The complete sequence of a human Y chromosome

Arang Rhie; Sergey Nurk; Monika Cechova; 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 Garrison; Ariel Gershman; Jennifer L. Gerton; Patrick G.S. Grady; Andrea Guarracino; Leanne Haggerty; Reza Halabian; Nancy F. Hansen; Robert Harris; Gabrielle A. Hartley; William T. Harvey; Marina Haukness; Jakob Heinz; Thibaut Hourlier; Robert M. Hubley; Sarah E. Hunt; Stephen Hwang; Miten Jain; Rupesh K. Kesharwani; Alexandra P. Lewis; Heng Li; Glennis A. Logsdon; Julian K. Lucas; Wojciech Makalowski; Christopher Markovic; Fergal J. Martin; Ann M. Mc Cartney; Rajiv C. McCoy; Jennifer McDaniel; Brandy M. McNulty; Paul Medvedev; Alla Mikheenko; Katherine M. Munson; Terence D. Murphy; Hugh E. Olsen; Nathan D. Olson; Luis F. Paulin; David Porubsky; Tamara Potapova; Fedor Ryabov; Steven L. Salzberg; Michael E.G. Sauria; Fritz J. Sedlazeck; Kishwar Shafin; Valery A. Shepelev; Alaina Shumate; Jessica M. Storer; Likhitha Surapaneni; Angela M. Taravella Oill; Françoise Thibaud-Nissen; Winston Timp; Marta Tomaszkiewicz; Mitchell R. Vollger; Brian P. Walenz; Allison C. Watwood; Matthias H. Weissensteiner; Aaron M. Wenger; Melissa A. Wilson; Samantha Zarate; Yiming Zhu; Justin M. Zook; Evan E. Eichler; Rachel J. O’Neill; Michael C. Schatz; Karen H. Miga; Kateryna D. Makova; Adam M. Phillippy

doi:10.1038/s41586-023-06457-y

The complete sequence of a human Y chromosome

Arang Rhie, Sergey Nurk, Monika Cechova, 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 GironErik Garrison, Ariel Gershman, Jennifer L. Gerton, Patrick G.S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E.G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel J. O’Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova, Adam M. Phillippy

Whiting School of Engineering

Research output: Contribution to journal › Article › peer-review

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^1–3. 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 finished^4,5. 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.

Original language	English (US)
Pages (from-to)	344-354
Number of pages	11
Journal	Nature
Volume	621
Issue number	7978
DOIs	https://doi.org/10.1038/s41586-023-06457-y
State	Published - Sep 14 2023

ASJC Scopus subject areas

General

Access to Document

10.1038/s41586-023-06457-y

Cite this

Rhie, A., Nurk, S., Cechova, M., Hoyt, S. J., Taylor, D. J., Altemose, N., Hook, P. W., Koren, S., Rautiainen, M., Alexandrov, I. A., Allen, J., Asri, M., Bzikadze, A. V., Chen, N. C., Chin, C. S., Diekhans, M., Flicek, P., Formenti, G., Fungtammasan, A., ... Phillippy, A. M. (2023). The complete sequence of a human Y chromosome. Nature, 621(7978), 344-354. https://doi.org/10.1038/s41586-023-06457-y

Rhie, 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, NC, Chin, CS, Diekhans, M, Flicek, P, Formenti, G, Fungtammasan, A, Garcia Giron, C, 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, Mc Cartney, AM, 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, Taravella Oill, AM, 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 2023, 'The complete sequence of a human Y chromosome', Nature, vol. 621, no. 7978, pp. 344-354. https://doi.org/10.1038/s41586-023-06457-y

@article{003591a878264d62add8ed37f3464a62,

title = "The complete sequence of a human Y chromosome",

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 duplications1–3. 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.",

author = "Arang Rhie and Sergey Nurk and Monika Cechova and Hoyt, {Savannah J.} and Taylor, {Dylan J.} and Nicolas Altemose and Hook, {Paul W.} and Sergey Koren and Mikko Rautiainen and Alexandrov, {Ivan A.} and Jamie Allen and Mobin Asri and Bzikadze, {Andrey V.} and Chen, {Nae Chyun} and Chin, {Chen Shan} and Mark Diekhans and Paul Flicek and Giulio Formenti and Arkarachai Fungtammasan and {Garcia Giron}, Carlos and Erik Garrison and Ariel Gershman and Gerton, {Jennifer L.} and Grady, {Patrick G.S.} and Andrea Guarracino and Leanne Haggerty and Reza Halabian and Hansen, {Nancy F.} and Robert Harris and Hartley, {Gabrielle A.} and Harvey, {William T.} and Marina Haukness and Jakob Heinz and Thibaut Hourlier and Hubley, {Robert M.} and Hunt, {Sarah E.} and Stephen Hwang and Miten Jain and Kesharwani, {Rupesh K.} and Lewis, {Alexandra P.} and Heng Li and Logsdon, {Glennis A.} and Lucas, {Julian K.} and Wojciech Makalowski and Christopher Markovic and Martin, {Fergal J.} and {Mc Cartney}, {Ann M.} and McCoy, {Rajiv C.} and Jennifer McDaniel and McNulty, {Brandy M.} and Paul Medvedev and Alla Mikheenko and Munson, {Katherine M.} and Murphy, {Terence D.} and Olsen, {Hugh E.} and Olson, {Nathan D.} and Paulin, {Luis F.} and David Porubsky and Tamara Potapova and Fedor Ryabov and Salzberg, {Steven L.} and Sauria, {Michael E.G.} and Sedlazeck, {Fritz J.} and Kishwar Shafin and Shepelev, {Valery A.} and Alaina Shumate and Storer, {Jessica M.} and Likhitha Surapaneni and {Taravella Oill}, {Angela M.} and Fran{\c c}oise Thibaud-Nissen and Winston Timp and Marta Tomaszkiewicz and Vollger, {Mitchell R.} and Walenz, {Brian P.} and Watwood, {Allison C.} and Weissensteiner, {Matthias H.} and Wenger, {Aaron M.} and Wilson, {Melissa A.} and Samantha Zarate and Yiming Zhu and Zook, {Justin M.} and Eichler, {Evan E.} and O{\textquoteright}Neill, {Rachel J.} and Schatz, {Michael C.} and Miga, {Karen H.} and Makova, {Kateryna D.} and Phillippy, {Adam M.}",

