Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileArang Rhie, View ORCID ProfileShane A. McCarthy, View ORCID ProfileOlivier Fedrigo, View ORCID ProfileJoana Damas, View ORCID ProfileGiulio Formenti, View ORCID ProfileSergey Koren, View ORCID ProfileMarcela Uliano-Silva, View ORCID ProfileWilliam Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin, View ORCID ProfileFrancoise Thibaud-Nissen, View ORCID ProfileLeanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim, View ORCID ProfileIliana Bista, Michelle Smith, View ORCID ProfileBettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, View ORCID ProfileSonja C. Vernes, View ORCID ProfileTanya M. Lama, View ORCID ProfileFrank Grutzner, View ORCID ProfileWesley C. Warren, View ORCID ProfileChristopher Balakrishnan, View ORCID ProfileDave Burt, View ORCID ProfileJulia M. George, Mathew Biegler, David Iorns, View ORCID ProfileAndrew Digby, Daryl Eason, View ORCID ProfileTaylor Edwards, View ORCID ProfileMark Wilkinson, View ORCID ProfileGeorge Turner, View ORCID ProfileAxel Meyer, View ORCID ProfileAndreas F. Kautt, View ORCID ProfilePaolo Franchini, View ORCID ProfileH William Detrich III, View ORCID ProfileHannes Svardal, View ORCID ProfileMaximilian Wagner, Gavin J.P. Naylor, View ORCID ProfileMartin Pippel, View ORCID ProfileMilan Malinsky, Mark Mooney, Maria Simbirsky, View ORCID ProfileBrett T. Hannigan, View ORCID ProfileTrevor Pesout, Marlys Houck, Ann Misuraca, View ORCID ProfileSarah B. Kingan, Richard Hall, View ORCID ProfileZev Kronenberg, View ORCID ProfileJonas Korlach, Ivan Sović, View ORCID ProfileChristopher Dunn, View ORCID ProfileZemin Ning, Alex Hastie, View ORCID ProfileJoyce Lee, Siddarth Selvaraj, View ORCID ProfileRichard E. Green, Nicholas H. Putnam, Jay Ghurye, View ORCID ProfileErik Garrison, View ORCID ProfileYing Sims, View ORCID ProfileJoanna Collins, View ORCID ProfileSarah Pelan, View ORCID ProfileJames Torrance, View ORCID ProfileAlan Tracey, View ORCID ProfileJonathan Wood, View ORCID ProfileDengfeng Guan, View ORCID ProfileSarah E. London, View ORCID ProfileDavid F. Clayton, View ORCID ProfileClaudio V. Mello, View ORCID ProfileSamantha R. Friedrich, View ORCID ProfilePeter V. Lovell, Ekaterina Osipova, View ORCID ProfileFarooq O. Al-Ajli, View ORCID ProfileSimona Secomandi, Heebal Kim, View ORCID ProfileConstantina Theofanopoulou, View ORCID ProfileYang Zhou, Robert S. Harris, View ORCID ProfileKateryna D. Makova, View ORCID ProfilePaul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, View ORCID ProfileFergal Martin, View ORCID ProfileKevin Howe, View ORCID ProfilePaul Flicek, View ORCID ProfileBrian P. Walenz, View ORCID ProfileWoori Kwak, Hiram Clawson, View ORCID ProfileMark Diekhans, Luis Nassar, View ORCID ProfileBenedict Paten, View ORCID ProfileRobert H.S. Kraus, View ORCID ProfileHarris Lewin, View ORCID ProfileAndrew J. Crawford, View ORCID ProfileM. Thomas P. Gilbert, View ORCID ProfileGuojie Zhang, Byrappa Venkatesh, View ORCID ProfileRobert W. Murphy, View ORCID ProfileKlaus-Peter Koepfli, View ORCID ProfileBeth Shapiro, View ORCID ProfileWarren E. Johnson, Federica Di Palma, Tomas Margues-Bonet, View ORCID ProfileEmma C. Teeling, View ORCID ProfileTandy Warnow, View ORCID ProfileJennifer Marshall Graves, View ORCID ProfileOliver A. Ryder, View ORCID ProfileDavid Hausler, Stephen J. O’Brien, View ORCID ProfileKerstin Howe, View ORCID ProfileEugene W. Myers, View ORCID ProfileRichard Durbin, Adam M. Phillippy, View ORCID ProfileErich D. Jarvis
doi: https://doi.org/10.1101/2020.05.22.110833
Arang Rhie
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Arang Rhie
Shane A. McCarthy
2Department of Genetics, University of Cambridge, Cambridge, UK
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Shane A. McCarthy
Olivier Fedrigo
4Vertebrate Genome Lab, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Olivier Fedrigo
Joana Damas
5The Genome Center, University of California Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joana Damas
Giulio Formenti
4Vertebrate Genome Lab, The Rockefeller University, New York City, USA
6Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Giulio Formenti
Sergey Koren
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sergey Koren
Marcela Uliano-Silva
7Leibniz Institute for Zoo and Wildlife Research, Department of Evolutionary Genetics, Berlin, Germany
8Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Marcela Uliano-Silva
William Chow
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for William Chow
Arkarachai Fungtammasan
9DNAnexus Inc.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gregory L. Gedman
5The Genome Center, University of California Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lindsey J. Cantin
5The Genome Center, University of California Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Francoise Thibaud-Nissen
10National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Francoise Thibaud-Nissen
Leanne Haggerty
11European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Leanne Haggerty
Chul Lee
12Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Byung June Ko
13Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Juwan Kim
12Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Iliana Bista
2Department of Genetics, University of Cambridge, Cambridge, UK
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Iliana Bista
Michelle Smith
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Bettina Haase
