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.