MBE Advance Access published online on October 31, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msh003
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario, Canada, K1N 6N5
* To whom correspondence should be addressed. E-mail: dhickey{at}uottawa.ca.
Amino acid sequences from several thousand homologous gene pairs were compared for two plant genomes, Oryza sativa and Arabidopsis thaliana. The Arabidopsis genes all have similar G+C (guanine plus cytosine) contents, whereas their homologs in rice span a wide range of G+C levels. The results show that those rice genes that display increased divergence in their nucleotide composition (specifically, increased G+C content) showed a corresponding, predictable change in the amino acid compositions of the encoded proteins relative to their Arabidopsis homologs. This trend was not seen in a "control" set of rice genes that had nucleotide contents closer to their Arabidopsis homologs. In addition to showing an overall difference in the amino acid composition of the homologous proteins, we were also able to investigate the biased patterns of amino acid substitution since the divergence of these two species. We found that the amino acid exchange matrix was highly asymmetric when comparing the High G+C rice genes to their Arabidopsis homologs. Finally, we investigated the possible causes of this biased pattern of sequence evolution. Our results indicate that the biased pattern of protein evolution is the consequence, rather than the cause, of the corresponding changes in nucleotide content. In fact, there is an even more marked asymmetry in the patterns of substitution at synonymous nucleotide sites. Surprisingly, there is a very strong negative correlation between the level of nucleotide bias and the length of the coding sequences within the rice genome. This difference in gene length may provide important clues about the underlying mechanisms. Key Words:
comparative genomics, angiosperm, nucleotide, amino acid
© 2003 Society for Molecular Biology and Evolution
Original Articles
Mutational Bias Affects Protein Evolution in Flowering Plants
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