Evolution of gene expression in Drosophila

Variation in gene expression is a major source of phenotypic diversity. This proposal takes advantage of the potential of next generation sequencing for comparative gene expression profiling. By measuring gene expression in males and females in seven species, this proposal will address 5 fundamental questions: 1) Evolution of sex- biased gene expression, 2) Evolution of cis- and trans-effects 3) Evolution of alternative splicing, 4) Influence of temperature stress on gene expression 5) Phylogenetic turnover of gene expression intensities.

In the frame of this project, we developed several tools and made them available to the scientific community. The first one is a new software tool, which permits the quantification of allele specific gene expression using RNA-Seq data. The second tool is the annotated reference genome of the fruit fly Drosophila simulans. The third tool enables users to map many short reads on a local computer cluster.The biological results fall into two themes: 1) the influence of temperature on the regulation of gene expression 2) evolutionary dynamics of de novo genesWe demonstrated that temperature is a major factor influencing the patterns of gene expression. We characterized the reaction norm of gene expression in dependence of temperature. The shape of the reaction norms differs among genes belonging to different functional classes (GO categories). The number of transcription factor binding sites was found to be the most important factor determining the expression dynamics across the different temperatures. While microRNA binding sites were also having a significant effect, it was smaller than the one caused by the number of transcription factor binding sites. Developmental temperature did not only have an effect on gene expression intensity, but also on the patterns of alternative splicing. Interestingly for both aspects of gene expression, we noted a similar pattern: at extreme temperatures the expression pattern between two Drosophila melanogaster genotypes was more diverged than at 18C, putatively the most benign temperature. This pattern has been interpreted as decanalization of gene expression in stressful environments. De novo genes arise from previously non-coding DNA stretches. While this type of evolutionary innovation has been considered extremely unlikely, more recent studies demonstrated that is, on the contrary, a very frequent process. With de novo genes emerging at such high rates, the question arose why this process did not lead to continuously increasing genomes. In this subproject, we have therefore focused on the death process of young de novo genes. Using D. pseudoobscura and closely related sister taxa we were able to show that many de novo genes have a very short evolutionary persistence time. We characterized the properties of de novo genes, which persisted for longer time spans and found that the level of gene expression is very important.