SELECTION ON THE CODON BIAS OF CHLOROPLAST AND CYANELLE GENES IN DIFFERENT PLANT AND ALGAL LINEAGES

In the plant chloroplast genome the codon usage of the highly expresse d psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study the role of selection on codon usage in each of the fully sequenced chloroplast g enomes, in addition to Chlamydomonas reinhardtii, is investigated by m easuring adaptation to this pattern of codon usage. A method is develo ped which tests selection on each gene individually by constructing se quences with the same amino acid composition as the gene and randomly assigning codons based on the nucleotide composition of noncoding regi ons of that genome. The codon bias of the actual gene is then compared to a distribution of random sequences. The data indicate that within the algae selection is strong in Cyanophora paradoxa, affecting a majo rity of genes, of intermediate intensity in Odontella sinensis, and we aker in Porphyra purpurea and Euglena gracilis. In the plants, selecti on is found to be quite weak in Pinus thunbergii and the angiosperms b ut there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then fu rther investigated in two comparative studies. It is shown that averag e relative codon bias is correlated with expression level and that, de spite saturation levels of substitution, there is a strong correlation among the algae genomes in the degree of codon bias of homologous gen es. All of these data indicate that selection for translation efficien cy plays a significant role in determining the codon bias of chloropla st genes but that it acts with different intensities in different line ages. In general it is stronger in the algae than the higher plants, b ut within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variat ion in intensity among the various genomes are discussed.