Molecular Biology and Evolution, Vol 14, 412-419, Copyright © 1997 by Society for Molecular Biology and Evolution
BR Morton
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.
ORIGINAL ARTICLE
Rates of synonymous substitution do not indicate selective constraints on the codon use of the plant psbA gene
Department of Biological Sciences, Barnard College, Columbia University, New York, New York 10027, USA. bmorton@barnard.columbia.edu
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