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. 2021 Nov 15;13(11):2282. doi: 10.3390/v13112282

Figure 8.

Figure 8

Analysis of factors mediating codon usage bias. (A) Parity Rule 2 (PR2) plot was used to analyze whether the effects of mutation pressure and natural selection on the use of the Rep codon were consistent. Figure 8A shows that mutation pressure and natural selection have unequal effects on the use of codons during evolution. (B) The ENC-GC3s plot was analyzed, with the ENC values plotted against the GC3S values to determine the main factors affecting codon use bias. The expected ENC values for each GC3S were estimated. Figure 8B shows that main factor affecting codon use bias was selection pressure. (C) Neutrality analysis was used to evaluate the effects of mutation pressure and natural selection on codon usage patterns. Figure 8C shows that the fitting curve (red line) deviates from the curve y = x (black line), indicating that selection pressure plays a dominant role, which is consistent with Figure 8B.