Additional file 1:

Harr plot analyses comparing the cp genome of C. taitungensis with those of E. globulus 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 cp genome. The pseudogene is indicated by ψ (pseudo-).

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Additional file 2:

The neighbor-joining tree of the rbcL gene in gymnosperms. The branch length indicates the number of substitutions. The numbers at each node denote the traditional bootstrap replicates that support the monophyly of the taxa in the subset designated by the node. Only bootstrap values higher than 50% are shown. The species highlighted in red represent the cp genomes of gymnosperms already determined.

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Additional file 3:

The character of dispersed repetitive sequences at expected inversion or translocation endpoints. The character of each repetitive sequence is indicated by similarity, length, repeat type, location, and sequence. The positions of each repetitive sequence correspond with the numbers (I-IV) above the gene segments of the C. japonica cp genome (see Figure 10). The bold characters indicate the location of repeat sequences, and IGS indicates the intergenic spacer region.

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