Figure 3. Codon usage bias of Cymbaria chloroplast genomes. (A) RSCU. (B) Correlation heatmap. (C) Neutral plot analysis. (D) PR2 plot analysis. (E) ENC plot analysis. Circle colors of green and orange represent C. mongolica (left) and C. daurica (right), respectively.
3.3. | Repetitive sequence variation
A total of 134 repeats, consisting of 78 forward, four reverse, one complementary, and 51 palindrome repeats, were detected from C. mongolica chloroplast genome. Meanwhile, a total of 225 repeats, including 106 forward, 18 reverse, 13 complementary, and 88 palindrome repeats, were identified from C. daurica chloroplast genome (Fig. 4A; Fig. 4B). The size of approximately 90% of the repeats ranged from 30 bp to 70 bp. C. mongolica and C. daurica contained 61 and 65 SSRs, and most were present in the LSC region (37 and 43 SSRs), respectively (Fig. 4A; Fig. 4C). Hexa-nucleotide SSRs were only detected in C. mongolica ; the remaining SSRs were identified in both species (Fig. 4D). Mono-nucleotides were the most plentiful, followed by di- and tetra-nucleotides. The mononucleotide motifs A/T had the highest proportion, accounting for 34.4% in C. mongolica and 32.3% inC. daurica (Fig. 4E).