Figure 2

The relationship between dif sites and GC skew. A. Correlation of the GC skew shift-point (corresponding to the replication terminus region, Y-axis) and the locations of dif sequences (X-axis) for genomes with predicted dif sequences. Genomes with no visible GC skew, as indicated by GC skew Index (GCSI) ≤ 0.05, are omitted. Both axes are shown as the relative distance in percentage of half of the genome size (replichore size), from the position directly opposite of the replication origin. For example, 0% means that the position is directly opposite of the replication origin identified by the GC skew shift-point, and 100% means that it is at the replication origin. In other words, the higher the percentage, the closer the distance to the replication origin. Here the positions of GC skew shift-points and dif sites are strongly correlated in all three phyla. B. Lack of correlation between the difference in the positions of GC skew shift-points and dif sites (Y-axis) and the GCSI (X-axis). GCSI is a quantitative measure of the degree of GC skew, where GCSI = 0 is no observable skew, and GCSI = 1 is extremely pronounced skew. Typically GC skew is visible at GCSI ≥ 0.1, and it is pronounced when GCSI ≥ 0.3. Since we see no correlation in these plots, stronger replication-related mutation bias (i.e. larger GCSI) does not necessarily result in closer positions of the GC skew shift-point and the dif site. These results suggest that the replication termination occurs near the dif site, but not at the dif site. The number of dif sites is 517 in all bacteria, 438 in Proteobacteria and 97 in Firmicutes. The ρ in this figure is Spearman's rank-correlation coefficient.