Gene-position plot with a reconstruction of vertical descent and potentially-transferred genes across F. nucleatum genome. Plus signs indicate genes whose phylogenetic affiliation to a certain group on the left is supported by BLAST analysis only. Crosses indicate genes whose phylogenetic origin is supported by BLAST and by one or two other methods (phylogenetic tree reconstruction and gene order conservation). Thirty-six clusters are indicated containing four or more consecutive genes that appear to have a xenologous origin (i.e. a phylogenetic affiliation outside the Firmicutes). Details of these clusters are explained in Table 2. Arrowheads at the top indicate the position of transposases. Arrowheads at the bottom indicate position of phage-related genes. Plus signs and crosses indicate potential transfers to/from Firmicutes (Firm), Spirochaetes (Sp), alpha-beta-gamma Proteobacteria (αβγ-Pr), delta-epsilon Proteobacteria (δε-Pr), Cytophaga-Flexibacter-Bacteroides Group (CFB), other bacterial groups (Others), Archaea, or genes that are consistent with the phylogeny (CWP) shown in Figure 1 and additional file 1.
Mira et al. BMC Evolutionary Biology 2004 4:50 doi:10.1186/1471-2148-4-50