Regulatory Divergence in Drosophila revealed by mRNA-seq

These data were generated in a study to analyze the genetic causes of gene regulatory divergence. mRNA-seq libraies were prepared from poly(A)+ RNA prepared from whole F1 hybrids of D. melanogaster and D. sechellia (female 0-3d post eclosion, "D_mel_x_D_sec"). A mixed mRNA- seq library was prepared from D. melanogaster and D. sechellia poly(A) + RNA (mixed before library preparation, "D_mel_+_D_sec). Finally, separate mRNA-seq libraries were prepared from poly(A)+ RNA from each species ("D_mel" and "D_sec"). The results of this study showed that 78% of genes expressed in the two species are differentially expressed, and that cis- and trans-regulatory divergence affect 51% and 66% of expressed genes, respectively. Keywords: RNA-Seq There were 4 total samples in this study. mRNA-seq was used to measure allele-specific gene expression levels from 9966 genes in the F1 hybrid, and mixed samples. Comparisons of relative gene expression levels between species and allele-specific expression levels within the F1 hybrid were used to assay the contributions of cis- and trans-regulatory divergence between the species.