The complete sequence of a human Y chromosome

Arang Rhie; Sergey Nurk; Monika Čechová; 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 P. Garrison; Ariel Gershman; Jennifer L. Gerton; Patrick G. S. Grady; Andrea Guarracino; Leanne S. Haggerty; Reza Halabian; Nancy Fisher Hansen; Robert Harris; Gabrielle A. Hartley

doi:10.1038/s41586-023-06457-y

GenomicsNatureAug 23, 2023

Peer-reviewed journal article

The complete sequence of a human Y chromosome

Arang Rhie iD, Sergey Nurk iD, Monika Čechová iD, Savannah J. Hoyt iD, Dylan J. Taylor iD, Nicolas Altemose iD, Paul W. Hook iD, Sergey Koren iD, Mikko Rautiainen iD, Ivan A. Alexandrov iD, Jamie Allen iD, Mobin Asri iD, Andrey V. Bzikadze iD, Nae-Chyun Chen iD, Chen-Shan Chin iD, Mark Diekhans iD, Paul Flicek iD, Giulio Formenti iD, Arkarachai Fungtammasan iD, Carlos Garcia Giron, Erik P. Garrison iD, Ariel Gershman iD, Jennifer L. Gerton iD, Patrick G. S. Grady iD, Andrea Guarracino iD, , Adam M. Phillippy iD

Abstract

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including 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, revealing the complete ampliconic structures of TSPY, DAZ, and RBMY gene families; 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 prior 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.

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