Research

Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans

Mara KN Lawniczak^1* , Alisha K Holloway^2* , David J Begun² and Corbin D Jones³

¹  Division of Cell and Molecular Biology, Imperial College London, London, SW7 2AZ, UK

²  Department of Evolution and Ecology and Center for Population Biology, University of California, Shields Avenue, Davis, CA 95616, USA

³  Department of Biology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC 27599, USA

author email corresponding author email* Contributed equally

Genome Biology 2008, 9:R125doi:10.1186/gb-2008-9-8-r125

Published:	12 August 2008

Subject areas: Evolution, Genome studies, Molecular biology

Abstract

Background

Understanding how DNA sequence polymorphism relates to variation in gene expression is essential to connecting genotypic differences with phenotypic differences among individuals. Addressing this question requires linking population genomic data with gene expression variation.

Results

Using whole genome expression data and recent light shotgun genome sequencing of six Drosophila simulans genotypes, we assessed the relationship between expression variation in males and females and nucleotide polymorphism across thousands of loci. By examining sequence polymorphism in gene features, such as untranslated regions and introns, we find that genes showing greater variation in gene expression between genotypes also have higher levels of sequence polymorphism in many gene features. Accordingly, X-linked genes, which have lower sequence polymorphism levels than autosomal genes, also show less expression variation than autosomal genes. We also find that sex-specifically expressed genes show higher local levels of polymorphism and divergence than both sex-biased and unbiased genes, and that they appear to have simpler regulatory regions.

Conclusion

The gene-feature-based analyses and the X-to-autosome comparisons suggest that sequence polymorphism in cis-acting elements is an important determinant of expression variation. However, this relationship varies among the different categories of sex-biased expression, and trans factors might contribute more to male-specific gene expression than cis effects. Our analysis of sex-specific gene expression also shows that female-specific genes have been overlooked in analyses that only point to male-biased genes as having unusual patterns of evolution and that studies of sexually dimorphic traits need to recognize that the relationship between genetic and expression variation at these traits is different from the genome as a whole.