Population genomics support PRDM9-dependent recombination landscapes in salmonids

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Raynaud, Marie | Gagnaire, Pierre-Alexandre | Galtier, Nicolas

Edité par CCSD -

International audience. In most mammals, the genomic localization of recombination hotspots is controlled by the PRDM9 protein. The complete or partial loss of a functional Prdm9 gene in other taxa such as birds, some teleost fishes or invertebrates, is associated with a different hotspot localization map and a more stable dynamics of recombination landscapes than in mammals. The role of PRDM9 in taxa that have retained a functional copy of this gene remains unclear, raising questions about its ancestral function in animals. Through a phylogenetic analysis, we discovered that salmonid fishes have retained a full-length functional copy of the Prdm9 gene. To further explore the role of PRDM9 in regulating recombination in salmonids, we used linkage disequilibrium information from whole-genome polymorphism data to build fine-scale recombination maps in wild populations of three Salmonid species: Oncorhynchus kisutch, O. mykiss and Salmo salar. The three species showed variation in recombination rates at both broad and fine scales, with a tendency for hotspots to be localized independently from transcription start sites and CpG islands, a typical signature of PRDM9-driven recombination in mammals. Moreover, the comparison of recombination landscapes among species and populations of salmonids revealed a rapid evolution of hotspot location. Finally, a DNA motif was found to be significantly enriched in a European lineage of Atlantic salmon, and this motif was eroded compared to the American lineages. These findings strongly suggest that PRDM9 has a function of directing DNA double strand breaks location in salmonids, arguing in favor of an ancestrally PRDM9-mediated recombination mechanism in vertebrates.

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