{
  "abstract": "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.",
  "abstract_shown": true,
  "affiliations": [
    "Crop Science Centre, Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom",
    "Institute of Microbiology, Department of Biology, ETH Zürich, Zürich, Switzerland",
    "Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands"
  ],
  "article_type": "Research Article",
  "arxiv": null,
  "author_total": 8,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Vincent C. T. Hanlon"
    },
    {
      "affs": [
        1
      ],
      "name": "Unnati Sonawala"
    },
    {
      "affs": [
        2
      ],
      "name": "Cian A. A. Raza"
    },
    {
      "name": "Luisa Kalkert"
    },
    {
      "name": "George Harpum"
    },
    {
      "name": "Lukas A. Burkhardt"
    },
    {
      "name": "Johannes Helder"
    },
    {
      "name": "Sebastian Eves-van den Akker"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5ncfhtpbja97k.bib",
  "cited_by": 0,
  "doi": "10.1371/journal.pone.0358232",
  "fulltext_url": null,
  "id": "5ncfhtpbja97k",
  "issns": [
    "1932-6203"
  ],
  "landing_url": "https://doi.org/10.1371/journal.pone.0358232",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1110|Nematode management and characterization studies"
    ],
    [
      "plos",
      "/Biology and life sciences/Biochemistry/Nucleotides"
    ],
    [
      "plos",
      "/Biology and life sciences/Ecology/Ecological metrics/Species diversity"
    ],
    [
      "plos",
      "/Biology and life sciences/Evolutionary biology/Population genetics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Genomics/Animal genomics/Amphibian genomics"
    ],
    [
      "plos",
      "/Biology and life sciences/Genetics/Population genetics"
    ],
    [
      "plos",
      "/Biology and life sciences/Molecular biology/Molecular biology techniques/Sequencing techniques/DNA sequencing"
    ],
    [
      "plos",
      "/Biology and life sciences/Organisms/Eukaryota/Fungi/Yeast"
    ],
    [
      "plos",
      "/Biology and life sciences/Population biology/Population genetics"
    ],
    [
      "plos",
      "/Ecology and environmental sciences/Ecology/Ecological metrics/Species diversity"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Bioinformatics/Sequence analysis/Sequence alignment"
    ],
    [
      "plos",
      "/Research and analysis methods/Database and informatics methods/Bioinformatics/Sequence analysis/Sequence motif analysis"
    ],
    [
      "plos",
      "/Research and analysis methods/Molecular biology techniques/Sequencing techniques/DNA sequencing"
    ]
  ],
  "openalex": "W7213361344",
  "pdf_url": "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0358232&type=printable",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-15",
  "publisher": "Public Library of Science",
  "ris": "https://research.draconitic.com/paper/5ncfhtpbja97k.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:49Z",
      "native_id": "10.1371/journal.pone.0358232",
      "source": "plos",
      "url": "https://doi.org/10.1371/journal.pone.0358232"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "plos:bioinformatics",
      "subfield": "bioinformatics"
    },
    {
      "field": "biology",
      "origin": "plos:ecology",
      "subfield": "ecology"
    },
    {
      "field": "biology",
      "origin": "plos:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations",
  "title_text": "Diversity at the HYP1 locus in potato cyst nematodes does not result from developmentally-programmed somatic mutations",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:49Z",
  "url": "https://research.draconitic.com/paper/5ncfhtpbja97k",
  "venue": "PLOS One",
  "versions": []
}