Rates of synonymous substitution do not indicate selective constraints on the codon use of the plant psbA gene.
The psbA gene of the flowering plant chloroplast genome has a pattern of codon bias that differs from all other angiosperm chloroplast genes. In psbA, unlike all other chloroplast genes, the third-codon-position composition does not reflect the general genome compositional bias of a high A+T content. Instead, in specific synonymous groups, the codon use of psbA more closely corresponds to the tRNA population available for translation. Since it requires a composition unlike the genome composition bias, this pattern of codon use is likely to be the result of selection. Selective constraints on codon use are expected to result in decreased rates of synonymous substitution, and it has been observed that psbA has the lowest rate of synonymous substitution among plant chloroplast genes. In the present study, this is examined further by testing whether or not those synonymous groups that specifically have an atypical codon use in psbA have correspondingly low rates of silent substitution. An analysis of synonymous substitution rate, performed separately for different degeneracy classes of amino acids, shows that, contrary to the expectation, those sites that are presumed, based on their codon use, to be under selective constraint in psbA do not show low rates of substitution and are not responsible for the overall low rate of synonymous substitution in this gene. Instead, they actually show increased rates of substitution relative to other chloroplast genes. Two hypotheses concerning the role of selection in psbA are advanced to explain the results.