Codon fitnesses for chloroplast genes were estimated using the relativ
e synonymous codon use of psbA, which has a different pattern of codon
use than other chloroplast genes and is the major translation product
of the chloroplast. These estimates were used to calculate the codon
adaptation index (CAI) of chloroplast genes from Marchantia polymorpha
, Nicotiana tabacum, and Chlamydomonas reinhardtii. The genes with the
highest CAI values in M. polymorpha correspond to those that are expr
essed at the highest levels. The rate of divergence between M. polymor
pha and both C. reinhardtii and N. tabacum is inversely related to the
CAI value of the M. polymorpha gene. The data suggest that selection
is acting on the synonymous codon use of the highly expressed genes of
the M. polymorpha chloroplast genome. The data set is inconclusive ab
out N. tabacum genes, but, as there is a weaker correspondence between
CAI value and expression level, it suggests that selection is not ope
rating in this lineage.