Molecular Biology and Evolution, Vol 5, 704-716, Copyright © 1988 by Society for Molecular Biology and Evolution
DC Shields, PM Sharp, DG Higgins and F Wright
The patterns of synonymous codon usage in 91 Drosophila melanogaster genes
have been examined. Codon usage varies strikingly among genes. This
variation is associated with differences in G+C content at silent sites,
but (unlike the situation in mammalian genes) these differences are not
correlated with variation in intron base composition and so are not easily
explicable in terms of mutational biases. Instead, those genes with high
G+C content at silent sites, resulting from a strong "preference" for a
particular subset of the codons that are mostly C- ending, appear to be the
more highly expressed genes. This suggests that G+C content is reduced in
sequences where selective constraints are weaker, as indeed seen in a
pseudogene. These and other data discussed are consistent with the effects
of translational selection among synonymous codons, as seen in unicellular
organisms. The existence of selective constraints on silent substitutions,
which may vary in strength among genes, has implications for the use of
silent molecular clocks.
ORIGINAL ARTICLE
"Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons
Department of Genetics, Trinity College, Dublin, Ireland.
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