Harr plot analyses comparing the cp genome of C. japonica with those of C. taitungensis and P. thunbergii. Each dotplot shows the positions where 45 out of 50 nucleotides match in the two sequences. The plot analysis was carried out using Pipmaker software. Sequences along the Y-axis are set from the top to the bottom, and along the X-axis are from left to right. Relative lengths of sequences are shown to the side and below the boxes. The colored gene segments along the X- and Y-axes correspond with common gene units of the seven cp genomes (shown in Figure 7). At the expected endpoint of inversion or translocation mutation, the gene name is attached based on the X-axis (C. japonica cp genome). The pseudogene is indicated by ψ (pseudo-). The representative inversion and translocation are represented by gene segment I (the trnT-UGU to trnQ-UUG of C. japonica cp genome) and gene segment II (thr trnV-GAC to pseudo-clpP of C. japonica cp genome). The detailed comparisons of the gene segment I and II are shown in the following Figure 9 and Figure 10.