Title: Parent–progeny sequencing indicates higher mutation rates in heterozygotes
Abstract: Mutation rates vary within genomes; here, by calling mutation events directly using a parent–offspring sequencing strategy in Arabidopsis, replicated in the rice and honey bee genomes, mutation rates are found to be higher in heterozygotes and in proximity to crossover events. To discover why mutations rates vary within genomes, Laurence Hurst and colleagues examined intragenomic variation in mutation rate directly in Arabidopsis, rice and the honey bee using a parent–offspring sequencing strategy. They find that mutation rates are higher in heterozygotes and in proximity to crossover events. Mutations occur disproportionately more often in heterozygous than in homozygous domains and gene clusters under purifying selection (commonly homozygous) and under balancing selection (mainly heterozygous) have low and high mutation rates, respectively. The authors suggest that extremely weak selection on the mutation rate may therefore not be necessary to explain why mutational hot and cold spots might correspond to regions under positive/balancing and purifying selection, respectively. Mutation rates vary within genomes, but the causes of this remain unclear1. As many prior inferences rely on methods that assume an absence of selection, potentially leading to artefactual results2, we call mutation events directly using a parent–offspring sequencing strategy focusing on Arabidopsis and using rice and honey bee for replication. Here we show that mutation rates are higher in heterozygotes and in proximity to crossover events. A correlation between recombination rate and intraspecific diversity is in part owing to a higher mutation rate in domains of high recombination/diversity. Implicating diversity per se as a cause, we find an ∼3.5-fold higher mutation rate in heterozygotes than in homozygotes, with mutations occurring in closer proximity to heterozygous sites than expected by chance. In a genome that is a patchwork of heterozygous and homozygous domains, mutations occur disproportionately more often in the heterozygous domains. If segregating mutations predispose to a higher local mutation rate, clusters of genes dominantly under purifying selection (more commonly homozygous) and under balancing selection (more commonly heterozygous), might have low and high mutation rates, respectively. Our results are consistent with this, there being a ten times higher mutation rate in pathogen resistance genes, expected to be under positive or balancing selection. Consequently, we do not necessarily need to evoke extremely weak1,2 selection on the mutation rate to explain why mutational hot and cold spots might correspond to regions under positive/balancing and purifying selection, respectively3,4.