Fig. 1.

—The three different structural haplotypes of chloroplast genomes detected in this study. The green region is the long single copy (LSC) region and blue region is the short single copy (SSC) region. The two black regions are the Inverted Repeat (IR) regions. The arrow denotes 5′–3′ orientation. psbA is in the minus strand of LSC region, whereas rrn23 is in the plus strand of IR regions. ndhF is in the minus strand of SSC region, while ccsA is in the plus strand of SSC region. For ease of communication, we use the relative order of three genes (psbA in LSC, and ndhF and ccsA in the SSC) to label these two haplotypes “A” and “B.” In haplotype A, these genes are ordered psbA–ndhF–ccsA. In haplotype B these genes are ordered psbA–ccsA–ndhF. For haplotype C, these three genes are ordered the same as haplotype A, but the repeat regions are in-line rather than inverted.