Evidence That Plant-Like Genes in <i>Chlamydia</i> Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast

<jats:p> An unusually high proportion of proteins encoded in <jats:italic>Chlamydia</jats:italic> genomes are most similar to plant proteins, leading to proposals that a <jats:italic>Chlamydia</jats:italic> ancestor obtained genes from a plant or plant-like host organism by horizontal gene transfer. However, during an analysis of bacterial–eukaryotic protein similarities, we found that the vast majority of plant-like sequences in <jats:italic>Chlamydia</jats:italic> are most similar to plant proteins that are targeted to the chloroplast, an organelle derived from a cyanobacterium. We present further evidence suggesting that plant-like genes in <jats:italic>Chlamydia</jats:italic> , and other Chlamydiaceae, are likely a reflection of an unappreciated evolutionary relationship between the Chlamydiaceae and the cyanobacteria-chloroplast lineage. Further analyses of bacterial and eukaryotic genomes indicates the importance of evaluating organellar ancestry of eukaryotic proteins when identifying bacteria-eukaryote homologs or horizontal gene transfer and supports the proposal that Chlamydiaceae, which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts. </jats:p> <jats:p> [Supplementary Material is available online at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.genome.org" xlink:type="simple">http://www.genome.org</jats:ext-link> and at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://www.pathogenomics.bc.ca/BAE-watch.html" xlink:type="simple">http://www.pathogenomics.bc.ca/BAE-watch.html</jats:ext-link> .] </jats:p>