within the grasses, the conserved chloroplast genes appear to exist in a very fluid medium of surrounding noncoding sequence.
Codon Bias of Chloroplast Genes. The codon utilization pattern of chloroplast genes of the green algae Chlamydomonas reinhardtii and Chlamydomonas moewusii appears to be closely adapted to the chloroplast tRNA population. In contrast, land plant chloroplast genes are dominated by a genomic bias towards a high A+T content, which is reflected in a high third-codon position A+T content. An interesting exception is the gene coding for the central protein of the photosystem II reaction center (denoted psbA) (Umesono et al., 1988). The psbA protein turns over at a very high rate and, consequently, is the most abundant translation product of the plant chloroplast (Mullet and Klein, 1987). The psbA gene of flowering plants has a codon use very similar to Chlamydomonas chloroplast genes (Morton, 1993). Given the tRNAs encoded by the sequenced chloroplast genomes, the pattern of codon bias of the Chlamydomonas genes appears to be the result of selection for an intermediate codon-anticodon interaction strength (Morton, unpublished data). Further, based on the fact that psbA is the sole flowering plant chloroplast gene following this codon utilization pattern, selection most likely acted on psbA codon use to increase translation efficiency (Morton, 1993).
Despite the difference in codon use by psbA relative to other plant chloroplast genes, this gene has a much lower bias in codon use than do Chlamydomonas chloroplast genes. In fact, there is good evidence that selection no longer acts on psbA codon use in flowering plant lineages; it is merely a remnant of the ancestral codon use. Further, the highly expressed gene rbcL displays a codon use more like psbA than does any other flowering plant chloroplast gene (Morton, 1994). These two factors, the apparently recent loss of selection on flowering plant psbA codon use and the similarity of rbcL to psbA, indicate that loss of selection for codon adaptation on plant chloroplast genes may have occurred at different times for each plant chloroplast gene, most likely as genome number increased over time (Morton, unpublished). Such a scenario may have important implications for studies of chloroplast origins because standard phylogenetic estimation methods are likely to be biased and, therefore, unreliable at very deep evolutionary levels. The codon bias results also suggest that nucleotide composition cannot be assumed to be at equilibrium, contrary to the assumptions incorporated in most distance estimators.