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Originally published as Genetics Published Articles Ahead of Print on June 3, 2005.
Genetics, Vol. 170, 1691-1700, August 2005, Copyright © 2005
doi:10.1534/genetics.104.038109
Patterns of Synonymous Codon Usage in Drosophila melanogaster Genes With Sex-Biased Expression
Tina M. Hambuch and John Parsch1
Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), 82152 Munich, Germany
1 Corresponding author: Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany.
E-mail: parsch{at}zi.biologie.uni-muenchen.de
The nonrandom use of synonymous codons (codon bias) is a well-established phenomenon in Drosophila. Recent reports suggest that levels of codon bias differ among genes that are differentially expressed between the sexes, with male-expressed genes showing less codon bias than female-expressed genes. To examine the relationship between sex-biased gene expression and level of codon bias on a genomic scale, we surveyed synonymous codon usage in 7276 D. melanogaster genes that were classified as male-, female-, or non-sex-biased in their expression in microarray experiments. We found that male-biased genes have significantly less codon bias than both female- and non-sex-biased genes. This pattern holds for both germline and somatically expressed genes. Furthermore, we find a significantly negative correlation between level of codon bias and degree of sex-biased expression for male-biased genes. In contrast, female-biased genes do not differ from non-sex-biased genes in their level of codon bias and show a significantly positive correlation between codon bias and degree of sex-biased expression. These observations cannot be explained by differences in chromosomal distribution, mutational processes, recombinational environment, gene length, or absolute expression level among genes of the different expression classes. We propose that the observed codon bias differences result from differences in selection at synonymous and/or linked nonsynonymous sites between genes with male- and female-biased expression.
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