A weak codon usage bias may be caused by natural selection when the viruses try to adapt to the host cell [ 51– 51].
The analysis of ENC showed an overall weak codon usage bias, as shown in Table S1, where DENV2 has the highest codon bias (48.80) and DENV4 has the lowest one (50.87).
D. willistoni was excluded from the analyses due to its weak codon usage bias and shifted pattern of preferred codons for a portion of amino acids [ 36, 52, 53].
It is notable, however, that P. aeruginosa, unlike most other bacteria with high G+C contents and relatively large genome sizes, displays weak codon usage bias in its highly expressed genes relative to its moderately expressed genes (Sharp et al. 2010), raising the possibility that additional forces contribute to base composition in some of the most G+C-rich bacterial genomes.
The regression model included participant age, gender, reporting of strong vs. weak opioid usage, severity of chronic pain on a scale of 0 10 (with increasing pain represented by increasing score), presence or absence of neuropathic pain, having fewer or more than three spontaneous bowel movements per week, and place of residence being a European or North American locale.
The significantly lower levels of CAI for the genes with rate accelerations, corresponding to weaker codon usage bias, were also confirmed in the limited data.
Furthermore, we found that the genes which experienced rate acceleration have lower expression levels and weaker codon usage bias than those which experienced rate deceleration.
Together with the results from analysis using mRNA abundance data, these results suggest that the rate-accelerated genes have lower expression levels, and have weaker codon usage biases, than the constant-rate and rate-decelerated genes.
In contrast, the gene (KS1) that encodes the enzyme involving a single step in the pathway has the highest dN/ dS ratio and much weaker codon usage bias (much higher ENC).
Furthermore, we found that the genes with rate accelerations tend to have lower expression level and weaker codon usage bias than those with rate decelerations, suggesting that selection for translational efficiency and accuracy may underlie the variability of the protein evolutionary rates.
