{
  "abstract": "The human Y chromosome remains underrepresented in genomic resources because its repetitive architecture is difficult to resolve and poorly represented by any single reference. Here, we present 142 curated near-complete de novo Y chromosome assemblies spanning 98 terminal-marker-defined lineages across 17 haplogroup clades and 180,000 years of evolution, establishing a population-scale sequence and annotation resource for the chromosome. Across 100 quality-filtered AZFc intervals, recurrent inversions, deletions and complex rearrangements resolve into 12 structural haplotypes, while DAZ, RBMY and TSPY families show distinct paralogue- and array-specific evolution. Complete centromere and Yq12 sequences reveal extensive lineage-specific change within comparatively stable higher-order architectures, and haplotype-resolved methylomes show distinct epigenetic states among similar repeat copies. The reference panel reduces analytical bias: in testis Iso-Seq data, the best-matching assembly increased median DAZ transcript alignment identity from 91.7% to 99.9% and improved isoform annotation. Together, this resource enables analysis of Y-chromosome structural, evolutionary and reproductive variation.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 43,
  "authors": [
    {
      "name": "P. Hallast"
    },
    {
      "name": "A. Rhie"
    },
    {
      "name": "M. Loftus"
    },
    {
      "name": "M. Mazzetto"
    },
    {
      "name": "P. Ebert"
    },
    {
      "name": "S. Gao"
    },
    {
      "name": "G. V. Martino"
    },
    {
      "name": "P. A. Audano"
    },
    {
      "name": "H. Ashraf"
    },
    {
      "name": "K. Pal"
    },
    {
      "name": "R. Siford"
    },
    {
      "name": "J. Ebler"
    },
    {
      "name": "S. Koren"
    },
    {
      "name": "D. Yoo"
    },
    {
      "name": "K. Kim"
    },
    {
      "name": "Y. Jiang"
    },
    {
      "name": "N. F. Hansen"
    },
    {
      "name": "P. Hebbar"
    },
    {
      "name": "T. Kanno"
    },
    {
      "name": "O. Purnoch"
    },
    {
      "name": "C. Montano"
    },
    {
      "name": "J. Lin"
    },
    {
      "name": "K. K. Oshima"
    },
    {
      "name": "L. Ren"
    },
    {
      "name": "A. Guarracino"
    },
    {
      "name": "M. Jensen"
    },
    {
      "name": "B. J. Pinto"
    },
    {
      "name": "D. Porubsky"
    },
    {
      "name": "S. Kuziel"
    },
    {
      "name": "L. Ni"
    },
    {
      "name": "J. Li"
    },
    {
      "name": "P. Balachandran"
    },
    {
      "name": "F. Yilmaz"
    },
    {
      "name": "Human Genome Structural Variation Consortium (HGSVC)"
    },
    {
      "name": "Human Pangenome Reference Consortium (HPRC)"
    },
    {
      "name": "J. O. Korbel"
    },
    {
      "name": "B. Paten"
    },
    {
      "name": "M. Gerstein"
    },
    {
      "name": "K. D. Makova"
    },
    {
      "name": "X. Shi"
    },
    {
      "name": "E. Eichler"
    },
    {
      "name": "C. R. Beck"
    },
    {
      "name": "M. Wilson"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/842cchx2m87gn.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.06.03.729890",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.06.03.729890v2.full",
  "id": "842cchx2m87gn",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.06.03.729890v2",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ],
    [
      "openalex",
      "1311|Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities"
    ]
  ],
  "openalex": "W7163761234",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.06.03.729890v2.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-06-03",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/842cchx2m87gn.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:26:13Z",
      "native_id": "10.64898/2026.06.03.729890",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.06.03.729890v2"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures",
  "title_text": "Population-scale Y chromosome assemblies reveal recurrent remodeling within constrained architectures",
  "type": "preprint",
  "updated_at": "2026-10-30T12:26:13Z",
  "url": "https://research.draconitic.com/paper/842cchx2m87gn",
  "venue": "bioRxiv",
  "versions": []
}