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Towards complete and error-free genome assemblies of all vertebrate species

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Towards complete and error-free genome assemblies of all vertebrate species. / Rhie, Arang; McCarthy, Shane A.; Fedrigo, Olivier et al.
In: Nature, Vol. 592, No. 7856, 28.04.2021, p. 737-746.

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

HarvardHarvard

Rhie, A, McCarthy, SA, Fedrigo, O, Damas, J, Formenti, G, Koren, S, Uliano-Silva, M, Chow, W, Fungtammasan, A, Kim, J, Lee, C, Ko, BJ, Chaisson, M, Gedman, GL, Cantin, LJ, Thibaud-Nissen, F, Haggerty, L, Bista, I, Smith, M, Haase, B, Mountcastle, J, Winkler, S, Paez, S, Howard, J, Vernes, SC, Lama, TM, Grutzner, F, Warren, WC, Balakrishnan, CN, Burt, D, George, JM, Biegler, MT, Iorns, D, Digby, A, Eason, D, Robertson, B, Edwards, T, Wilkinson, M, Turner, G, Meyer, A, Kautt, AF, Franchini, P, Detrich, HW, Svardal, H, Wagner, M, Naylor, GJP, Pippel, M, Malinsky, M, Mooney, M, Simbirsky, M, Hannigan, BT, Pesout, T, Houck, M, Misuraca, A, Kingan, SB, Hall, R, Kronenberg, Z, Sović, I, Dunn, C, Ning, Z, Hastie, A, Lee, J, Selvaraj, S, Green, RE, Putnam, NH, Gut, I, Ghurye, J, Garrison, E, Sims, Y, Collins, J, Pelan, S, Torrance, J, Tracey, A, Wood, J, Dagnew, RE, Guan, D, London, SE, Clayton, DF, Mello, CV, Friedrich, SR, Lovell, PV, Osipova, E, Al-Ajli, FO, Secomandi, S, Kim, H, Theofanopoulou, C, Hiller, M, Zhou, Y, Harris, RS, Makova, KD, Medvedev, P, Hoffman, J, Masterson, P, Clark, K, Martin, F, Howe, K, Flicek, P, Walenz, BP, Kwak, W, Clawson, H, Diekhans, M, Nassar, L, Paten, B, Kraus, RHS, Crawford, AJ, Gilbert, MTP, Zhang, G, Venkatesh, B, Murphy, RW, Koepfli, K-P, Shapiro, B, Johnson, WE, Di Palma, F, Marques-Bonet, T, Teeling, EC, Warnow, T, Graves, JM, Ryder, OA, Haussler, D, O’Brien, SJ, Korlach, J, Lewin, HA, Howe, K, Myers, EW, Durbin, R, Phillippy, AM & Jarvis, ED 2021, 'Towards complete and error-free genome assemblies of all vertebrate species', Nature, vol. 592, no. 7856, pp. 737-746. https://doi.org/10.1038/s41586-021-03451-0

APA

Rhie, A., McCarthy, S. A., Fedrigo, O., Damas, J., Formenti, G., Koren, S., Uliano-Silva, M., Chow, W., Fungtammasan, A., Kim, J., Lee, C., Ko, B. J., Chaisson, M., Gedman, G. L., Cantin, L. J., Thibaud-Nissen, F., Haggerty, L., Bista, I., Smith, M., ... Jarvis, E. D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746. https://doi.org/10.1038/s41586-021-03451-0

CBE

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, et al. 2021. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592(7856):737-746. https://doi.org/10.1038/s41586-021-03451-0

MLA

Rhie, Arang et al. "Towards complete and error-free genome assemblies of all vertebrate species". Nature. 2021, 592(7856). 737-746. https://doi.org/10.1038/s41586-021-03451-0

VancouverVancouver

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 2021 Apr 28;592(7856):737-746. doi: 10.1038/s41586-021-03451-0

Author

Rhie, Arang ; McCarthy, Shane A. ; Fedrigo, Olivier et al. / Towards complete and error-free genome assemblies of all vertebrate species. In: Nature. 2021 ; Vol. 592, No. 7856. pp. 737-746.

RIS

TY - JOUR

T1 - Towards complete and error-free genome assemblies of all vertebrate species

AU - Rhie, Arang

AU - McCarthy, Shane A.

