The complete sequence of a human Y chromosome

Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer L. Gerton, Patrick G. S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E. G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel J. O’Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova and Adam M. Phillippy ()
Additional contact information
Arang Rhie: National Institutes of Health
Sergey Nurk: National Institutes of Health
Monika Cechova: Masaryk University
Savannah J. Hoyt: University of Connecticut
Dylan J. Taylor: Johns Hopkins University
Nicolas Altemose: University of California
Paul W. Hook: Johns Hopkins University
Sergey Koren: National Institutes of Health
Mikko Rautiainen: National Institutes of Health
Ivan A. Alexandrov: Federal Research Center of Biotechnology of the Russian Academy of Sciences
Jamie Allen: Wellcome Genome Campus, Hinxton
Mobin Asri: University of California Santa Cruz
Andrey V. Bzikadze: University of California
Nae-Chyun Chen: Johns Hopkins University
Chen-Shan Chin: GeneDX Holdings Corp
Mark Diekhans: University of California Santa Cruz
Paul Flicek: Wellcome Genome Campus, Hinxton
Giulio Formenti: The Rockefeller University
Arkarachai Fungtammasan: DNAnexus, Inc.
Carlos Garcia Giron: Wellcome Genome Campus, Hinxton
Erik Garrison: University of Tennessee Health Science Center
Ariel Gershman: Johns Hopkins University
Jennifer L. Gerton: Stowers Institute for Medical Research
Patrick G. S. Grady: University of Connecticut
Andrea Guarracino: University of Tennessee Health Science Center
Leanne Haggerty: Wellcome Genome Campus, Hinxton
Reza Halabian: University of Münster
Nancy F. Hansen: National Institutes of Health
Robert Harris: Pennsylvania State University
Gabrielle A. Hartley: University of Connecticut
William T. Harvey: University of Washington School of Medicine
Marina Haukness: University of California Santa Cruz
Jakob Heinz: Johns Hopkins University
Thibaut Hourlier: Wellcome Genome Campus, Hinxton
Robert M. Hubley: Institute for Systems Biology
Sarah E. Hunt: Wellcome Genome Campus, Hinxton
Stephen Hwang: Johns Hopkins University
Miten Jain: Northeastern University
Rupesh K. Kesharwani: One Baylor Plaza
Alexandra P. Lewis: University of Washington School of Medicine
Heng Li: Dana-Farber Cancer Institute
Glennis A. Logsdon: University of Washington School of Medicine
Julian K. Lucas: University of California Santa Cruz
Wojciech Makalowski: University of Münster
Christopher Markovic: Genome Technology Access Center at the McDonnell Genome Institute, Washington University
Fergal J. Martin: Wellcome Genome Campus, Hinxton
Ann M. Mc Cartney: National Institutes of Health
Rajiv C. McCoy: Johns Hopkins University
Jennifer McDaniel: National Institute of Standards and Technology
Brandy M. McNulty: University of California Santa Cruz
Paul Medvedev: Pennsylvania State University
Alla Mikheenko: Saint Petersburg State University
Katherine M. Munson: University of Washington School of Medicine
Terence D. Murphy: National Library of Medicine, National Institutes of Health
Hugh E. Olsen: University of California Santa Cruz
Nathan D. Olson: National Institute of Standards and Technology
Luis F. Paulin: One Baylor Plaza
David Porubsky: University of Washington School of Medicine
Tamara Potapova: Stowers Institute for Medical Research
Fedor Ryabov: Masters Program in National Research University Higher School of Economics
Steven L. Salzberg: Johns Hopkins University
Michael E. G. Sauria: Johns Hopkins University
Fritz J. Sedlazeck: One Baylor Plaza
Kishwar Shafin: Google Inc.
Valery A. Shepelev: Institute of Molecular Genetics
Alaina Shumate: Johns Hopkins University
Jessica M. Storer: Institute for Systems Biology
Likhitha Surapaneni: Wellcome Genome Campus, Hinxton
Angela M. Taravella Oill: Arizona State University
Françoise Thibaud-Nissen: National Library of Medicine, National Institutes of Health
Winston Timp: Johns Hopkins University
Marta Tomaszkiewicz: Pennsylvania State University
Mitchell R. Vollger: University of Washington School of Medicine
Brian P. Walenz: National Institutes of Health
Allison C. Watwood: Pennsylvania State University
Matthias H. Weissensteiner: Pennsylvania State University
Aaron M. Wenger: Pacific Biosciences
Melissa A. Wilson: Arizona State University
Samantha Zarate: Johns Hopkins University
Yiming Zhu: One Baylor Plaza
Justin M. Zook: National Institute of Standards and Technology
Evan E. Eichler: University of Washington School of Medicine
Rachel J. O’Neill: University of Connecticut
Michael C. Schatz: Johns Hopkins University
Karen H. Miga: University of California Santa Cruz
Kateryna D. Makova: Pennsylvania State University
Adam M. Phillippy: National Institutes of Health

Nature, 2023, vol. 621, issue 7978, 344-354

Abstract: Abstract The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1–3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Date: 2023
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Citations: View citations in EconPapers (7)

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DOI: 10.1038/s41586-023-06457-y

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