Selection pressure and codon usage bias analysis
An analysis of selection pressure can be used to explore whether the existence of variability is related to selection pressure. The results showed three positive selection sites of TMUV detected by three methods, and six positive selection sites detected by two methods; details are shown in Table 2.
To investigate the evolutionary characteristics of TMUV, the ORF gene sequence was analyzed for codon usage bias. The mean value of G% was the highest, followed by A%, C%, and T%, which indicates a strong compositional bias in favor of G or A. Furthermore, in terms of synonymous codons, we found that at the third position (A3%, T3%, C3%, G3%), the highest value was observed for nucleotide G for all genotypes.
At the same time, to investigate the effects of selective pressure and mutation pressure on the evolution of TMUV, an ENC-plot and neutrality plot analyses were conducted. The mean ENC value was 53.2575 ± 0.458, which was higher than 35, indicating a low codon bias in TMUV. The ENC-plot and neutrality plot analyses (Fig. 4a and 4b) indicated mutation pressure rather than natural selection pressure.