specificity. For example, an additional 17 families (light green bars) are common to at least 50% of the eukaryotic genomes while 25 families possessed promiscuous sequences from only a single genome (purple bar). This specificity has led to a clear grouping of genomes into the three domains of life (as indicated on the left of the figure) with the exceptions of Cryptosporidium parvum (placed by itself outside the main group of eukaryotes) and Plasmodium falciparum, which has been grouped with two strains of Tropheryma whipplei and Leifsonia xyli. Both species are members of the Apicomplexa, a group of related protist parasites and appear to lack representative sequences from several of the 17 gene families that help define the other eukaryotes as a single group.