Expected inversion or translocation endpoints and dispersed repetitive sequences of the C. japonica cp genome. The expected inversion corresponds with gene segment II in Figure 8. Genes are represented by boxes extending above or below the base-line depending on the direction of transcription. The colored boxes indicate the same gene units among the seven cp genomes including C. japonica. The number above the gene segments of the C. japonica cp genome correspond with positions of each repetitive sequence, and the character (similarity, length, repeat type, location, and sequence) of each repetitive sequence is shown in additional file 3. The trnL-CAA gene sequence of the C. japonica cp genome is shown with its secondary structure. The trnL-CAA with ψ (pseudo-) is incomplete in length to form its secondary structure.