Gene order structures of the BaGTA and ROR segments.

<p>Comparative analysis of the DNA segments covering the BaGTA genes (A) and the ROR genes (B). Genes are colored according to their phylogenetic classification (see methods), without manual intervention: vertically inherited (magenta), imported (green), <i>Bartonella</i>-specific (blue) and ORFans (red). Genes acquired in the common ancestor of <i>Bartonella</i> and conserved in length and present in all genomes are marked with a thick border around the arrow depicting the gene. Those that are not bordered were presumably acquired in the common ancestor but have since then been lost or slightly modified in one or a few species. Pseudogenes are marked with a dotted border. Proteins experimentally detected by mass-spectrometry as part of the BaGTA phage particles <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003393#pgen.1003393-Berglund1" target="_blank">[9]</a> are marked with a filled black circle inside the arrow depicting the gene in <i>B. henselae</i> or <i>B. grahamii</i>. Genes shown in grey represent core genes not part of the BaGTA or the ROR. Horizontal grey lines indicate tblastx hits, with grey intensity reflecting the tblastx e-values. The repeat structure and GC content of gene number 4 in the ROR region is shown in (C). Blue lines indicate palindromic repeats. The graphs above the gene (grey bands) show the GC content in a 50-bp window. The average is indicated with a horizontal line. Abbreviations of <i>Bartonella</i> species names are as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003393#pgen-1003393-t001" target="_blank">Table 1</a>.