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.

Biosystems and Biomaterials Division National Institute of Standards and Technology Gaithersburg MD USA

Cancer Genetics and Comparative Genomics Branch National Human Genome Research Institute National Institutes of Health Bethesda MD USA

Center for Algorithmic Biotechnology Saint Petersburg State University St Petersburg Russia

Center for Computational Biology and Bioinformatics Pennsylvania State University University Park PA USA

Center for Evolution and Medicine School of Life Sciences Arizona State University Tempe AZ USA

Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry Sackler Faculty of Medicine Tel Aviv University Tel Aviv Yafo Israel

Department of Biochemistry and Molecular Biology Pennsylvania State University University Park PA USA

Department of Bioengineering Department of Physics Northeastern University Boston MA USA

Department of Biology Johns Hopkins University Baltimore MD USA

Department of Biology Pennsylvania State University University Park PA USA

Department of Biomedical Engineering Johns Hopkins University Baltimore MD USA

Department of Biomedical Engineering Pennsylvania State University State College PA USA

Department of Biomedical Informatics Harvard Medical School Boston MA USA

Department of Biomolecular Engineering University of California Santa Cruz Santa Cruz CA USA

Department of Computer Science and Engineering Pennsylvania State University University Park PA USA

Department of Computer Science Johns Hopkins University Baltimore MD USA

Department of Computer Science Rice University Houston TX USA

Department of Data Sciences Dana Farber Cancer Institute Boston MA USA

Department of Genetics and Genome Sciences UConn Health Farmington CT USA

Department of Genetics Genomics and Informatics University of Tennessee Health Science Center Memphis TN USA

Department of Genetics University of Cambridge Cambridge UK

Department of Genome Sciences University of Washington School of Medicine Seattle WA USA

Department of Molecular and Cell Biology University of California Berkeley CA USA

Department of Molecular and Cell Biology University of Connecticut Storrs CT USA

Departments of Biomedical Engineering Computer Science and Biostatistics Johns Hopkins University Baltimore MD USA

DNAnexus Inc Mountain View CA USA

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge UK

Faculty of Informatics Masaryk University Brno Czech Republic

Federal Research Center of Biotechnology of the Russian Academy of Sciences Moscow Russia

Foundation of Biological Data Science Belmont CA USA

GeneDX Holdings Corp Stamford CT USA

Genome Informatics Section Computational and Statistical Genomics Branch National Human Genome Research Institute National Institutes of Health Bethesda MD USA

Genome Technology Access Center at the McDonnell Genome Institute Washington University St Louis MO USA

Genomics Research Centre Human Technopole Milan Italy

Google Inc Mountain View CA USA

Graduate Program in Bioinformatics and Systems Biology University of California San Diego CA USA

Human Genome Sequencing Center Baylor College of Medicine One Baylor Plaza Houston TX USA

Institute for Systems Biology Seattle WA USA

Institute for Systems Genomics University of Connecticut Storrs CT USA

Institute of Bioinformatics Faculty of Medicine University of Münster Münster Germany

Institute of Molecular Genetics Moscow Russia

Investigator Howard Hughes Medical Institute University of Washington Seattle WA USA

Masters Program in National Research University Higher School of Economics Moscow Russia

National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD USA

Oxford Nanopore Technologies Inc Oxford UK

Pacific Biosciences Menlo Park CA USA

Stowers Institute for Medical Research Kansas City MO USA

The Rockefeller University New York NY USA

UC Santa Cruz Genomics Institute University of California Santa Cruz Santa Cruz CA USA

UCL Queen Square Institute of Neurology UCL London UK

University of Kansas Medical Center Kansas City MO USA

XDBio Program Johns Hopkins University Baltimore MD USA

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Non-canonical DNA in human and other ape telomere-to-telomere genomes

Sexy ways: approaches to studying plant sex chromosomes