A comparison of the relative positions of the orthologous genes in Porphyromonas gingivalis and Chlamydia trachomatis was compiled using the BugSpray Genome Comparison Tool. These genes have significant similarity to genes in the compared genome, using an E-value threshold of 0.0001. The blue line indicates the 5' to 3' strand of the genome. The purple line is directed 3' to 5'. The small boxes represent genes and are positioned at each gene's start coordinate. Green lines connect orthologous pairs of genes that are oriented in the same direction. Red lines connect orthologous pairs of genes that are oriented in the opposite direction. The P. gingivalis genome is located above the C. trachomatis genome.

P. gingivalis and C. trachomatis have many orthologous genes, but the relative positions of these orthologs are not conserved between the two genomes. This suggests a distant phylogenetic relationship. When this map is compared to the orthologous gene map of C. trachomatis and Chlamydia pneumoniae, it becomes obvious that C. trachomatis and C. pneumoniae have a closer phylogenetic relationship than P. gingivalis and C. trachomatis.