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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\n                    <jats:italic>HYP1<\/jats:italic>\n                    , the most highly expressed gene that encodes a protein secreted by potato cyst nematodes during parasitism. Importantly,\n                    <jats:italic>HYP1<\/jats:italic>\n                    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\n                    <jats:italic>HYP1<\/jats:italic>\n                    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\n                    <jats:italic>de novo<\/jats:italic>\n                    mutations at\n                    <jats:italic>HYP1<\/jats:italic>\n                    , and we interpret our findings in light of key population genetic parameters as well as the genetic diversity surrounding\n                    <jats:italic>HYP1<\/jats:italic>\n                    and across the genome.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0358232","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T17:46:52Z","timestamp":1789494412000},"page":"e0358232","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2008-8957","authenticated-orcid":true,"given":"Vincent C. 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A.","family":"Raza","sequence":"additional","affiliation":[{"name":"Crop Science Centre","place":["Cambridge, United Kingdom"],"department":["Department of Plant Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luisa","family":"Kalkert","sequence":"additional","affiliation":[{"name":"Crop Science Centre","place":["Cambridge, United Kingdom"],"department":["Department of Plant Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Harpum","sequence":"additional","affiliation":[{"name":"Crop Science Centre","place":["Cambridge, United Kingdom"],"department":["Department of Plant Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lukas A.","family":"Burkhardt","sequence":"additional","affiliation":[{"name":"ETH Z\u00fcrich","place":["Z\u00fcrich, Switzerland"],"department":["Institute of Microbiology, Department of 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