EXploring genomic stability in HYBrids – ExHyb

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The notion of species, whose delineation is fundamental for current policies of biodiversity, is classically defined on the basis of viability and fertility of the descendants from a cross between two individuals. These events are possible when the union of the maternal and paternal genomes is stable. When two species diverged or when reproductive isolation is taking place between two distant populations, the union of the two genomes results in what we will call a genomic stress, which can activate genomic parasites such as transposable elements (TEs). Hybridization challenges species frontiers; the present project intends to study the variability of mechanisms that allow the maintaining of genomic stability, using the analysis of the consequences of the genomic stress in hybrids. We will use the activity and regulation of TEs as markers of genomic stability, together with the analysis of genome structure and expression. It is now widely recognized that epigenetic regulation is the primary control mechanism of the TEs in the genomes. Therefore, we propose to analyze the regulation of TEs at epigenetic level, and to measure the impact of TEs in the expression of nearby genes, at different evolutionary scales in Drosophila. Drosophila is a powerful genetic model, as Drosophila melanogaster’s genome has been fully sequenced, annotated and well-described, alike closely related species. In order to provide the most complete landscape of the effects of hybridization in genomes, we propose to perform the study at different scales of divergence: intra- and inter-specific. At the intra-specific scale, we will analyze populations of both D. melanogaster and D. simulans species, each species being well described, for which a lot of genomic data are available and for which we have a long-term experience in the group. For the inter-specific level, the D. melanogaster / D. simulans pair is not suitable, since they show high degree of reproductive isolation. Therefore, we propose to take advantage of the D. mojavensis / D. arizonae couple of species, which diverged more recently (<1 million years ago), and for which hybridization is still possible. We will first characterize the parental populations at the genomic level (using pooled whole-genomes sequencing), and describe the global pattern of TE insertion polymorphism and dynamics of each natural population and species. This will be possible thanks to an incredible advance in technological methods regarding next generation sequencing. At both evolutionary levels we propose to generate transcriptomic dataset for species / parental populations and their hybrids. We can thus measure the expression activity of genes and of TEs. From the same samples, producing epigenetic data (piRNA sequencing for regulation by RNA interference and ChIPseq for regulation by modifications of chromatin structure) will allow us to analyze different mechanisms of regulation of TEs and genes involved in their regulation. Also, we will be able to map chromatin histone marks on TEs and genes, and thus better understand the impact of TEs on the genome and especially following hybridization. The data produced during this project will allow us to further understand intragenomic conflicts. In particular, we should be able to design a complete panorama on the equilibrium established between TEs and their host genome and to bring light on how hybridization may affect this TE-regulation equilibrium.