Towards complete and error-free genome assemblies of all vertebrate species
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 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 Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries.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.
Citation
Vertebrate Genome Project , 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 , Haase , B , Mountcastle , J , Winkler , S , Paez , S , Howard , J , Vernes , S C , Lama , T M , Grutzner , F , Warren , W C , Balakrishnan , C N , Burt , D , George , J M , Biegler , M T , Iorns , D , Digby , A , Eason , D , Robertson , B , Edwards , T , Wilkinson , M , Turner , G , Meyer , A , Kautt , A F , Franchini , P , Detrich , H W , Svardal , H , Wagner , M , Naylor , G J P , Pippel , M , Malinsky , M & Mooney , M 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
Publication
Nature
Status
Peer reviewed
ISSN
0028-0836Type
Journal article
Rights
Copyright © The Author(s) 2021. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.
Description
Funding: S.C.V. was funded by a Max Planck Research Group award from the Max Planck Society, and a Human Frontiers Science Program (HFSP) Research grant (RGP0058/2016).Collections
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