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
Date Published2023 Sep
KeywordsChromosomes, Human, Y, Genomics, Humans, Segmental Duplications, Genomic, Tandem Repeat Sequences, Telomere

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.

Alternate JournalNature
PubMed ID37612512
PubMed Central ID3975068
Grant ListR01 HG011274 / HG / NHGRI NIH HHS / United States
R21 HG010548 / HG / NHGRI NIH HHS / United States
U01 HG010971 / HG / NHGRI NIH HHS / United States

Similar Publications

Chen F, Zhang Y, Chandrashekar DS, Varambally S, Creighton CJ. Global impact of somatic structural variation on the cancer proteome. Nat Commun. 2023;14(1):5637.
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, et al.. The complete sequence of a human Y chromosome. Nature. 2023;621(7978):344-354.
Saengboonmee C, Sorin S, Sangkhamanon S, Chomphoo S, Indramanee S, Seubwai W, et al.. γ-aminobutyric acid B2 receptor: A potential therapeutic target for cholangiocarcinoma in patients with diabetes mellitus. World J Gastroenterol. 2023;29(28):4416-4432.
Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, et al.. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet. 2023;110(8):1229-1248.
Chin C-S, Behera S, Khalak A, Sedlazeck FJ, Sudmant PH, Wagner J, et al.. Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes. Nat Methods. 2023;20(8):1213-1221.
Zhao N, Teles F, Lu J, Koestler DC, Beck J, Boerwinkle E, et al.. Epigenome-wide association study using peripheral blood leukocytes identifies genomic regions associated with periodontal disease and edentulism in the Atherosclerosis Risk in Communities study. J Clin Periodontol. 2023;50(9):1140-1153.
Harris RA, McAllister JM, Strauss JF. Single-Cell RNA-Seq Identifies Pathways and Genes Contributing to the Hyperandrogenemia Associated with Polycystic Ovary Syndrome. Int J Mol Sci. 2023;24(13).
Qian X, Srinivasan T, He J, Chen R. The Role of Ceramide in Inherited Retinal Disease Pathology. Adv Exp Med Biol. 2023;1415:303-307.
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, et al.. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet. 2023;110(8):1394-1413.
Walker KA, Chen J, Shi L, Yang Y, Fornage M, Zhou L, et al.. Proteomics analysis of plasma from middle-aged adults identifies protein markers of dementia risk in later life. Sci Transl Med. 2023;15(705):eadf5681.