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The complete sequence of a human Y chromosome

Author

Listed:
  • Arang Rhie

    (National Institutes of Health)

  • Sergey Nurk

    (National Institutes of Health
    Oxford Nanopore Technologies Inc.)

  • Monika Cechova

    (Masaryk University
    University of California Santa Cruz)

  • 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
    Saint Petersburg State University
    Tel Aviv University)

  • 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
    Foundation of Biological Data Science)

  • Mark Diekhans

    (University of California Santa Cruz)

  • Paul Flicek

    (Wellcome Genome Campus, Hinxton
    University of Cambridge)

  • 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
    University of Kansas Medical Center)

  • Patrick G. S. Grady

    (University of Connecticut)

  • Andrea Guarracino

    (University of Tennessee Health Science Center
    Human Technopole)

  • Leanne Haggerty

    (Wellcome Genome Campus, Hinxton)

  • Reza Halabian

    (University of Münster)

  • Nancy F. Hansen

    (National Institutes of Health
    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
    Harvard Medical School)

  • Glennis A. Logsdon

    (University of Washington School of Medicine)

  • Julian K. Lucas

    (University of California Santa Cruz
    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
    University of California Santa Cruz)

  • Paul Medvedev

    (Pennsylvania State University
    Pennsylvania State University
    Pennsylvania State University)

  • Alla Mikheenko

    (Saint Petersburg State University
    UCL Queen Square Institute of Neurology, UCL)

  • 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
    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
    Rice University)

  • 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
    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
    University of Washington)

  • Rachel J. O’Neill

    (University of Connecticut
    University of Connecticut
    UConn Health)

  • Michael C. Schatz

    (Johns Hopkins University
    Johns Hopkins University)

  • Karen H. Miga

    (University of California Santa Cruz
    University of California Santa Cruz)

  • Kateryna D. Makova

    (Pennsylvania State University)

  • Adam M. Phillippy

    (National Institutes of Health)

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.

Suggested Citation

  • 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 & And, 2023. "The complete sequence of a human Y chromosome," Nature, Nature, vol. 621(7978), pages 344-354, September.
    • Handle: RePEc:nat:nature:v:621:y:2023:i:7978:d:10.1038_s41586-023-06457-y
    DOI: 10.1038/s41586-023-06457-y
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    Citations

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    Cited by:

    1. Zhantao Shao & Jack Hu & Allison Jandura & Ronit Wilk & Matthew Jachimowicz & Lingfeng Ma & Chun Hu & Abby Sundquist & Indrani Das & Phillip Samuel-Larbi & Julie A. Brill & Henry M. Krause, 2024. "Spatially revealed roles for lncRNAs in Drosophila spermatogenesis, Y chromosome function and evolution," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Asa'a, S. & Reher, T. & Rongé, J. & Diels, J. & Poortmans, J. & Radhakrishnan, H.S. & van der Heide, A. & Van de Poel, B. & Daenen, M., 2024. "A multidisciplinary view on agrivoltaics: Future of energy and agriculture," Renewable and Sustainable Energy Reviews, Elsevier, vol. 200(C).
    3. Pengfei Liu & Jeromine Vigneau & Rory J. Craig & Josué Barrera-Redondo & Elena Avdievich & Claudia Martinho & Michael Borg & Fabian B. Haas & Chang Liu & Susana M. Coelho, 2024. "3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Chen Sun & Kunal Kathuria & Sarah B. Emery & ByungJun Kim & Ian E. Burbulis & Joo Heon Shin & Daniel R. Weinberger & John V. Moran & Jeffrey M. Kidd & Ryan E. Mills & Michael J. McConnell, 2024. "Mapping recurrent mosaic copy number variation in human neurons," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    5. Temitayo A. Olagunju & Benjamin D. Rosen & Holly L. Neibergs & Gabrielle M. Becker & Kimberly M. Davenport & Christine G. Elsik & Tracy S. Hadfield & Sergey Koren & Kristen L. Kuhn & Arang Rhie & Kati, 2024. "Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content," Nature Communications, Nature, vol. 15(1), pages 1-12, December.

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