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Статья
Towards complete and error-free genome assemblies of all vertebrate species
A. Rhie,
S. McCarthy,
O. Fedrigo,
J. Damas,
G. Formenti,
S. Koren,
M. Uliano-Silva,
W. Chow,
A. Fungtammasan,
J. Kim,
C. Lee,
B. Ko,
M. Chaisson,
G. Gedman,
L. Cantin,
F. Thibaud-Nissen,
L. Haggerty,
I. Bista,
M. Smith,
B. Haase,
J. Mountcastle,
S. Winkler,
S. Paez,
J. Howard,
S. Vernes,
T. Lama,
F. Grutzner,
W. Warren,
C. Balakrishnan,
D. Burt,
J. George,
M. Biegler,
D. Iorns,
A. Digby,
D. Eason,
B. Robertson,
T. Edwards,
M. Wilkinson,
G. Turner,
A. Meyer,
A. Kautt,
P. Franchini,
H. Detrich,
H. Svardal,
M. Wagner,
G. Naylor,
M. Pippel,
M. Malinsky,
M. Mooney,
M. Simbirsky,
B. Hannigan,
T. Pesout,
M. Houck,
A. Misuraca,
S. Kingan,
R. Hall,
Z. Kronenberg,
I. Sović,
C. Dunn,
Z. Ning,
A. Hastie,
J. Lee,
S. Selvaraj,
R. Green,
N. Putnam,
I. Gut,
J. Ghurye,
E. Garrison,
Y. Sims,
J. Collins,
S. Pelan,
J. Torrance,
A. Tracey,
J. Wood,
R. Dagnew,
D. Guan,
S. London,
D. Clayton,
C. Mello,
S. Friedrich,
P. Lovell,
E. Osipova,
F. Al-Ajli,
S. Secomandi,
H. Kim,
C. Theofanopoulou,
M. Hiller,
Y. Zhou,
R. Harris,
K. Makova,
P. Medvedev,
J. Hoffman,
P. Masterson,
K. Clark,
F. Martin,
K. Howe,
P. Flicek,
B. Walenz,
W. Kwak,
H. Clawson,
2021
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 . To address this issue, the international Genome 10K (G10K) consortium 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 Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries.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. 1–4 5,6
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Версии
- 1. Version of Record от 2021-04-29
Метаданные
Об авторах
-
A. Rhie
National Human Genome Research Institute (NHGRI) -
S. McCarthy
University of Cambridge, Wellcome Sanger Institute -
O. Fedrigo
Rockefeller University -
J. Damas
University of California, Davis -
G. Formenti
Rockefeller University, Rockefeller University -
S. Koren
National Human Genome Research Institute (NHGRI) -
M. Uliano-Silva
Leibniz-Institut für Zoo- und Wildtierforschung, Berlin Center for Genomics in Biodiversity Research -
W. Chow
Wellcome Sanger Institute -
A. Fungtammasan
DNAnexus -
J. Kim
Seoul National University -
C. Lee
Seoul National University -
B. Ko
Department of Food and Animal Biotechnology -
M. Chaisson
University of Southern California -
G. Gedman
Rockefeller University -
L. Cantin
Rockefeller University -
F. Thibaud-Nissen
National Center for Biotechnology Information (NCBI) -
L. Haggerty
European Bioinformatics Institute -
I. Bista
University of Cambridge, Wellcome Sanger Institute -
M. Smith
Wellcome Sanger Institute -
B. Haase
Rockefeller University -
J. Mountcastle
Rockefeller University -
S. Winkler
Max Planck Institute of Molecular Cell Biology and Genetics, Technische Universität Dresden -
S. Paez
Rockefeller University, Rockefeller University -
J. Howard
Novogene -
S. Vernes
Max Planck Institute for Psycholinguistics, Donders Institute for Brain, Cognition and Behaviour, University of St Andrews -
T. Lama
University of Massachusetts Amherst -
F. Grutzner
The University of Adelaide -
W. Warren
University of Missouri -
C. Balakrishnan
East Carolina University -
D. Burt
The University of Queensland -
J. George
Clemson University -
M. Biegler
Rockefeller University -
D. Iorns
Genetic Rescue Foundation -
A. Digby
Te Papa Atawhai -
D. Eason
Te Papa Atawhai -
B. Robertson
University of Otago -
T. Edwards
The University of Arizona -
