Evidence map›Paper›PMID 42561917›Full record

ArticleCell2026

The complete genome of a songbird.

Giulio Formenti, Nivesh Jain, Jack A Medico, Marco Sollitto, Dmitry Antipov, Suziane Barcellos, Matthew Biegler, Inês Borges, J King Chang, Ying Chen and 39 more

Abstract read
PubMed Publisher
In one paragraph

Article in Cell, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. The diploid reference genome of a human embryonic stem cell line.bioRxiv : the preprint server for biology · 2026
    Article
  4. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

49 authors.

Giulio FormentiThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA. Electronic address: gformenti@rockefeller.edu.
Nivesh JainThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Jack A MedicoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Marco SollittoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; Department of Biology, University of Florence, Sesto Fiorentino, Florence 5001, Italy.
Dmitry AntipovGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Suziane BarcellosThe Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
Matthew BieglerThe Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
Inês BorgesCentre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany.
J King ChangEvolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia.
Ying ChenThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Haoyu ChengDepartment of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06520, USA.
Helena B da ConceiçãoCentro de Oncologia Molecular, Hospital Sirio Libanes, São Paulo 01308-050, Brazil.
Matthew DavenportThe Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
Lorraine De OliveiraCentro de Oncologia Molecular, Hospital Sirio Libanes, São Paulo 01308-050, Brazil.
Erick DuarteThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Gillian DurhamField Research Center, The Rockefeller University, Millbrook, NY 12545, USA.
Jonathan FennComputational 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.
Niamh FordeDiscovery 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.
Pedro A GalanteCentro de Oncologia Molecular, Hospital Sirio Libanes, São Paulo 01308-050, Brazil.
Kenji GerhardtDepartment of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
Alice M GianiNash 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.
Simona GiuntaLaboratory of Genome Evolution, Department of Biology & Biotechnologies, Charles Darwin University of Rome "La Sapienza", Rome 00185, Italy.
Juhyun KimGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Aleksey KomissarovNeapolis University Pafos, Paphos, Cyprus.
Bonhwang KooThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Sergey KorenGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Denis LarkinDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of London, 4 Royal College St., London NW10TU, UK.
Chul LeeThe Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
Heng LiDepartment of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Kateryna D MakovaDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Patrick MastersonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Terence MurphyNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Kirsty McCaffreyThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Rafael L V MercuriDepartment of Biomedical Informatics and Data Science, Yale School of Medicine, New Haven, CT 06520, USA.
Yeojung NaDepartment of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
Mary J O'ConnellComputational 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; Natural History Museum, Cromwell Rd., South Kensington, London SW7 5BD, UK.
Shujun OuDepartment of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
Adam M PhillippyGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Marina PopovaThe Center for Bio- and Medical Technologies, Moscow 121205, Russia.
Arang RhieGenome Informatics Section, Center for Genomics and Data Science Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
Francisco J Ruiz-RuanoCentre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany; Bonn Institute for Organismal Biology, Animal Biodiversity, University of Bonn, 53115 Bonn, Germany.
Simona SecomandiThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; The Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA.
Linnéa SmedsDepartment of Biology, Penn State University, University Park, PA 16802, USA.
Alexander SuhCentre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany; Bonn Institute for Organismal Biology, Animal Biodiversity, University of Bonn, 53115 Bonn, Germany.
Tatiana TilleyThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Niki VontzouCentre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, Adenauerallee 160, 53113 Bonn, Germany; School of Biological Sciences, University of East Anglia, Norwich, UK.
Paul D WatersEvolution & Ecology Research Centre, School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia.
Jennifer BalaccoThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA.
Erich D JarvisThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY 10065, USA; The Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY 10065, USA; Field Research Center, The Rockefeller University, Millbrook, NY 12545, USA. Electronic address: ejarvis@rockefeller.edu.

Funding

Gfastar: a C++ library and a tool suite to aid Telomere-to-Telomere genome assemblyR03HG013362 · NHGRI · ROCKEFELLER UNIVERSITY · PI FORMENTI, GIULIO · 2024 to 2024
$170k
NHGRI NIH HHS R03 HG013362
6 · The paper itself

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.

Indexed as

FinchesGenomeSongbirdsAnimalsCentromereCentromere Protein BGenomicsTelomereCentromere Protein Bampliconic gene arraysCENPsatellitessegmental duplicationsT2TTaeniopygia guttatatelomere-to-telomereTgut191ATgut716Azebra finch

Identifiers

PMID42561917

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.