Evidence for purifying selection on conserved noncoding elements in the genome of Drosophila melanogaster

Identification of regulatory regions within genomes is a key challenge for understanding the influence of functional traits on species evolution. Development of whole-genome sequencing programs in the early 2000s has been associated with the rise of comparative genomics as a powerful tool for predicting functional regions in genomes, using structural characteristics of DNA sequences. Conserved Noncoding Elements (CNEs, i.e. untranslated sequences highly similar across divergent species) were early identified as candidate regulatory regions in metazoans, plants, and fungi. CNEs have been repeatedly discriminated from mutational cold-spots, but only few studies have assessed their functional relevance at a genome-wide scale. In the present study, we used a whole-genome alignment of 27 insect species to build a coherent mapping of CNEs in the genome of Drosophila melanogaster. We then exploited polymorphism data from 48 European populations of D. melanogaster to estimate levels of nucleotide diversity and adaptive evolution in CNEs. We show here that about 35% of D. melanogaster autosomes fall into conserved noncoding regions that exhibit reduced genetic diversity and undergo purifying selection. In addition, we report six insertions of Transposable Elements (TEs) in the genome of D. melanogaster showing high levels of conservation across Drosophila species. Half of these insertions are located in untranslated transcribed regions (UTRs) of genes involved in developmental pathways and thus represent potential relics of ancient TE domestication events.