Originally published as Genetics Published Articles Ahead of Print on August 10, 2009.

Genetics, Vol. 183, 547-561, October 2009, Copyright © 2009
doi:10.1534/genetics.109.105957

Regulatory Divergence in Drosophila melanogaster and D. simulans, a Genomewide Analysis of Allele-Specific Expression

Rita M. Graze^*,, Lauren M. McIntyre^*,,,1, Bradley J. Main, Marta L. Wayne^*,** and Sergey V. Nuzhdin^,

^* Genetics Institute, University of Florida, Gainesville, Florida 32610-3610, Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610-0266, Department of Evolution and Ecology, University of California, Davis, California 95616, ^** Department of Zoology, University of Florida, Gainesville, Florida, 32611-8525, Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089-2910 and Department of Statistics, University of Florida, Gainesville, Florida 32611-8545

¹ Corresponding author: 1376 Mowry Road, CG Research Building, University of Florida, Gainesville, FL 32607.
E-mail: mcintyre{at}ufl.edu

Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces that shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genomewide in female adult heads of Drosophila melanogaster, D. simulans, and their F₁ hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.

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