The complete sequence of a human Y chromosome

Published

August 23, 2023

Author(s)

Arang Rhie, Sergey Nurk, Monika Cechova, Savannah Hoyt, Dylan Taylor, Nathanael David Olson, Justin Zook, Adam Phillippy

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 duplications1,2,3. 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.

Citation

Nature

Volume

621

Pub Type

Journals

Download Paper

https://doi.org/10.1038/s41586-023-06457-y

Local Download

Keywords

human genome assembly

Citation

Rhie, A. , Nurk, S. , Cechova, M. , Hoyt, S. , Taylor, D. , Olson, N. , Zook, J. and Phillippy, A. (2023), The complete sequence of a human Y chromosome, Nature, [online], https://doi.org/10.1038/s41586-023-06457-y, https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=935967 (Accessed October 8, 2025)