{
  "abstract": "The Drosophila melanogaster Y chromosome is currently known to contain 13 single-copy protein-coding genes, 6 of which are essential for male fertility, as well as several noncoding genes and abundant repetitive DNA. Localization of Y-linked sequences has traditionally relied on labor-intensive crosses using Kennison's translocation strains, which map Y-linked loci by generating flies deficient for each of the 6 Y chromosome fertility regions (ks-1, ks-2, kl-1, kl-2, kl-3, and kl-5). Here, we present Digital Kennison, a computational pipeline that recasts this classical mapping strategy as a sequence-based analysis. The pipeline queries 8 genomic databases derived from Kennison's strains using BLAST and read coverage, assigning sequences to fertility regions or the centromeric region with a calibrated confidence score. We benchmarked the method on 60 Y-linked sequences spanning all 7 regions, including single-copy protein-coding genes, Mst77Y family members, noncoding RNAs, and the centromere. Digital Kennison achieved 97% precision while resolving challenging cases, including boundary-spanning genes (PRY and Ppr-Y), fragmented Mst77Y copies, and FDY, which has a closely related autosomal paralog. Beyond validating known localizations, the pipeline localized the unmapped gene CG41561 to the kl-1region and reassigned the transcript CR40629-RC from the kl-2 region to kl-5. It also localized 7 of 16 recently transferred Y-linked sequences, including 4 with high confidence. Applied to 904 R6 scaffolds, Digital Kennison assigned 75% to fertility regions, including 5 currently annotated as autosomal-pericentromeric. Digital Kennison reduces sequence localization from weeks of genetic crosses to minutes of computation while preserving the power of classical translocation mapping.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Fabiana Uno",
      "orcid": "0000-0001-9310-2185"
    },
    {
      "name": "A Bernardo Carvalho",
      "orcid": "0000-0001-8959-6469"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/90n4we57czyf4.bib",
  "cited_by": 0,
  "doi": "10.1093/g3journal/jkag253",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13732432/",
  "id": "90n4we57czyf4",
  "issns": [
    "2160-1836"
  ],
  "landing_url": "https://doi.org/10.1093/g3journal/jkag253",
  "language": "en",
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "AcademicSubjects/SCI01140"
    ],
    [
      "heading",
      "AcademicSubjects/SCI01180"
    ],
    [
      "heading",
      "Investigation"
    ],
    [
      "openalex",
      "1311|Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities"
    ]
  ],
  "openalex": "W7212131307",
  "pdf_url": "https://academic.oup.com/g3journal/advance-article-pdf/doi/10.1093/g3journal/jkag253/71022018/jkag253.pdf",
  "pmcid": "PMC13732432",
  "pmid": "42721288",
  "published": "2026-09-10",
  "publisher": "Oxford University Press",
  "ris": "https://research.draconitic.com/paper/90n4we57czyf4.ris",
  "sources": [
    {
      "first_seen": "2026-11-08T12:22:25Z",
      "native_id": "PMC13732432",
      "source": "pmc",
      "url": "https://doi.org/10.1093/g3journal/jkag253"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1311|Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Digital Kennison: a bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome",
  "title_text": "Digital Kennison: a bioinformatics pipeline for rapid mapping of sequences to the Drosophila melanogaster Y chromosome",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T12:22:25Z",
  "url": "https://research.draconitic.com/paper/90n4we57czyf4",
  "venue": "G3: Genes | Genomes | Genetics",
  "versions": []
}