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.