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Peer-reviewedCC BYCell

The complete genome of a songbird

  • Giulio Formenti1,2
  • Nivesh Jain3,2
  • Jack A Medico3,2
  • Marco Sollitto4,5,6
  • Dmitry Antipov7,8
  • Suziane Alves Barcellos9,2
  • Matthew T. Biegler9,10
  • Ines Borges11,10
  • Jong-How Chang12,13
  • Ying Chen3,12
  • Haoyu Cheng14,2
  • Helena B. Conceição15,16
37 more authors
  • Matthew H. Davenport9,17
  • Zhongwang Li15,10
  • Erick Duarte3,17
  • Gillian P. Durham18,2
  • Jonathan Fenn19,20
  • Niamh Forde21,22,23
  • Pedro A. F. Galante15,24,25
  • Kenji Gerhardt26,8
  • Alice Maria Giani27,28
  • Simona Giunta29,2
  • Juhyun Kim7,8
  • Aleksey S. Komissarov30,17
  • Bonhwang Koo3,31
  • Sergey Koren7,32,33
  • Denis M. Larkin34,35
  • Chul Lee9,36
  • Heng Li37,10
  • Kateryna D. Makova38,39,40
  • Patrick Masterson
  • Terence D. Murphy
  • Kirsty McCaffrey3
  • Rafael L. V. Mercuri14,2
  • Yeojung Na26,17
  • Mary J. O’Connell31
  • Shujun Ou26,22,23
  • Adam M. Phillippy7,31
  • Marina A. Popova8
  • Arang Rhie7,28
  • Francisco J. Ruíz-Ruano8
  • Simona Secomandi
  • Linnéa Smeds38,2
  • Alexander Suh
  • Tatiana Tilley3
  • Niki Vontzou2
  • Paul D. Waters12
  • Jennifer Balacco3,12
  • Erich David Jarvis2
40 affiliations
  1. 1The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA. Electronic address: [email protected]
  2. 2The Vertebrate Genome Laboratory, The Rockefeller University, 230 York Ave, New York, USA
  3. 3The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA
  4. 4The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; Department of Biology, University of Florence, Sesto Fiorentino, Florence 5001, Italy
  5. 5Department of Biology, University of Florence, 50019, Sesto Fiorentino, FI, Italy
  6. 6The Vertebrate Genome Laboratory, The Rockefeller University, 130 York Ave, New York, USA
  7. 7Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
  8. 8Genome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, USA
  9. 9The Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA
  10. 10The Laboratory of Neurogenetics of Language, The Rockefeller University, 1230 York Ave, New York, USA
  11. 11Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany
  12. 12Evolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
  13. 13Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Zoologisches Forschungsmuseum A. Koenig, Adenauerallee 160, D-3113 Bonn, Germany
  14. 14Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06520, USA
  15. 15Centro de Oncologia Molecular, Hospital Sirio Libanes, São Paulo 01308-050, Brazil
  16. 16Department of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT, 06520 USA
  17. 17Hospital Sirio-Libanes, Sao Paulo, Brazil
  18. 18Field Research Center, The Rockefeller University, Millbrook, NY 12545, USA
  19. 19Computational 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
  20. 20Field Research Center, The Rockefeller University, 45 Tyrrel Road, Millbrook, NY, USA
  21. 21Discovery 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
  22. 22Computational and Molecular Evolutionary Biology Group, School of Life Sciences, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
  23. 23Division of Evolution, Infection and Genomics, School of Biological Sciences
  24. 24Centre for Reproductive Health, Institute for Regeneration and Repair, University of Edinburgh
  25. 25Discovery and Translational Sciences Department, Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
  26. 26Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
  27. 27Nash 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
  28. 28Aglabx, Paphos, Cyprus
  29. 29Laboratory of Genome Evolution, Department of Biology & Biotechnologies, Charles Darwin University of Rome "La Sapienza", Rome 00185, Italy
  30. 30Neapolis University Pafos, Paphos, Cyprus
  31. 31Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA, 43210
  32. 32Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
  33. 33Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
  34. 34Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College St., London NW10TU, UK
  35. 35Giunta Laboratory of Genome Evolution, Department of Biology & Biotechnology Charles Darwin, University of Rome "La Sapienza", Rome, Italy, 00185
  36. 36Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College St, London, UK NW10TU
  37. 37Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
  38. 38Department of Biology, Penn State University, University Park, PA 16802, USA
  39. 39Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115
  40. 40Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215
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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.

