Genome-wide recombination map construction from single individuals using linked-read sequencing

Meiotic recombination rates vary across the genome, often involving localized crossover ”hotspots” and ”coldspots”. Studying the molecular basis and mechanisms underlying this variation has been challenging due to the high cost and effort to construct individualized genome-wide maps of recombination crossovers. Here we introduce a new method, called ReMIX, to detect crossovers from gamete DNA of a single individual using Illumina sequencing of 10X Genomics linked-read libraries. ReMIX reconstructs haplotypes and identifies the valuable rare molecules spanning crossover breakpoints, allowing quantification of the genomic location and intensity of meiotic recombination. Using a single mouse and stickleback fish, we demonstrate how ReMIX faithfully recovers recombination hotspots and landscapes that have previously been built using hundreds of offspring. ReMIX provides a high-resolution, high-throughput, low-cost approach to quantify recombination variation across the genome, providing an exciting opportunity to study recombination among multiple individuals in diverse organisms. ReMIX is publicly available at https://github.com/adreau/ReMIX.