Fine-scale recombination patterns in salmonid fishes support PRDM9-directed hotspot location

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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. We evaluated the accuracy of our reconstructions via simulations Raynaud et al. (2023). The three species showed variation in recombination rates at both broad and fine scales, with a tendency for hotspots to be localized away from transcription start sites, 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. 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. Confirmation of these results via ChipSeq and binding motif analysis is on its way.

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