Regulatory divergence in Drosophila revealed by mRNA-seq

Abstract

The regulation of gene expression is critical for organismal function and is an important source of phenotypic diversity between species. Understanding the genetic and molecular mechanisms responsible for regulatory divergence is therefore expected to provide insight into evolutionary change. Using deep sequencing, we quantified total and allele-specific mRNA expression levels genome-wide in two closely related Drosophila species (D. melanogaster and D. sechellia) and their F 1 hybrids. We show that 78% of expressed genes have divergent expression between species, and that cis-and trans-regulatory divergence affects 51% and 66% of expressed genes, respectively, with 35% of genes showing evidence of both. This is a relatively larger contribution of trans-regulatory divergence than was expected based on prior studies, and may result from the unique demographic history of D. sechellia. Genes with antagonistic cis-and trans-regulatory changes were more likely to be misexpressed in hybrids, consistent with the idea that such regulatory changes contribute to hybrid incompatibilities. In addition, cis-regulatory differences contributed more to divergent expression of genes that showed additive rather than nonadditive inheritance. A correlation between sequence similarity and the conservation of cisregulatory activity was also observed that appears to be a general feature of regulatory evolution. Finally, we examined regulatory divergence that may have contributed to the evolution of a specific trait-divergent feeding behavior in D. sechellia. Overall, this study illustrates the power of mRNA sequencing for investigating regulatory evolution, provides novel insight into the evolution of gene expression in Drosophila, and reveals general trends that are likely to extend to other species.

Evolution of splicing regulatory networks in Drosophila

“…Of the splicing events analyzed, genes exhibiting divergent splicing were not enriched for any GO categories. To further examine possible links between tissue abundance and splicing divergence, we asked whether genes with divergent splicing were enriched in species differences in mRNA abundance, calculated as described previously (McManus et al 2010a). In all comparisons, divergently spliced genes were no more likely to be divergently expressed than genes with conserved splicing (Supplemental Table S4).…”

“…In F1 hybrids, pre-mRNA from both parental alleles are subject to the same regulatory environments, thus observed differences in allele-specific splicing reflect cis-regulatory divergence. We used this approach previously to dissect cis-and trans-regulatory changes in mRNA abundance (McManus et al 2010a). By applying this to alternative splicing, we find that divergent regulation of intron retention and alternative splice sites has occurred almost exclusively through changes in cis-acting sequences, while divergence of exon skipping results from both cis and trans-acting regulatory changes.…”

Gene Regulatory Evolution During Speciation in a Songbird

“…One caveat, which appears to be common to various tests of regulatory divergence and requires further examination, is that cis and trans tests may differ in statistical power (e.g., Suvorov et al 2013). Divergence (spread) along the cis axis tends to be greater (Figure 3, see also Mack et al 2016), even in cases of abundant trans divergence (e.g., McManus et al 2010). Furthermore, due to the incorporation of biological variation, a large number of sites and genes are left with ambiguity in their mode of inheritance.…”

“…Astoundingly, fully fertile hybrids have been documented from bird species that have diverged for up to 10 million years (Tubaro and Lijtmaer 2002;Lijtmaer et al 2003;Price 2008;Arrieta et al 2013). In many other taxa, studies of gene expression have pointed to frequent misexpression in F1 hybrids (Landry et al 2005;McManus et al 2010;Malone and Michalak 2008;Renaut et al 2009;Bell et al 2013;Coolon et al 2014). If gene misexpression in hybrids is reflective of the buildup of postzygotic reproductive incompatibilities, then we may expect to see a reduced frequency of misexpression in bird species relative to other taxa of similar age.…”

“…The advent of RNA-seq technology has added a new dimension to the study of regulatory evolution, as it is now possible to estimate the relative expression of alternative alleles across all expressed polymorphisms (McManus et al 2010;Bell et al 2013). Because F1 hybrids share the same trans regulatory environment, allelic imbalance (allelespecific expression) in F1 hybrids allows the further categorization of regulatory divergence into the contributions of cis and trans regulatory evolution and the interaction of the two (Wittkopp et al 2004).…”