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

Abstract

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 coldspots, 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.

The discovery, distribution, and diversity of DNA viruses associated withDrosophila melanogasterin Europe

“…In general, the level of constraint on virus genes appeared low, with global π A /π S 0.39 and local π A /π S = 0.58. These patterns of diversity are markedly different to those of the host, in which π S (at four-fold degenerate sites) is on the order of 1 per cent with π A /π S (zero- and four-fold) around 0.2, and differentiation approximately F ST = 0.03 ( Kapun et al 2020 ; Tristan, Aurelie, and Annabelle 2019 ). Given that large dsDNA virus mutation rates can be ten- to 100-fold higher than animal mutation rates ( Duffy 2018 ), the overall lower diversity in Drosophila Kallithea nudivirus is consistent with bottlenecks during infection and the smaller population size that corresponds to a 2.1 per cent prevalence.…”

The discovery, distribution and diversity of DNA viruses associated withDrosophila melanogasterin Europe

“…In general, the level of constraint on virus genes seemed low, with global πA/πS 0.39 and local πA/πS = 0.58. These patterns of diversity are markedly different to those of the host, in which πS (fourfold sites) is on the order of 1% with πA/πS (zero-fold and four-fold) around 0.2, and differentiation approximately FST = 0.03 (Tristan et al 2019, Kapun et al 2020. Given that large dsDNA virus mutation rates can be 10-100 fold higher than animal mutation rates (Duffy 2018), the overall lower diversity in Kallithea virus is consistent with bottlenecks during infection and the smaller population size that corresponds to a 2.1% prevalence.…”

“…In general, the level of constraint on virus genes appeared low, with global TT A /TT S 0.39 and local TT A /TT S = 0.58. These patterns of diversity are markedly different to those of the host, in which πS (at fourfold degenerate sites) is on the order of 1% with TT A /TT S (zero-fold and four-fold) around 0.2, and differentiation approximately F ST = 0.03 (Tristan et al . 2019, Kapun et al .…”