Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila

[Abstract] Promoters are structurally and functionally diverse gene regulatory regions. The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters. Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contribute to promote diversity. In this work, we analyzed in detail one of the transposable element insertions, named FBti0019985, that has been co-opted to drive expression of CG18446, a candidate stress response gene. We analyzed strains from different natural populations and we found that besides FBti0019985, there are another eight independent transposable elements inserted in the proximal promoter region of CG18446. All nine insertions are solo-LTRs that belong to the roo family. We analyzed the sequence of the nine roo insertions and we investigated whether the different insertions were functionally equivalent by performing 5’-RACE, gene expression, and cold-stress survival experiments. We found that different insertions have different molecular and functional consequences. The exact position where the transposable elements are inserted matters, as they all showed highly conserved sequences but only two of the analyzed insertions provided alternative transcription start sites, and only the FBti0019985 insertion consistently affects CG18446 expression. The phenotypic consequences of the different insertions also vary: only FBti0019985 was associated with cold-stress tolerance. Interestingly, the only previous report of transposable elements inserting repeatedly and independently in a promoter region in D. melanogaster, were also located upstream of a stress response gene. Our results suggest that functional validation of individual structural variants is needed to resolve the complexity of insertion clusters.[Author Summary] The presence of several transposable element insertions in the promoter region of a Drosophila melanogaster gene has only been described in heat shock protein genes. In this work, we have discovered and characterized in detail several naturally occurring independent transposable element insertions in the promoter region of a cold-stress response gene in the fruitfly Drosophila melanogaster. The nine transposable element insertions described are clustered in a small 368 bp region and all belong to the same family of transposable elements: the roo family. Each individual insertion is present at relatively low population frequencies, ranging from 1% to 17%. However, the majority of strains analyzed contain one of these nine roo insertions suggesting that this region might be evolving under positive selection. Although the sequence of these insertions is highly similar, their molecular and functional consequences are different. Only one of them, FBti0019985, is associated with increased viability in nonstress and in cold-stress conditions.This work was supported by the Ministerio de Economía y Competitividad (MINECO: http://www.idi.mineco.gob.es) BFU-2011-24397 and RYC-2010-07306 to JG, and BES-2012-052999 to AU, Ministerio de Economía y Competitividad and Fondo Europeo de Desarrollo Regional (MINECO/FEDER:http://www.idi.mineco.gob.es) BFU2014-57779-P, the European Commission (https://ec.europa.eu) FP7-PEOPLE-2011-CIG-293860, the Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (http://agaur.gencat.cat) 2014-SGR-201 to JG, and by the Agence Nationale de la Recherche (http://www.agence-nationale-recherche.fr) ANR-14-CE02-0003 to MARdC.USD 2250 APC fee funded by the EC FP7 Post-Grant Open Access PilotPeer reviewe

Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster

Organisms must cope with altered environmental conditions such as high concentrations of heavy metals. Stress response to heavy metals is mediated by the metal-responsive transcription factor 1 (MTF-1), which is conserved from Drosophila to humans. MTF-1 binds to metal response elements (MREs) and changes the expression of target genes. kuzbanian (kuz), a metalloendopeptidase that activates the evolutionary conserved Notch signaling pathway, has been identified as an MTF-1 target gene. We have previously identified a putatively adaptive transposable element in the Drosophila melanogaster genome, named FBti0019170, inserted in a kuz intron. In this work, we investigated whether a laboratory mutant stock overexpressing kuz is associated with zinc stress phenotypes. We found that both embryos and adult flies overexpressing kuz are more tolerant to zinc compared with wild-type flies. On the other hand, we found that the effect of FBti0019170 on zinc stress tolerance depends on developmental stage and genetic background. Moreover, in the majority of the genetic backgrounds analyzed, FBti0019170 has a deleterious effect in unpolluted environments in pre-adult stages. These results highlight the complexity of natural mutations and suggest that besides laboratory mutations, natural mutations should be studied in order to accurately characterize gene function and evolution.H.L.M. was a VAST-CSIC fellow, L.G. was a FI/DGR fellow (2012FI-B-00676) and J.G. is a Ramón y Cajal fellow (RYC-2010-07306). This work was supported by grants from the European Community’s Seven Framework Programme (FP7-PEOPLE-2011-CIG-293860), from the Spanish Government (BFU2011-24397 and BFU2014-57779-P), and from the Generalitat de Catalunya (2014 SGR 201).EUR 1,305 APC fee funded by the EC FP7 Post-Grant Open Access PilotPeer reviewe

A new species in the Anopheles gambiae complex reveals new evolutionary relationships between vector and non-vector species

Complexes of closely related species provide key insights about the rapid and independent evolution of adaptive traits. Here, we described and studied a presumably new species in the Anopheles gambiae complex, Anopheles fontenillei, recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. In particular, we detected recent introgression with An. gambiae and An. coluzzii of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species also allowed us to resolve the evolutionary history of inversion 3La. Overall, Anopheles fontenillei has implemented our understanding about the relationship of species within the gambiae complex and provides insight into the evolution of vectorial capacity traits, relevant for the successful control of malaria in Africa.Funding was provided by the “Institut de Recherche pour le Developpément”, the “Agence Universitaire de la Francophonie” (grant: OKANDA), the “Centre National de la Recherche Scientifique” (CNRS) and the “Consejo Superior de Investigaciones Cientificas” (CSIC) (grant PICS ANCESTRAL to DA and JG), the “ANR” (grant ANR--18-CE35-0002-01-WILDING to DA), and the “Ministerio de Ciencia, Innovación y Universidades/AEI” (grant BFU2017-82937-P to JG).N

Genomic analysis of European Drosophila melanogaster populations reveals longitudinal structure, continent-wide selection, and previously unknown DNA viruses

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.Publisher PDFPeer reviewe

The Drosophila melanogaster Genetic Reference Panel

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics

The Drosophila melanogaster Genetic Reference Panel

A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype–phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype–phenotype mapping using the power of Drosophila genetics

Indispensability Argument and Set Theory

One may take several different positions with respect to the ontological status of scientific entities such as, for example, quarks (quarks can't be observed even in principle). Do quarks "really exist", or are they only a (currently successful) theoretical construct used by physicists in their models? Perhaps, the "least committed" position could be the formalist one: let us define the "real existence" of some scientific entity as its invariance in future scientific theories

Mapping blocks of linkend selection throughout the drosophila melanogaster genome

Trabajo presentado en la 4th Meeting of the Spanish Society of the Evolutionary Biology (SESBE 2013) celebrada en Barcelona del 27 al 29 de noviembre de 2013.N