Long-read sequencing of primate testis and human sperm allows identification of recombination events in individuals

Homologous recombination rearranges genetic information during meiosis, creating new combinations of the genome while also introducing mutations, and influencing GC content. Here we report direct detection of recombination events using highly accurate long-read sequencing from testis tissue of 16 individuals across six primate species and three human sperm samples. Based on methylation patterns, we classify sequencing reads as originating from either somatic or germline cells. We identify 2881 crossovers, 2314 simple gene conversions, and 555 complex events, and analyze their chromosomal distribution. Crossovers are more telomeric, showing stronger concordance with recombination maps than gene conversions. Human samples align with a double-strand break map, whereas other species differ, consistent with variation in PRDM9-directed breaks, although the recombination process is otherwise conserved. Gene conversion tracts are short and of similar length across species (mean 22-95 bp), implying that most non-crossover events are undetectable. We observe GC-biased gene conversion for both single and multiple-SNV events, including sites flanking crossovers. We infer longer gene conversion tracts associated with crossovers (318-688 bp) than with non-crossovers. Highly accurate long-read sequencing combined with methylation-based classification of reads to specific cell types provides a powerful way of studying recombination events in single individuals of any mammalian species.