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