FIGURE 1. Comparison of the two sequenced H.pylori genomes based on the chromosomal organization of strain 26695.

a, Genome-wide view. Circles are numbered starting from the outermost concentric ring. Circle 1, nucleotide and circle 2, amino-acid similarity between each J99 and 26695 orthologue. The relative location and amount of each J99-specific sequence are shown immediately inside the second circle (the height of each line is proportional to the amount of unique sequence, and for larger regions the size relative to the equivalent 26695 region is indicated by a triangle proportional to the 26695 scale). The largest J99-specific region shown is composed of two segments separated by 150 bp (see b for details). Circles 3 and 4, which flank the solid reference circle, show the locations of rRNA, insertion-sequence (IS) and repeat elements, for 26695 (circle 3) and J99 (circle 4). Circles 5 and 6 represent the locations of the NotI sites in the 26695 and J99 genomes, respectively. Circle 7 represents the relative transcriptional direction of J99 genes compared to their 26695 orthologues. Regions that are not coloured and translocations are transcribed in the same relative direction in J99 and 26695, whereas inversions result in genes being transcribed in the opposite relative direction in J99. Circle 8 represents the organization of the J99 genome relative to the 26695 genome, incorporating artificial end points needed to allow the alignment. The required inversions and/or translocations are numbered consecutively for J99. b, c, An expanded view of the complex organizational differences 7–10 (b) and 3A/3B (c) shown in circle 8 of a. The 26695 ORFs are shown in the order and location that they are found (black numbers). The J99 ORFs are shown as red numbers. ORFs and other elements in parentheses are found in 26695 but not J99. The organization of J99 segments that share >90% identity to 26695 are depicted by the solid black lines, with arrows indicating the relative orientation of the J99 segments with respect to 26695 segments. The open triangles represent J99-specific DNA, drawn to scale, with the size and genes shown. The order of these regions in J99 is indicated by lower-case blue letters. The circled numbers correspond to the inversions/translocations referred to in a. Sizes of regions in a are shown in megabases (Mb).