(A) Schematic representation of the polymorphism. Two regions specifically inserted into the MC58 genome are indicated by black solid line and dotted line, respectively, along the vertical axis. Two duplicated segments are also found at the joints of these insertions, which are indicated by the red and blue arrowheads, respectively.
(B)-(D) Representation in CGAT. This structure is easily seen by CGAT using the function for independent scaling of the horizontal or vertical axis. In (C), zooming the vertical axis clearly shows the presence of a MC58-specific insertion between the boundaries of the inversion sites, while in (B), zooming the horizontal axis shows the presence of two duplicated segments in the MC58 genome at the joints of the inversion. Whereas the difference between these structures is quite clear in (B) and (C), it is difficult to distinguish them on the global view of the dotplot display (D).
A plausible explanation for the formation of this polymorphism is given in the paper.
Reference: Kawai, M., Nakao, K., Uchiyama, I, and Kobayashi, I. (2006), How genomes rearrange: genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms. Gene, 383, 52-63 (2006) [PubMed]
The figure was provided by M. Kawai.