Figure 10

Generation of single-strandedness and thereby, deamination gradients during the course of chloroplast genome replication. The cartoon features steps in the course of replication for the region between replication origin pairs on each inverted repeat. The two bubbles represent the displaced parental strands at origins A2 and A1 of each inverted repeat. These bubbles expand towards each other respectively, on each inverted repeat to form a Cairns replication intermediate. Replication forks move in the respective directions to synthesize two complete daughter strands. The parental strands are represented by complete lines, while the daughter strands are represented as dotted lines. The arrows indicate the direction of new strand synthesis. The growing windows of single-strandedness and therefore, A → G deamination gradients are indicated at each step, in parallel (Figures 10A and 10B respectively). The representation in Figure 10C shows the deamination gradients as we observe from analyzing nucleotide compositions of all chloroplast genomes for the region between A1 and A1-C origin copies on each inverted repeat, if we assume it to be overlapping the SSC or the region between A2 and A2-C origin copies, if we assume that it overlaps the LSC. This signature is possible only if replication proceeds as per steps indicated in Figure 10A.