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Cite

BibTeXRIS
BibTeX
@article{formenti2026complete,
  title = {{The complete genome of a songbird}},
  author = {Giulio Formenti and Nivesh Jain and Jack A Medico and Marco Sollitto and Dmitry Antipov and Suziane Alves Barcellos and Matthew T. Biegler and Ines Borges and Jong-How Chang and Ying Chen and Haoyu Cheng and Helena B. Conceição and Matthew H. Davenport and Zhongwang Li and Erick Duarte and Gillian P. Durham and Jonathan Fenn and Niamh Forde and Pedro A. F. Galante and Kenji Gerhardt and Alice Maria Giani and Simona Giunta and Juhyun Kim and Aleksey S. Komissarov and Bonhwang Koo and Sergey Koren and Denis M. Larkin and Chul Lee and Heng Li and Kateryna D. Makova and Patrick Masterson and Terence D. Murphy and Kirsty McCaffrey and Rafael L. V. Mercuri and Yeojung Na and Mary J. O’Connell and Shujun Ou and Adam M. Phillippy and Marina A. Popova and Arang Rhie and Francisco J. Ruíz-Ruano and Simona Secomandi and Linnéa Smeds and Alexander Suh and Tatiana Tilley and Niki Vontzou and Paul D. Waters and Jennifer Balacco and Erich David Jarvis},
  journal = {Cell},
  year = {2026},
  month = aug,
  doi = {10.1016/j.cell.2026.07.018},
  url = {https://doi.org/10.1016/j.cell.2026.07.018},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - The complete genome of a songbird
AU  - Giulio Formenti
AU  - Nivesh Jain
AU  - Jack A Medico
AU  - Marco Sollitto
AU  - Dmitry Antipov
AU  - Suziane Alves Barcellos
AU  - Matthew T. Biegler
AU  - Ines Borges
AU  - Jong-How Chang
AU  - Ying Chen
AU  - Haoyu Cheng
AU  - Helena B. Conceição
AU  - Matthew H. Davenport
AU  - Zhongwang Li
AU  - Erick Duarte
AU  - Gillian P. Durham
AU  - Jonathan Fenn
AU  - Niamh Forde
AU  - Pedro A. F. Galante
AU  - Kenji Gerhardt
AU  - Alice Maria Giani
AU  - Simona Giunta
AU  - Juhyun Kim
AU  - Aleksey S. Komissarov
AU  - Bonhwang Koo
AU  - Sergey Koren
AU  - Denis M. Larkin
AU  - Chul Lee
AU  - Heng Li
AU  - Kateryna D. Makova
AU  - Patrick Masterson
AU  - Terence D. Murphy
AU  - Kirsty McCaffrey
AU  - Rafael L. V. Mercuri
AU  - Yeojung Na
AU  - Mary J. O’Connell
AU  - Shujun Ou
AU  - Adam M. Phillippy
AU  - Marina A. Popova
AU  - Arang Rhie
AU  - Francisco J. Ruíz-Ruano
AU  - Simona Secomandi
AU  - Linnéa Smeds
AU  - Alexander Suh
AU  - Tatiana Tilley
AU  - Niki Vontzou
AU  - Paul D. Waters
AU  - Jennifer Balacco
AU  - Erich David Jarvis
PY  - 2026
DA  - 2026/08/01
JO  - Cell
DO  - 10.1016/j.cell.2026.07.018
UR  - https://doi.org/10.1016/j.cell.2026.07.018
AB  - 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.
SN  - 0092-8674
SN  - 1097-4172
ER  -