Data from: PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids

Usage notes Data and scripts related for the study entitled "PRDM9 drives the location and rapid evolution of recombination hotspots in salmonids" by Raynaud, Sanna et al. are provided. ChIP-Seq: Fragments and peak coordinates obtained from DMC1 ChIP-seq (SSDS) experiments on rainbow trout testes are given, as well as fragments obtained from ChIP-seq experiments for H3K4me3 and H3K36me3 from testes and peak coordinates obtained from ChIP-seq experiments for H3K4me3 from brain tissue. Files generated during DSB hotspot motif analysis are also provided. LD-based recombination landscapes: VCFs: VCF files generated by GATK for 3 salmon species: coho salmon Oncorhynchus kisutch (one population), rainbow trout Oncorhynchus mykiss (one population) and Atlantic salmon Salmo salar (three populations: GP, BS and NS). Filtered and phased VCF files are also provided for the 5 populations. Population recombination landscapes: Population recombination rates estimated by LDhelmet for each chromosome of 5 populations belonging to three different salmonid species: coho salmon Oncorhynchus kisutch (one population), rainbow trout Oncorhynchus mykiss (one population) and Atlantic salmon Salmo salar (three populations: GP, BS and NS). The LDhelmet estimates for the 5 independent replicate runs for each chromosome and the whole-genome recombination landscapes averaged over the five runs are given. The whole-genome recombination landscapes averaged over five replicates are also given for sea bass Dicentrarchus labrax. Processed LD-based maps and recombination hotspots: LDhelmet recombination maps smoothed in 2-kb and 100-kb windows and hotspot list called from the 2-kb smooth maps and the raw LDhelmet maps are given for the 5 salmon populations and for D. labrax. Transposable element annotations: File containing the location and type of transposable elements mapped with RepeatMasker are provided for O. kisutch, O. mykiss and S. salar. PRDM9 paralog alignment in Salmonids: Fasta sequences and multiple alignments in mase format of the PRDM9α and β paralogues of the 12 salmonid species, northern pike (Esox lucius) and sea bass (Dicentrarchus labrax) are provided. PRDM9 alleles in rainbow trout and Atlantic salmon: Fasta sequences of the PRDM9α alleles identified in two paralogs (α1.a.1-2 and α2.2) in two salmonid species, Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss), as well as their allele frequencies and their amino acid diversity at the DNA-binding residues are provided. Prediction of CGI-associated TSS in salmonids: Data and scripts in the S2 analysis to predict CGI-associated TSSs in salmonids are given. Scripts: Scripts are provided to reproduce read mapping, variant calling, physical and statistical phasing, polarisation, reconstruction of the LD-based map, analysis of the LD-based maps, analysis of the DMC1 ChIP-seq data and final figures of the paper. Data_Scripts_Raynaud_et_al_2024.tar.gz