The complete sequence of a human Y chromosome.

TitleThe complete sequence of a human Y chromosome.
Publication TypeJournal Article
Year of Publication2023
AuthorsRhie, A, Nurk, S, Cechova, M, Hoyt, SJ, Taylor, DJ, Altemose, N, Hook, PW, Koren, S, Rautiainen, M, Alexandrov, IA, Allen, J, Asri, M, Bzikadze, AV, Chen, N-C, Chin, C-S, Diekhans, M, Flicek, P, Formenti, G, Fungtammasan, A, Girón, CGarcía, Garrison, E, Gershman, A, Gerton, JL, Grady, PGS, Guarracino, A, Haggerty, L, Halabian, R, Hansen, NF, Harris, R, Hartley, GA, Harvey, WT, Haukness, M, Heinz, J, Hourlier, T, Hubley, RM, Hunt, SE, Hwang, S, Jain, M, Kesharwani, RK, Lewis, AP, Li, H, Logsdon, GA, Lucas, JK, Makalowski, W, Markovic, C, Martin, FJ, Cartney, AMMc, McCoy, RC, McDaniel, J, McNulty, BM, Medvedev, P, Mikheenko, A, Munson, KM, Murphy, TD, Olsen, HE, Olson, ND, Paulin, LF, Porubsky, D, Potapova, T, Ryabov, F, Salzberg, SL, Sauria, MEG, Sedlazeck, FJ, Shafin, K, Shepelev, VA, Shumate, A, Storer, JM, Surapaneni, L, Oill, AMTaravell, Thibaud-Nissen, F, Timp, W, Tomaszkiewicz, M, Vollger, MR, Walenz, BP, Watwood, AC, Weissensteiner, MH, Wenger, AM, Wilson, MA, Zarate, S, Zhu, Y, Zook, JM, Eichler, EE, O'Neill, RJ, Schatz, MC, Miga, KH, Makova, KD, Phillippy, AM
JournalNature
Volume621
Issue7978
Pagination344-354
Date Published2023 Sep
ISSN1476-4687
KeywordsBase Sequence, Chromosomes, Human, Y, DNA, Satellite, Genetic Variation, Genetics, Population, Genomics, Heterochromatin, Humans, Multigene Family, Reference Standards, Segmental Duplications, Genomic, Sequence Analysis, DNA, Tandem Repeat Sequences, Telomere
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 duplications. 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 finished. 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 genome and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
DOI10.1038/s41586-023-06457-y
Alternate JournalNature
PubMed ID37612512
PubMed Central IDPMC10752217
Grant ListU01 HG010961 / HG / NHGRI NIH HHS / United States
R35 GM124827 / GM / NIGMS NIH HHS / United States
R01 GM130691 / GM / NIGMS NIH HHS / United States
Z99 HG999999 / ImNIH / Intramural NIH HHS / United States
R01 HG002939 / HG / NHGRI NIH HHS / United States
K99 GM147352 / GM / NIGMS NIH HHS / United States
R01 HG009190 / HG / NHGRI NIH HHS / United States
ZIA HG200398 / ImNIH / Intramural NIH HHS / United States
R35 GM133747 / GM / NIGMS NIH HHS / United States
U24 HG010263 / HG / NHGRI NIH HHS / United States
R01 GM136684 / GM / NIGMS NIH HHS / United States
R01 HG010040 / HG / NHGRI NIH HHS / United States
U41 HG010972 / HG / NHGRI NIH HHS / United States
R21 CA240199 / CA / NCI NIH HHS / United States
R01 CA266339 / CA / NCI NIH HHS / United States
R00 GM147352 / GM / NIGMS NIH HHS / United States
U41 HG006620 / HG / NHGRI NIH HHS / United States
R01 HG010169 / HG / NHGRI NIH HHS / United States
U41 HG007234 / HG / NHGRI NIH HHS / United States
U01 CA253481 / CA / NCI NIH HHS / United States
U24 HG007234 / HG / NHGRI NIH HHS / United States
R01 HG011274 / HG / NHGRI NIH HHS / United States
U24 HG006620 / HG / NHGRI NIH HHS / United States
U24 HG010136 / HG / NHGRI NIH HHS / United States
R21 HG010548 / HG / NHGRI NIH HHS / United States
S10 OD028587 / OD / NIH HHS / United States
U01 HG010971 / HG / NHGRI NIH HHS / United States
U01 DA047638 / DA / NIDA NIH HHS / United States
R01 GM123312 / GM / NIGMS NIH HHS / United States
R01 GM072264 / GM / NIGMS NIH HHS / United States
R01 HG002385 / HG / NHGRI NIH HHS / United States
U01 HG011758 / HG / NHGRI NIH HHS / United States
/ HHMI / Howard Hughes Medical Institute / United States

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