Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations

Most genetic diversity stems from spontaneous mutations, that is, errors in DNA repair or replication. But for dozens of organisms across the tree of life, mutations at specific loci are not spontaneous but developmentally programmed: effectively, some organisms edit their own DNA sequences. This is perhaps most common among pathogens and parasites, many of which use editing to diversify genes that produce important antigens. Plant-parasitic potato cyst nematodes are damaging agricultural pests that establish a lifelong feeding site inside the root of their host plant. We previously observed extensive diversity of rare alleles at HYP1, the most highly expressed gene that encodes a protein secreted by potato cyst nematodes during parasitism. Importantly, HYP1 alleles differ from each other by complex, in-frame rearrangements of short repeated sequence motifs within a single exon. Combining several lines of evidence, we previously hypothesized that potato cyst nematodes use developmentally-programmed mutations, or editing, to diversify HYP1 alleles in the soma. In the current work, we now test this hypothesis. We employ highly accurate long-read DNA sequencing of a simplified genetic system to identify potential rare edited alleles, we use a transgenic yeast system to describe large de novo mutations at HYP1, and we interpret our findings in light of key population genetic parameters as well as the genetic diversity surrounding HYP1 and across the genome. Significance StatementIn parasites, genetic diversity is valuable fuel for the coevolutionary arms race with their hosts. However, in parasitic nematode worms, low genetic diversity is often observed. Several other parasites and pathogens (e.g., single-celled eukaryotes) generate genetic diversity in an unusual way: they edit the DNA sequence of an important gene in their own genome, instead of waiting for rare spontaneous mutations to occur. This has never been observed in a plant parasite, but we previously described a major parasitism gene (HYP1) in plant-parasitic nematodes with such diverse DNA sequences that it looks like it could perhaps be edited. Now, we generate better data for a simplified genetic system and show that much of the observed HYP1 diversity was actually cryptic DNA sequencing errors. Although there is real genetic diversity at HYP1, it is best explained not by editing but by fundamental evolutionary forces that operate across the genome.