Substitution frequency at nonsynonymous and synonymous sites plotted by genes present in different numbers of species

The nonsynonymous substitution frequency (dN) values were plotted against the synonymous substitution frequency (dS) values for R7 core genes and strain-variable open reading frames (ORFs) present in two to seven species and core genes and strain-variable ORFs present in seven species that are longer than one kilobase in size.<p><b>Copyright information:</b></p><p>Taken from "Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction"</p><p>http://genomebiology.com/2008/9/2/R42</p><p>Genome Biology 2008;9(2):R42-R42.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2374718.</p><p></p

Visualization of variable segments using the GenComp visualization tool

Segments are shown that contain variable open reading frames (ORFs) that are present in all seven species, in most but not all species, in members of the spotted fever group (SFG) , and in a single species. The visualization tool displays (in blue) the location of positional orthologs that are conserved across all seven 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 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 (Rp), (Rt), (Rf), (Ra), (Rc), (Rs), and (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.<p><b>Copyright information:</b></p><p>Taken from "Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction"</p><p>http://genomebiology.com/2008/9/2/R42</p><p>Genome Biology 2008;9(2):R42-R42.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2374718.</p><p></p

Number of R7 core genes and strain-variable ORFs placed at different nodes of the species tree

The relative proportions of R7 core genes (open boxes) and strain-variable open reading frames (ORFs; black boxes) are indicated at each node of the tree. Arrows show the nodes that contain the majority of core genes (ROW*) and strain-variable ORFs (R8). Species abbreviations are as in Figure 3, plus Ot (), wMel ([]), and wBm ([]). The underlying phylogenetic tree was constructed using the maximum likelihood method from a concatenated alignment of adenylate kinase, SecY, and ribosomal proteins S3, S8, S10, S11, S13, S14, S19 and L2, L3, L4, L5, L6, L14, L16, L18, L22, L23, L24 and L29.<p><b>Copyright information:</b></p><p>Taken from "Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction"</p><p>http://genomebiology.com/2008/9/2/R42</p><p>Genome Biology 2008;9(2):R42-R42.</p><p>Published online 26 Feb 2008</p><p>PMCID:PMC2374718.</p><p></p