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

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  • Lawniczak, Mara KN
    • Other Affiliation: Division of Cell and Molecular Biology, Imperial College London
  • Holloway, Alisha K
    • Other Affiliation: Department of Evolution and Ecology and Center for Population Biology, University of California, Davis
  • Begun, David J
    • Other Affiliation: Department of Evolution and Ecology and Center for Population Biology, University of California, Davis
  • Jones, Corbin
    • Affiliation: School of Medicine, Carolina Center for Genome Sciences
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.
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Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Mara KN Lawniczak et al.; licensee BioMed Central Ltd.
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Journal title
  • Genome Biology
Journal volume
  • 9
Journal issue
  • 8
Page start
  • R125
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1465-6906
Bibliographic citation
  • Genome Biology. 2008 Aug 12;9(8):R125
Publisher
  • BioMed Central Ltd
Access right
  • Open Access
Date uploaded
  • August 23, 2012

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file details gb-2008-9-8-r125.pdf 2019-05-07 Public Download
file details The relationship between expression variation and divergence for the gene features discussed in this manuscript. 2019-05-07 Public Download
file details gb-2008-9-8-r125.xml 2019-05-07 Public Download
file details Details of the statistical results summarized in Table 4. 2019-05-07 Public Download
file details The results presented in Table 1 and Figure 1 are robust to increasing the minimum coverage to four sequences per probe. 2019-05-07 Public Download