M. Wilkinson
The Natural History Museum, London -
G. Turner
Bangor University -
A. Meyer
Universität Konstanz -
A. Kautt
Universität Konstanz, Harvard University -
P. Franchini
Universität Konstanz -
H. Detrich
Northeastern University -
H. Svardal
Universiteit Antwerpen, Naturalis Biodiversity Center -
M. Wagner
Karl-Franzens-Universitat Graz -
G. Naylor
Florida Museum of Natural History -
M. Pippel
Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden -
M. Malinsky
Wellcome Sanger Institute, Universität Basel, Zoologisches Institut -
M. Mooney
Tag.bio -
M. Simbirsky
DNAnexus -
B. Hannigan
DNAnexus -
T. Pesout
University of California, Santa Cruz -
M. Houck
San Diego Zoo Global -
A. Misuraca
San Diego Zoo Global -
S. Kingan
Pacific Biosciences -
R. Hall
Pacific Biosciences -
Z. Kronenberg
Pacific Biosciences -
I. Sović
Pacific Biosciences, Digital BioLogic -
C. Dunn
Pacific Biosciences -
Z. Ning
Wellcome Sanger Institute -
A. Hastie
Bionano Genomics, Inc. -
J. Lee
Bionano Genomics, Inc. -
S. Selvaraj
Arima Genomics -
R. Green
University of California, Santa Cruz, Dovetail Genomics -
N. Putnam
Independent -
I. Gut
Centro de Regulacion Genomica, Barcelona, Universitat Pompeu Fabra Barcelona -
J. Ghurye
Dovetail Genomics, University of Maryland, College Park (UMD) -
E. Garrison
University of California, Santa Cruz -
Y. Sims
Wellcome Sanger Institute -
J. Collins
Wellcome Sanger Institute -
S. Pelan
Wellcome Sanger Institute -
J. Torrance
Wellcome Sanger Institute -
A. Tracey
Wellcome Sanger Institute -
J. Wood
Wellcome Sanger Institute -
R. Dagnew
University of Southern California -
D. Guan
University of Cambridge, Harbin Institute of Technology -
S. London
The Department of Psychology, The University of Chicago -
D. Clayton
Clemson University -
C. Mello
OHSU School of Medicine -
S. Friedrich
OHSU School of Medicine -
P. Lovell
OHSU School of Medicine -
E. Osipova
Max Planck Institute of Molecular Cell Biology and Genetics, Center for Systems Biology Dresden, Max Planck Institute for the Physics of Complex Systems -
F. Al-Ajli
Monash University Malaysia, Monash University Malaysia, Qatar Falcon Genome Project -
S. Secomandi
Università degli Studi di Milano -
H. Kim
Seoul National University, Department of Food and Animal Biotechnology -
C. Theofanopoulou
Rockefeller University -
M. Hiller
LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Forschungsinstitut und Naturmuseum, Goethe-Universität Frankfurt am Main -
Y. Zhou
BGI-Shenzhen -
R. Harris
Pennsylvania State University -
K. Makova
Pennsylvania State University, Pennsylvania State University, Pennsylvania State University -
P. Medvedev
Pennsylvania State University, Pennsylvania State University, Pennsylvania State University, Pennsylvania State University -
J. Hoffman
National Center for Biotechnology Information (NCBI) -
P. Masterson
National Center for Biotechnology Information (NCBI) -
K. Clark
National Center for Biotechnology Information (NCBI) -
F. Martin
European Bioinformatics Institute -
K. Howe
European Bioinformatics Institute -
P. Flicek
European Bioinformatics Institute -
B. Walenz
National Human Genome Research Institute (NHGRI) -
W. Kwak
Hoonygen -
H. Clawson
University of California, Santa Cruz
Название журнала
- Nature
Том
- 592
Выпуск
- 7856
Страницы
- 737-746
Финансирующая организация
- Wellcome Trust
Номер гранта
- 750747
Тип документа
- journal article
Тип лицензии Creative Commons
- CC BY
Правовой статус документа
- Свободная лицензия
Источник
- scopus
