Figure 2

Two genomes, with their real and observed breakpoint graphs. Genes are g1, g2, g3, ordered in one linear chromosome in a blue and a red genome: in the order g1g2g3 on the red chromosome, and in the order g3g2g1 on the blue chromosome. In (A) the two non augmented genomes are depicted. In (B) and (C), augmented genomes are depicted. Both augmented genomes are identical in both parts. Only the correspondence of the telomeric vertices between the blue and red genomes vary, which illustrates the possible difference between the real and observed breakpoint graph. There are two breakpoints in the red genome with respect to the blue genome. In the situation (B) the blue genome can be obtained from the red by three DCJs. But the adjacencies leading to t vertices are not observed, so another possibility is (C), where a scenario with only two DCJs exist. Case (C) is the observed breakpoint graph because it maximizes the number of cycles in the breakpoint graph. The real breakpoint graph can be either (B) or (C), but to determine it requires a knowledge of the evolutionary scenario that have shaped these two genomes.