AU - Fedrigo, Olivier

AU - Damas, Joana

AU - Formenti, Giulio

AU - Koren, Sergey

AU - Uliano-Silva, Marcela

AU - Chow, William

AU - Fungtammasan, Arkarachai

AU - Kim, Juwan

AU - Lee, Chul

AU - Ko, Byung June

AU - Chaisson, Mark

AU - Gedman, Gregory L.

AU - Cantin, Lindsey J.

AU - Thibaud-Nissen, Francoise

AU - Haggerty, Leanne

AU - Bista, Iliana

AU - Smith, Michelle

AU - Haase, Bettina

AU - Mountcastle, Jacquelyn

AU - Winkler, Sylke

AU - Paez, Sadye

AU - Howard, Jason

AU - Vernes, Sonja C.

AU - Lama, Tanya M.

AU - Grutzner, Frank

AU - Warren, Wesley C.

AU - Balakrishnan, Christopher N.

AU - Burt, Dave

AU - George, Julia M.

AU - Biegler, Matthew T.

AU - Iorns, David

AU - Digby, Andrew

AU - Eason, Daryl

AU - Robertson, Bruce

AU - Edwards, Taylor

AU - Wilkinson, Mark

AU - Turner, George

AU - Meyer, Axel

AU - Kautt, Andreas F.

AU - Franchini, Paolo

AU - Detrich, H. William

AU - Svardal, Hannes

AU - Wagner, Maximilian

AU - Naylor, Gavin J. P.

AU - Pippel, Martin

AU - Malinsky, Milan

AU - Mooney, Mark

AU - Simbirsky, Maria

AU - Hannigan, Brett T.

AU - Pesout, Trevor

AU - Houck, Marlys

AU - Misuraca, Ann

AU - Kingan, Sarah B.

AU - Hall, Richard

AU - Kronenberg, Zev

AU - Sović, Ivan

AU - Dunn, Christopher

AU - Ning, Zemin

AU - Hastie, Alex

AU - Lee, Joyce

AU - Selvaraj, Siddarth

AU - Green, Richard E.

AU - Putnam, Nicholas H.

AU - Gut, Ivo

AU - Ghurye, Jay

AU - Garrison, Erik

AU - Sims, Ying

AU - Collins, Joanna

AU - Pelan, Sarah

AU - Torrance, James

AU - Tracey, Alan

AU - Wood, Jonathan

AU - Dagnew, Robel E.

AU - Guan, Dengfeng

AU - London, Sarah E.

AU - Clayton, David F.

AU - Mello, Claudio V.

AU - Friedrich, Samantha R.

AU - Lovell, Peter V.

AU - Osipova, Ekaterina

AU - Al-Ajli, Farooq O.

AU - Secomandi, Simona

AU - Kim, Heebal

AU - Theofanopoulou, Constantina

AU - Hiller, Michael

AU - Zhou, Yang

AU - Harris, Robert S.

AU - Makova, Kateryna D.

AU - Medvedev, Paul

AU - Hoffman, Jinna

AU - Masterson, Patrick

AU - Clark, Karen

AU - Martin, Fergal

AU - Howe, Kevin

AU - Flicek, Paul

AU - Walenz, Brian P.

AU - Kwak, Woori

AU - Clawson, Hiram

AU - Diekhans, Mark

AU - Nassar, Luis

AU - Paten, Benedict

AU - Kraus, Robert H. S.

AU - Crawford, Andrew J.

AU - Gilbert, M. Thomas P.

AU - Zhang, Guojie

AU - Venkatesh, Byrappa

AU - Murphy, Robert W.

AU - Koepfli, Klaus-Peter

AU - Shapiro, Beth

AU - Johnson, Warren E.

AU - Di Palma, Federica

AU - Marques-Bonet, Tomas

AU - Teeling, Emma C.

AU - Warnow, Tandy

AU - Graves, Jennifer Marshall

AU - Ryder, Oliver A.

AU - Haussler, David

AU - O’Brien, Stephen J.

AU - Korlach, Jonas

AU - Lewin, Harris A.

AU - Howe, Kerstin

AU - Myers, Eugene W.

AU - Durbin, Richard

AU - Phillippy, Adam M.

AU - Jarvis, Erich D.

PY - 2021/4/28

Y1 - 2021/4/28

N2 - High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

AB - High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1–4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

U2 - 10.1038/s41586-021-03451-0

DO - 10.1038/s41586-021-03451-0

M3 - Article

VL - 592

SP - 737

EP - 746

JO - Nature

JF - Nature

SN - 1476-4687

IS - 7856

ER -