Towards complete and error-free genome assemblies of all vertebrate species
Creators: name: Rhie, Arang
name: McCarthy, Shane A
name: Fedrigo, Olivier
name: Damas, Joana
name: Formenti, Giulio
name: Koren, Sergey
name: Uliano-Silva, Marcela
name: Chow, William
name: Fungtammasan, Arkarachai
name: Kim, Juwan
name: Lee, Chul
name: Ko, Byung June
name: Chaisson, Mark
name: Gedman, Gregory L
name: Cantin, Lindsey J
name: Thibaud-Nissen, Francoise
name: Haggerty, Leanne
name: Bista, Iliana
name: Smith, Michelle
name: Haase, Bettina
name: Mountcastle, Jacquelyn
name: Winkler, Sylke
name: Paez, Sadye
name: Howard, Jason
name: Vernes, Sonja C
name: Lama, Tanya M
name: Grutzner, Frank
name: Warren, Wesley C
name: Balakrishnan, Christopher N
name: Burt, Dave
name: George, Julia M
name: Biegler, Matthew T
name: Iorns, David
name: Digby, Andrew
name: Eason, Daryl
name: Robertson, Bruce
name: Edwards, Taylor
name: Wilkinson, Mark
name: Turner, George
name: Meyer, Axel
name: Kautt, Andreas F
name: Franchini, Paolo
name: Detrich, H William
name: Svardal, Hannes
name: Wagner, Maximilian
name: Naylor, Gavin JP
name: Pippel, Martin
name: Malinsky, Milan
name: Mooney, Mark
name: Simbirsky, Maria
name: Hannigan, Brett T
name: Pesout, Trevor
name: Houck, Marlys
name: Misuraca, Ann
name: Kingan, Sarah B
name: Hall, Richard
name: Kronenberg, Zev
name: Sović, Ivan
name: Dunn, Christopher
name: Ning, Zemin
name: Hastie, Alex
name: Lee, Joyce
name: Selvaraj, Siddarth
name: Green, Richard E
name: Putnam, Nicholas H
name: Gut, Ivo
name: Ghurye, Jay
name: Garrison, Erik
name: Sims, Ying
name: Collins, Joanna
name: Pelan, Sarah
name: Torrance, James
name: Tracey, Alan
name: Wood, Jonathan
name: Dagnew, Robel E
name: Guan, Dengfeng
name: London, Sarah E
name: Clayton, David F
name: Mello, Claudio V
name: Friedrich, Samantha R
name: Lovell, Peter V
name: Osipova, Ekaterina
name: Al-Ajli, Farooq O
name: Secomandi, Simona
name: Kim, Heebal
name: Theofanopoulou, Constantina
name: Hiller, Michael
name: Zhou, Yang
name: Harris, Robert S
name: Makova, Kateryna D
name: Medvedev, Paul
name: Hoffman, Jinna
name: Masterson, Patrick
name: Clark, Karen
name: Martin, Fergal
name: Howe, Kevin
name: Flicek, Paul
name: Walenz, Brian P
name: Kwak, Woori
name: Clawson, Hiram
name: Diekhans, Mark
name: Nassar, Luis
name: Paten, Benedict
name: Kraus, Robert HS
name: Crawford, Andrew J
name: Gilbert, M Thomas P
name: Zhang, Guojie
name: Venkatesh, Byrappa
name: Murphy, Robert W
name: Koepfli, Klaus-Peter
name: Shapiro, Beth
name: Johnson, Warren E
name: Di Palma, Federica
name: Marques-Bonet, Tomas
name: Teeling, Emma C
name: Warnow, Tandy
name: Graves, Jennifer
name: Ryder, Oliver A
name: Haussler, David
name: O’Brien, Stephen J
name: Korlach, Jonas
name: Lewin, Harris A
name: Howe, Kerstin
name: Myers, Eugene W
name: Durbin, Richard
name: Phillippy, Adam M
name: Jarvis, Erich D
Publisher: name: La Trobe
Year: 2022
Subjects: classificationCode: 31
subject: Biological sciences
subject: FOS: Biological sciences
classificationCode: 3102
subject: Bioinformatics and computational biology
classificationCode: 3105
subject: Genetics

description: 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.