Figure 3.
Site-specific evolutionary conservation of codon optimality. (a) Optimal (O) and nonoptimal (N) codons are projected onto an exemplary sequence alignment of the S. cerevisiae gene RIB5, and shown together with positional conservation scores. Significantly conserved optimal codons are indicated in blue, and nonoptimal codons in red. (b) Comparison of the distributions of random (grey histogram and black line) and observed (red line) conservation scores. Sites with higher conservation scores than expected by chance, i.e. outside the alignment-specific significance thresholds (dotted lines), are considered significantly conserved sites. (c) Fraction of analyzed ORFs that show a higher number of significantly conserved optimal and nonoptimal sites than would be expected by chance, thus can be assumed under selective pressure. (d) Distributions of significance thresholds for conserved optimal and nonoptimal codons for highly and lowly expressed genes, obtained using the nTE scale. (e) Fraction of ORFs under selective pressure computed with classical codon optimality. If perfect site-specific conservation of optimal codons can already be observed by chance, selection for the site-specific conservation of optimal codons cannot be assumed, and these cases are thus indicated as ‘not significant’. (f) Distributions of significance thresholds for conserved optimal and nonoptimal codons for highly and lowly expressed genes, obtained using the cTE scale.