Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages |
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Authors: | Brian R Morton |
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Institution: | (1) Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA, US |
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Abstract: | In the plant chloroplast genome the codon usage of the highly expressed 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 genomes, in addition to Chlamydomonas reinhardtii, is investigated by measuring adaptation to this pattern of codon usage. A method is developed which tests selection on each
gene individually by constructing sequences with the same amino acid composition as the gene and randomly assigning codons
based on the nucleotide composition of noncoding regions 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 majority of genes, of intermediate intensity in Odontella sinensis, and weaker in Porphyra purpurea and Euglena gracilis. In the plants, selection is found to be quite weak in Pinus thunbergii and the angiosperms but there is evidence that an intermediate level of selection exists in the liverwort Marchantia polymorpha. The role of selection is then further investigated in two comparative studies. It is shown that average relative codon bias
is correlated with expression level and that, despite saturation levels of substitution, there is a strong correlation among
the algae genomes in the degree of codon bias of homologous genes. All of these data indicate that selection for translation
efficiency plays a significant role in determining the codon bias of chloroplast genes but that it acts with different intensities
in different lineages. In general it is stronger in the algae than the higher plants, but within the algae Euglena is found to have several unusual features which are noted. The factors that might be responsible for this variation in intensity
among the various genomes are discussed.
Received: 6 June 1997 / Accepted: 24 July 1997 |
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Keywords: | : Chloroplast DNA — Codon usage — Natural selection |
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