{
  "abstract": "Bird genomes are the smallest among amniotes; however, they remain challenging to assemble due to their structural complexity. This study presents a fully phased diploid telomere-to-telomere reference genome for the zebra finch (Taeniopygia guttata), a model organism for neuroscience and evolutionary genomics. Combining sequencing strategies allowed the closing of nearly all gaps, adding ∼90 Mbp of sequence (7.8%). The assembly contains gapless sequences for all microchromosomes, including the elusive dot chromosomes with their distinctive architecture. The genome was comprehensively annotated for genes, repeats, and structural variants. Complete centromeres were identified, along with candidate DNA-binding centromere protein B (CENP-B) homologs, suggesting that birds possess a kinetochore-associated CENP system similar to that of mammals. Relative to the previous reference generated by the Vertebrate Genomes Project, 2,710 (8.13%) previously unassembled or unannotated genes were identified. This complete genome of a songbird serves as a public reference and illuminates avian genome architecture and function.",
  "abstract_shown": true,
  "affiliations": [
    "The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA. Electronic address: gformenti@rockefeller.edu",
    "The Vertebrate Genome Laboratory, The Rockefeller University, 230 York Ave, New York, USA",
    "The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA",
    "The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; Department of Biology, University of Florence, Sesto Fiorentino, Florence 5001, Italy",
    "Department of Biology, University of Florence, 50019, Sesto Fiorentino, FI, Italy",
    "The Vertebrate Genome Laboratory, The Rockefeller University, 130 York Ave, New York, USA",
    "Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA",
    "Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, USA",
    "The Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA",
    "The Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Ave, New York, USA",
    "Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany",
    "Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia",
    "Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoologisches Forschungsmuseum A. Koenig, Adenauerallee 160, D-3113 Bonn, Germany",
    "Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06520, USA",
    "Centro de Oncologia Molecular, Hospital Sirio Libanes, São Paulo 01308-050, Brazil",
    "Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, 06520 USA",
    "Hospital Sirio-Libanes, Sao Paulo, Brazil",
    "Field Research Center, The Rockefeller University, Millbrook, NY 12545, USA",
    "Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2RD, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK",
    "Field Research Center, The Rockefeller University, 45 Tyrrel Road, Millbrook, NY, USA",
    "Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK; Centre for Reproductive Health, Institute for Regeneration and Repair, University of Edinburgh, 5 Little France Drive, Edinburgh EH16 4UU, UK",
    "Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2RD, UK",
    "Division of Evolution, Infection and Genomics, School of Biological Sciences",
    "Centre for Reproductive Health, Institute for Regeneration and Repair, University of Edinburgh",
    "Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK",
    "Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA",
    "Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA",
    "Aglabx, Paphos, Cyprus",
    "Laboratory of Genome Evolution, Department of Biology & Biotechnologies, Charles Darwin University of Rome \"La Sapienza\", Rome 00185, Italy",
    "Neapolis University Pafos, Paphos, Cyprus",
    "Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA, 43210",
    "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029",
    "Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029",
    "Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College St., London NW10TU, UK",
    "Giunta Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, University of Rome \"La Sapienza\", Rome, Italy, 00185",
    "Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College St, London, UK NW10TU",
    "Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA",
    "Department of Biology, Penn State University, University Park, PA 16802, USA",
    "Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115",
    "Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215"
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 49,
  "authors": [
    {
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        0,
        1
      ],
      "name": "Giulio Formenti",
      "orcid": "0000-0002-7554-5991"
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        1
      ],
      "name": "Nivesh Jain",
      "orcid": "0000-0002-8134-2904"
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    {
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        1
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      "name": "Jack A Medico",
      "orcid": "0000-0003-1855-0855"
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        4,
        5
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      "name": "Marco Sollitto",
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      "name": "Dmitry Antipov",
      "orcid": "0000-0002-6087-0660"
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      "name": "Suziane Alves Barcellos",
      "orcid": "0000-0003-2863-9976"
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      "name": "Matthew T. Biegler",
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      "name": "Ines Borges"
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      "name": "Jong-How Chang",
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      "name": "Ying Chen",
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      "name": "Haoyu Cheng",
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      "name": "Helena B. Conceição",
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      "name": "Matthew H. Davenport",
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      "name": "Zhongwang Li",
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        16
