3.3. Sequence divergence
The Primula chloroplast genomes exhibited moderate sequence
divergence. Furthermore, the results showed that the sequence of coding
regions and the two IR regions were significantly more conserved than
that of LSC and SSC regions. In the coding regions, most genes were
relatively conserved, except for matK , rpl22 , ndhFand ycf1 . In contrast, the intergenic regions were shown to be
highly divergent (Figure 3). Then, we found that the variation level of
DNA polymorphism was from 0.00067 to 0.02633. The greatest differences
among the five Primula species were located in the two SC
regions, while IR regions were the least different. About 17
hyper-variable regions were discovered with a nucleotide diversity
(Pi ) value that was greater than 0.01 (Figure 4).
Some relatively high Pi value were detected in
CDS, such as psbA (0.02633), ycf1 (0.01533), psaJ(0.01333), rpl32 (0.01233), petL (0.01167) and ndhA(0.01033). Consistently, the gene ycf1 exhibited higher diversity
and showed abundant variation. In addition, we revealed five highly
divergent regions among noncoding regions, including ccsA-ndhD(0.01733), ndhF-rpl32 (0.01583), petA-psbJ (0.01567),trnE (UUC)-trnT (GGU) (0.01267) and rps15-ycf1(0.01167). These mutational hotspots can serve as potential loci when
developing novel DNA barcodes for plant classification.