Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie, Shane McCarthy, Olivier Fédrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano‐Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim, Chul Lee, Byung June Ko, Mark Chaisson, Gregory Gedman, Lindsey Cantin, Françoise Thibaud‐Nissen, Leanne Haggerty, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason T. Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grützner, Wesley C. Warren, Christopher N. Balakrishnan, David W. Burt, Julia M. George, Matthew T. Biegler, David Iorns, Andrew Digby, Daryl Eason, Bruce C. Robertson, Taylor Edwards, Mark Wilkinson, George F. Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H. William Detrich, Hannes Svardal, Maximilian Wagner, Gavin J. P. Naylor, Martin Pippel, Milan Malinsky, Mark P. Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys L. Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Marta Gut, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, Robel E. Dagnew, Dengfeng Guan, Sarah E. London, David F. Clayton, Claudio V. Mello, Samantha R. Friedrich, Peter V. Lovell, Ekaterina Osipova, Farooq O. Al-Ajli, Simona Secomandi, Heebal Kim, Constantina Theofanopoulou, Michael Hiller, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal J. Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson
Abstract
Abstract 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 species 1–4 . To address this issue, the international Genome 10K (G10K) consortium 5,6 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.