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      "name": "Erick Duarte",
      "orcid": "0009-0009-1100-6583"
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      "name": "Gillian P. Durham"
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      "name": "Jonathan Fenn",
      "orcid": "0000-0002-9255-6975"
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        21,
        22
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      "name": "Niamh Forde",
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        24
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      "name": "Pedro A. F. Galante",
      "orcid": "0000-0002-4820-4155"
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        7
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      "name": "Kenji Gerhardt"
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        26,
        27
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      "name": "Alice Maria Giani",
      "orcid": "0000-0001-8805-7826"
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        1
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      "name": "Simona Giunta",
      "orcid": "0000-0002-6666-9271"
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    {
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        6,
        7
      ],
      "name": "Juhyun Kim",
      "orcid": "0000-0002-0321-9388"
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    {
      "affs": [
        29,
        16
      ],
      "name": "Aleksey S. Komissarov",
      "orcid": "0000-0001-6981-7316"
    },
    {
      "affs": [
        2,
        30
      ],
      "name": "Bonhwang Koo",
      "orcid": "0000-0002-5181-6267"
    },
    {
      "affs": [
        6,
        31,
        32
      ],
      "name": "Sergey Koren",
      "orcid": "0000-0002-1472-8962"
    },
    {
      "affs": [
        33,
        34
      ],
      "name": "Denis M. Larkin",
      "orcid": "0000-0001-7859-6201"
    },
    {
      "affs": [
        8,
        35
      ],
      "name": "Chul Lee",
      "orcid": "0000-0002-9403-0774"
    },
    {
      "affs": [
        36,
        9
      ],
      "name": "Heng Li",
      "orcid": "0000-0003-4874-2874"
    },
    {
      "affs": [
        37,
        38,
        39
      ],
      "name": "Kateryna D. Makova",
      "orcid": "0000-0002-6212-9526"
    },
    {
      "name": "Patrick Masterson"
    },
    {
      "name": "Terence D. Murphy",
      "orcid": "0000-0001-9311-9745"
    },
    {
      "affs": [
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      ],
      "name": "Kirsty McCaffrey",
      "orcid": "0009-0005-4760-6653"
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      "affs": [
        13,
        1
      ],
      "name": "Rafael L. V. Mercuri",
      "orcid": "0000-0003-0223-3089"
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    {
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        25,
        16
      ],
      "name": "Yeojung Na"
    },
    {
      "affs": [
        30
      ],
      "name": "Mary J. O’Connell"
    },
    {
      "affs": [
        25,
        21,
        22
      ],
      "name": "Shujun Ou",
      "orcid": "0000-0001-5938-7180"
    },
    {
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        6,
        30
      ],
      "name": "Adam M. Phillippy",
      "orcid": "0000-0003-2983-8934"
    },
    {
      "affs": [
        7
      ],
      "name": "Marina A. Popova",
      "orcid": "0009-0000-4472-0497"
    },
    {
      "affs": [
        6,
        27
      ],
      "name": "Arang Rhie",
      "orcid": "0000-0002-9809-8127"
    },
    {
      "affs": [
        7
      ],
      "name": "Francisco J. Ruíz-Ruano",
      "orcid": "0000-0002-5391-301X"
    },
    {
      "name": "Simona Secomandi",
      "orcid": "0000-0001-8597-6034"
    },
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        37,
        1
      ],
      "name": "Linnéa Smeds",
      "orcid": "0000-0002-8415-9259"
    },
    {
      "name": "Alexander Suh",
      "orcid": "0000-0002-8979-9992"
    },
    {
      "affs": [
        2
      ],
      "name": "Tatiana Tilley",
      "orcid": "0009-0001-9277-7743"
    },
    {
      "affs": [
        1
      ],
      "name": "Niki Vontzou",
      "orcid": "0000-0003-3276-6599"
    },
    {
      "affs": [
        11
      ],
      "name": "Paul D. Waters",
      "orcid": "0000-0002-4689-8747"
    },
    {
      "affs": [
        2,
        11
      ],
      "name": "Jennifer Balacco",
      "orcid": "0000-0001-7102-1632"
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      "affs": [
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      "name": "Erich David Jarvis",
      "orcid": "0000-0001-8931-5049"
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  ],
  "bibtex": "https://research.draconitic.com/paper/bavjf8fv7hyk7.bib",
  "cited_by": 16,
  "doi": "10.1016/j.cell.2026.07.018",
  "fulltext_url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC13723774/",
  "id": "bavjf8fv7hyk7",
  "issns": [
    "0092-8674",
    "1097-4172"
  ],
  "landing_url": "https://doi.org/10.1016/j.cell.2026.07.018",
  "language": "en",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
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      "Article"
    ],
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      "1312|Genomics and Phylogenetic Studies"
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  "openalex": "W4415189576",
  "pdf_url": null,
  "pmcid": "PMC12754717",
  "pmid": "41480146",
  "published": "2026-08-01",
  "publisher": "Cell Press",
  "ris": "https://research.draconitic.com/paper/bavjf8fv7hyk7.ris",
  "sources": [
    {
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      "url": "https://doi.org/10.1016/j.cell.2026.07.018"
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  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
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  ],
  "title": "The complete genome of a songbird",
  "title_text": "The complete genome of a songbird",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T13:20:41Z",
  "url": "https://research.draconitic.com/paper/bavjf8fv7hyk7",
  "venue": "Cell",
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}