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Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome

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Abstract

The patterns and processes of molecular evolution may differ between the X chromosome and the autosomes in Drosophila melanogaster. This may in part be due to differences in the effective population size between the two chromosome sets and in part to the hemizygosity of the X chromosome in Drosophila males. These and other factors may lead to differences both in the gene complements of the X and the autosomes and in the properties of the genes residing on those chromosomes. Here we show that codon bias and recombination rate are correlated strongly and negatively on the X chromosome, and that this correlation cannot be explained by indirect relationships with other known determinants of codon bias. This is in dramatic contrast to the weak positive correlation found on the autosomes. We explored possible explanations for these patterns, which required a comprehensive analysis of the relationships among multiple genetic properties such as protein length and expression level. This analysis highlights conserved features of coding sequence evolution on the X and the autosomes and illuminates interesting differences between these two chromosome sets.

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Acknowledgments

This work was supported in part by the Stanford Genome Training Program (funded by 5 T32 HG00044 from the National Human Genome Research Institute) to N.D.S. and a Sloan Fellowship to D.A.P. Comments from two anonymous reviews, an associate editor, and the editor-in-chief considerably improved this manuscript.

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Authors and Affiliations

  1. Department of Biological Sciences, Stanford University, 371 Serra Mall, Stanford, California, 90305-5020, USA

    Nadia D. Singh, Jerel C. Davis & Dmitri A. Petrov

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  1. Nadia D. Singh
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  2. Jerel C. Davis
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  3. Dmitri A. Petrov
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Correspondence to Nadia D. Singh.

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[Reviewing editor: Dr. Richard Kliman]

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Singh, N.D., Davis, J.C. & Petrov, D.A. Codon Bias and Noncoding GC Content Correlate Negatively with Recombination Rate on the Drosophila X Chromosome. J Mol Evol 61, 315–324 (2005). https://doi.org/10.1007/s00239-004-0287-1

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  • DOI: https://doi.org/10.1007/s00239-004-0287-1

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