Comparison of Ultra-Conserved Elements in Drosophilids and Vertebrates

Abstract

Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption.

Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants

“…It is possible that functional differences between these two types of data may lead to incompatible branch length estimation. All of our Sanger data were protein-coding or ribosomal DNA sequence from nuclear genes, whereas many UCE loci in general do not overlap with protein-coding regions, but rather appear to act as enhancers or splicing regulators [ 48 ]. Methods that jointly estimate divergence ages and tree topology, such as BEAST, have further seldom been employed to date with UCE or other genomic-scale data due to computational constraints.…”

Conserved noncoding elements influence the transposable element landscape inDrosophila

“…Thus, CNEs represent an abundant class of noncoding features under purifying selection that may influence the landscape of TE insertions. Previous work showed that artificially-induced TE insertions are depleted in the most highly conserved CNEs (so-called “ultra-conserved elements”) (Makunin et al , 2013). However the non-random target preferences, requirement for marker gene activation in TE detection, and experimental origin of the TEs analyzed by Makunin et al (2013) do not allow conclusions to be drawn about CNE-based constraints on insertion of the endogenous set of TE families in natural populations.…”

“…Previous work showed that artificially-induced TE insertions are depleted in the most highly conserved CNEs (so-called “ultra-conserved elements”) (Makunin et al , 2013). However the non-random target preferences, requirement for marker gene activation in TE detection, and experimental origin of the TEs analyzed by Makunin et al (2013) do not allow conclusions to be drawn about CNE-based constraints on insertion of the endogenous set of TE families in natural populations. Resolving whether CNEs influence the landscape of TE insertion in natural populations of D. melanogaster will provide further insight into the factors governing TE dynamics in this species, and contribute to our broader understanding of the forces that shape genome organization and molecular evolution in general.…”

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

“…Three of these insertions are partially located in UTRs of genes involved in developmental processes (grh, pld, ssdp). There is therefore strong support for proposing that these "conserved noncoding insertions" became domesticated in the common ancestor of the melanogaster group (15)(16)(17)(18)(19)(20) My (24)).…”

“…The complementarity of these approaches is at the core of many methods for identifying selection, such as the McDonald & Kreitman test (14) or, more recently, the estimation of deleterious fitness effects (DFE) (15)(16)(17). In the fruitfly, Drosophila melanogaster, many characterizations of highly conserved elements have been proposed, based on different sets of species and identity criteria (2,12,18). However, no systematic study of selection in CNEs combining genome-wide interspecific comparisons with analysis of intra-population polymorphism and selection yet exists in melanogaster.…”