Figure 3

Genome rearrangements plots comparing two genomes. Genome plots can provide information on the kind of rearrangements undergone. These plots represent the location of each gene in one axis for one of the genomes against the location of the found ortholog in the other axis for the second genome. a Comparative genomic plot when comparing two genomes showing no lineage-specific genome rearrangements. In this case, the plot was produced for the comparison of two primary symbiotic bacteria of insects (B. aphidicola strain A. pisum versus B. aphidicola strain Schizaphis graminum). Since no rearrangements have occurred in any of the two genomes, the comparison yields a straight diagonal line. b Comparative genomic plot for two genomes showing lineage-specific genome rearrangements. In this case, the plot was comparing the genome of other patterns that can be observed and are x-like patterns b (in this case, B. aphidicola, A. pisum, and E. coli k12) where the rearrangements have occurred over the replication axis E. coli K12 to the genome of B. aphidicola strain A. pisum. c This is the comparison between Chlamydophila pneumoniae CWL029 and Chlamydia trachomatis 434/Bu that show an even better example of rearrangements that have occurred over the replication axis (this example have also been shown in [102]). As shown, many rearrangements including inversions and translocations have occurred, and consequently, the orthologs are not located in the major diagonal of the plot but rather show an X-shape distribution. This is expected if an inversion has taken place near the centromer of the chromosome.