Figure 4. Sliding window analysis of the whole chloroplast genomes of five Primula species. The nucleotide variability of the five Primula species was assessed by DnaSP with window length of 600 bp and step size of 200 bp. The X-axis represents the regions of chloroplast genome and Y-axis represents nucleotide diversity for each window.
3.4. IR expansion and contraction analyses
The IR/SC junction regions showed slight differences in gene content and gene order. As shown in Figure 5, genes rps19 /rpl2 ,ndhF , ycf1 and rpl2 /trnH were present at the junction of the LSC/IRb, IRb/SSC, SSC/IRa and IRa/LSC borders, respectively. The LSC/IRb boundary was located in the rps19region, which crossed into the IRb region in all the six chloroplast genomes, resulting in a variable expansion (14–102 bp) of IRb region toward the rps19 gene. The ndhF gene was entirely located in the SSC region in the chloroplast genomes of P. secundifloraand P. poissonii , whereas the IRb region extended 42 bp into thendhF gene in all the other Primula chloroplast genomes. The SSC/IRa junction was situated in the ycf1 coding region, which crossed into the IRa region in all five chloroplast genomes. However, the length of ycf1 in the IRa region varied from 5,468 to 5,483 bp, indicating the dynamic variation of the SSC/IRa junctions. The gene trnH was located in LSC, 0–14 bp away from the IRa/LSC border (Figure 5). Taken together, these data indicate that the contractions and expansions of the IR regions exhibited relatively stable patterns within these Primula species , with slight variations.