Figure 2

Orthologous genes in alpha-proteobacteria. Presence (black) or absence (white) of genes (found using bidirectional best blast hit, BBH) described in Figure 1 and involved in cell cycle regulation in the alpha-proteobacterial genomes. Proteins are indicated in the uppermost row and they are ordered on the basis of their co-occurrence patterns (see Material and Methods). We show here a reduced dataset comprising one species for each considered genus, for a total of 37 out of 65 alpha-proteobacteria analyzed (the complete results are listed in Table S2, Additional file 4). Organisms are ordered on the basis of their phylogenetic relationships as assessed by using a 5000-residue long concatamer of universal proteins [65], the Neighbor-Joining method with a Dayhoff evolutionary model and 100 bootstrap replicates. A tree representation where nodes with a statistical support of less than 75% have been collapsed (Figure 2, left) was chosen; Dark gray cells indicate the presence of a BBH with respect to the protein corresponding to that column. Medium dark gray cells correspond to DivK proteins in those organisms that have an ambiguous position in the phylogenetic tree (Additional file 3, Figure S1); light gray cells correspond to organisms that have PleC but where DivK is absent or in doubt.