Recombination processes inferred from long-read sequencing of primate testis and human sperm

Homologous recombination rearranges genetic information during meiosis to generate new combinations of the genome. Recombination also causes new mutations, affects the GC content of the genome and reduces selective interference. Here, we use HiFi long-read sequencing to directly detect crossover and gene conversion events from switches between the two haplotypes along single HiFi-reads from testis tissue of 16 individuals from six primate species as well as three human sperm samples. Based on DNA methylation calls, we classify the cellular origin of reads to either somatic or germline cells in the testis tissue. We identify 2881 simple crossovers, 2314 simple gene conversions, and 555 complex exchange events in the 19 samples and investigate their chromosomal distribution. We also find recombination among acrocentric chromosomes and between segmental duplication. Crossovers are more telomeric and correlate better with recombination maps than gene conversions. We show a strong concordance between a human double-strand break map and the human samples, but not for the other species, supporting differences in PRDM9-programmed double-strand breaks among species. We estimate the average gene conversion tract lengths to be similar and very short in all species (mean lengths 22-95 bp, fitting a geometric distribution). As a consequence of this, we estimate that 95-98% of all non-crossover events are not detectable, because they do not include any polymorphism. We detect a GC bias in the gene conversion of both single and multiple SNVs. GC-biased gene conversion also affects SNVs flanking crossover events. We use this to estimate that gene conversion events associated with crossover events have longer tract lengths (estimated averages 275-898 bp) than those associated with non-crossover events. Highly accurate long-read sequencing combined with methylation-based classification of reads to specific cell types provides a new, powerful way to identify many recombination events in single individuals of any mammalian species.