note = "Publisher Copyright: {\textcopyright} 2023, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.",

year = "2023",

month = sep,

day = "14",

doi = "10.1038/s41586-023-06457-y",

language = "English (US)",

volume = "621",

pages = "344--354",

journal = "Nature",

issn = "0028-0836",

publisher = "Nature Research",

number = "7978",

}

TY - JOUR

T1 - The complete sequence of a human Y chromosome

AU - Rhie, Arang

AU - Nurk, Sergey

AU - Cechova, Monika

AU - Hoyt, Savannah J.

AU - Taylor, Dylan J.

AU - Altemose, Nicolas

AU - Hook, Paul W.

AU - Koren, Sergey

AU - Rautiainen, Mikko

AU - Alexandrov, Ivan A.

AU - Allen, Jamie

AU - Asri, Mobin

AU - Bzikadze, Andrey V.

AU - Chen, Nae Chyun

AU - Chin, Chen Shan

AU - Diekhans, Mark

AU - Flicek, Paul

AU - Formenti, Giulio

AU - Fungtammasan, Arkarachai

AU - Garcia Giron, Carlos

AU - Garrison, Erik

AU - Gershman, Ariel

AU - Gerton, Jennifer L.

AU - Grady, Patrick G.S.

AU - Guarracino, Andrea

AU - Haggerty, Leanne

AU - Halabian, Reza

AU - Hansen, Nancy F.

AU - Harris, Robert

AU - Hartley, Gabrielle A.

AU - Harvey, William T.

AU - Haukness, Marina

AU - Heinz, Jakob

AU - Hourlier, Thibaut

AU - Hubley, Robert M.

AU - Hunt, Sarah E.

AU - Hwang, Stephen

AU - Jain, Miten

AU - Kesharwani, Rupesh K.

AU - Lewis, Alexandra P.

AU - Li, Heng

AU - Logsdon, Glennis A.

AU - Lucas, Julian K.

AU - Makalowski, Wojciech

AU - Markovic, Christopher

AU - Martin, Fergal J.

AU - Mc Cartney, Ann M.

AU - McCoy, Rajiv C.

AU - McDaniel, Jennifer

AU - McNulty, Brandy M.

AU - Medvedev, Paul

AU - Mikheenko, Alla

AU - Munson, Katherine M.

AU - Murphy, Terence D.

AU - Olsen, Hugh E.

AU - Olson, Nathan D.

AU - Paulin, Luis F.

AU - Porubsky, David

AU - Potapova, Tamara

AU - Ryabov, Fedor

AU - Salzberg, Steven L.

AU - Sauria, Michael E.G.

AU - Sedlazeck, Fritz J.

AU - Shafin, Kishwar

AU - Shepelev, Valery A.

AU - Shumate, Alaina

AU - Storer, Jessica M.

AU - Surapaneni, Likhitha

AU - Taravella Oill, Angela M.

AU - Thibaud-Nissen, Françoise

AU - Timp, Winston

AU - Tomaszkiewicz, Marta

AU - Vollger, Mitchell R.

AU - Walenz, Brian P.

AU - Watwood, Allison C.

AU - Weissensteiner, Matthias H.

AU - Wenger, Aaron M.

AU - Wilson, Melissa A.

AU - Zarate, Samantha

AU - Zhu, Yiming

AU - Zook, Justin M.

AU - Eichler, Evan E.

AU - O’Neill, Rachel J.

AU - Schatz, Michael C.

AU - Miga, Karen H.

AU - Makova, Kateryna D.

AU - Phillippy, Adam M.

PY - 2023/9/14

Y1 - 2023/9/14

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85168596669&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85168596669&partnerID=8YFLogxK

U2 - 10.1038/s41586-023-06457-y

DO - 10.1038/s41586-023-06457-y

M3 - Article

C2 - 37612512

AN - SCOPUS:85168596669

SN - 0028-0836

VL - 621

SP - 344

EP - 354

JO - Nature

JF - Nature

IS - 7978

ER -

The complete sequence of a human Y chromosome

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this