Moreover, of the 12 silent mutations that may be at fixation (Figure 2), 75% of them generated synonymous codons with high frequency usage in C. trachomatis [25].
Similarly, we have found that 75% of all silent mutations that are likely at evolutionary fixation resulted in synonymous codons with high frequency usage in C. trachomatis [25].
However, 16 codons with high frequency are observed in the mtDNA.
It was found that the ORFs with higher frequencies of the following codons (AAC, TCT, ACC, TCC, GCC, GCT, CCA) tend to have higher rate of protein synthesis; on the other hand, higher frequency of the codons (ATA, CGA, TGC, GTA, GGA, CTT, AGG, CGG, TAT) relates to lower translation efficiency.
This means that the significantly over-represented co-occurrence of two codons does not necessarily imply that the corresponding hexanucleotide sequences occur with high frequency.
Similarly, two out of six Ser codons with low expected frequency were over-represented as well, while two out of three Ile codons with high expected frequency were under-represented.
Only 35 codons, rather than all 61 codons, appeared as the second codon in high-frequency codon pairs.
The codon bias observed for highly expressed genes of the dataset is different from codons used at highest frequency in naturally highly expressed E. coli genes [5], [7].
Among 18 amino acids with degenerate codons, 16 showed higher frequencies of translationally preferred codons in the remaining region (5' boundary plus central) compared to those in the 3' boundary region (see Additional file 1).
Consequently, nPTB and ROD1 have a very distinctive codon composition, with a high frequency of codons ending in A or T, while PTB has a much higher proportion of codons ending in G or C. Strikingly, codon bias in the human genome shows an overall preference for G or C in the third codon position (∼59%) [33].
Codons with higher (or lower) selected frequencies have higher (or lower) RSCU values.
