Figure 3

Visualization of variable segments using the GenComp visualization tool. Segments are shown that contain variable open reading frames (ORFs) that are present in (a) all seven species, (b) in most but not all species, (c) in members of the spotted fever group (SFG) Rickettsia, and (d) in a single species. The visualization tool displays (in blue) the location of positional orthologs that are conserved across all seven Rickettsia spp. and differ by less than 20% in size. Interspersed among these are segments with strain-variable ORFs shown (in green) that differ in sizes and are normally present in only a subset of the Rickettsia spp. Vertical lines show positional orthologs and horizontal lines indicate the six frames (+1, +2, +3, -1, -2, and -3, in that order). Each set of six lines represents a species, with R. prowazekii (Rp), R. typhi (Rt), R. felis (Rf), R. akari (Ra), R. conorii (Rc), R. sibirica (Rs), and R. rickettsii (Rr) shown from the top to the bottom, in accordance with their phylogenetic relationships. Numbers inside boxes show ORF numbers, and designations above boxes show gene annotations. The first digits in the numbers below the boxes indicate homologous strain-variable ORFs that are members of the same ORF-cluster, and the last two digits indicate ORFs in the ORF-clusters that differ by less than 80% in size. Arrows illustrate the fragmentation process for sequences that are similar across species.