Nucleic Acids Research, 1994, Vol. 22, No. 13 2437-2446
© 1994
SURVEY AND SUMMARY |
Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases
Department of Genetics, Trinity College Dublin 2, Ireland 1Department of Genetics, University of Nottingham, Queens Medical Centre Nottingham NG7 2UH, UK
*To whom correspondence should be addressed
Received April 20, 1994. Revised May 26, 1994. Accepted May 26, 1994.
Synonymous codon usage varies considerably among Caenorhabditis elegans genes. Multivariate statistical analyses reveal a single major trend among genes. At one end of the trend lie genes with relatively unbiased codon usage. These genes appear to be lowly expressed, and their patterns of codon usage are consistent with mutational biases influenced by the neighbouring nucleotide. At the other extreme lie genes with extremely biased codon usage. These genes appear to be highly expressed, and their codon usage seems to have been shaped by selection favouring a limited number of translationally optimal codons. Thus, the frequency of these optimal codons in a gene appears to be correlated with the level of gene expression, and may be a useful indicator in the case of genes (or open reading frames) whose expression levels (or even function) are unknown. A second, relatively minor trend among genes is correlated with the frequency of G at synonymously variable sites. It is not yet clear whether this trend reflects variation in base composition (or mutational biases) among regions of the C.elegans genome, or some other factor. Sequence divergence between C.elegans and C.briggsae has also been studied.
+Present address: Dipartimento di Biologia, Universita di Padova, 35121 Padova, Italy
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