The phylogenetic distance of XerCD in each organism. The phylogenetic distances of bacterial genomes to three seed organisms, Escherichia coli (Proteobacteria), Bacillus subtilis (Firmicutes) and Frankia alni (Actinobacteria), were calculated as the average of phylogenetic distances of XerC and XerD. Detailed example is given in Additional file 1, Figure S1. A to C are scatter plots of the distances of these genomes to the seed organisms. Axes represent average distances as calculated by ClustalW. A, Distances from Escherichia coli K-12 and Bacillus subtilis 168; B, distance from Escherichia coli K-12 and Frankia alni ACN14a; and C, distance from Bacillus subtilis 168 and Frankia alni ACN14a. Blue represent the genomes of Proteobacteria, green represent Firmicutes, yellow represent Actinobacteria, and the gray marks represent other phyla. All phyla show strong preferences for seeds from the same phylum.