Figure 2. Heat map depicting the chloroplast gene content across 54 Orobanchaceae species. Blocks in green, blue, and orange indicate intact genes, pseudogenes, and lost genes, respectively. Background colors in green, blue, and orange indicate autotrophs, hemiparasites, and holoparasites, respectively.
3.2. | Codon usage bias
The PCGs in the C. mongolica and C. daurica comprised 18,482 and 15,896 codons, respectively. Leucine (Leu, 10.50% and 10.62%) was the most commonamino acid, and cysteine (Cys, 1.09% and 1.07%) was the least common amino acid. A total of 30 codons (RSCU > 1) were A/T-ending codons, with the exception of UUG (Fig. 3A). The range of the ENC in C. mongolica and C. daurica was 35.24–56.04 and 35.75–59.41, respectively, which suggested weak codon usage bias. ENC was significantly negatively correlated with GC2 in both species; a significant positive correlation between ENC and GC3 was only detected in C. mongolica (Fig. 3B). There was no significant correlation between GC3 and GC12 according to neutral plot analysis (Fig. 3C); the regression coefficient was 0.049 and 0.193 in C. mongolica and C. daurica , respectively. Most genes were below and around the standard curve according to ENC plot analysis (Fig. 3D), and the ENC ratio was from 0.05 to 0.15. PR2-plot analysis (Fig. 3E) showed that T > A and G > C in the base usage frequency. A total of 16 codons were identified as preferred codons, of which 10 were shared by the two species.