4Vertebrate Genome Lab, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bettina Haase
Jacquelyn Mountcastle
4Vertebrate Genome Lab, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sylke Winkler
14Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
15DRESDEN concept Genome Center, Dresden, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sadye Paez
4Vertebrate Genome Lab, The Rockefeller University, New York City, USA
6Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jason Howard
6Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
16Novogene, Durham, North Carolina, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sonja C. Vernes
17Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
18Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sonja C. Vernes
Tanya M. Lama
19University of Massachusetts Cooperative Fish and Wildlife Research Unit, Amherst, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tanya M. Lama
Frank Grutzner
20Shool of Biological Science, The Environment Insitute, University of Adelaide, Adelaide, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Frank Grutzner
Wesley C. Warren
21Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Wesley C. Warren
Christopher Balakrishnan
22Department of Biology, East Carolina University, Greenville, North Carolina, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christopher Balakrishnan
Dave Burt
23UQ Genomics, University of Queensland, Brisbane, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Dave Burt
Julia M. George
24School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Julia M. George
Mathew Biegler
6Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
David Iorns
25The Genetic Rescue Foundation, Wellington, New Zealand
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Andrew Digby
26Department of Conservation, Invercargill, New Zealand
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrew Digby
Daryl Eason
27Kākāpō Recovery, Department of Conservation, Invercargill, New Zealand
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Taylor Edwards
28University of Arizona Genetics Core, Tucson, Arizona, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Taylor Edwards
Mark Wilkinson
29Department of Life Sciences, Natural History Museum, London, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mark Wilkinson
George Turner
30School of Natural Sciences, Bangor University, Gwynedd, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for George Turner
Axel Meyer
31Department of Biology, University of Konstanz, Konstanz, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Axel Meyer
Andreas F. Kautt
32Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
33Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andreas F. Kautt
Paolo Franchini
31Department of Biology, University of Konstanz, Konstanz, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Paolo Franchini
H William Detrich III
33Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for H William Detrich III
Hannes Svardal
34Department of Biology, University of Antwerp, Belgium
35Naturalis Biodiversity Center, Leiden, The Netherlands
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Hannes Svardal
Maximilian Wagner
36Institute of Biology, Karl-Franzens University of Graz, Austria
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Maximilian Wagner
Gavin J.P. Naylor
37Florida Museum of Natural History, University of Florida, Gainesville, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Martin Pippel
14Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
38Center for Systems Biology, Dresden, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Martin Pippel
Milan Malinsky
3Wellcome Sanger Institute, Hinxton, UK
39Zoological Institute, University of Basel, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Milan Malinsky
Mark Mooney
40Tag.bio
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Maria Simbirsky
9DNAnexus Inc.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Brett T. Hannigan
9DNAnexus Inc.
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Brett T. Hannigan
Trevor Pesout
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Trevor Pesout
Marlys Houck
42San Diego Zoo Global, Escondido, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ann Misuraca
43Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah B. Kingan
43Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sarah B. Kingan
Richard Hall
43Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zev Kronenberg
43Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zev Kronenberg
Jonas Korlach
43Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jonas Korlach
Ivan Sović
43Pacific Biosciences, Menlo Park, CA, USA
44Digital BioLogic, Ivanić-Grad, Croatia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christopher Dunn
43Pacific Biosciences, Menlo Park, CA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christopher Dunn
Zemin Ning
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Zemin Ning
Alex Hastie
45Bionano Genomics, San Diego, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Joyce Lee
45Bionano Genomics, San Diego, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joyce Lee
Siddarth Selvaraj
46Arima Genomics, San Diego, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Richard E. Green
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
47Dovetail Genomics, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Richard E. Green
Nicholas H. Putnam
48no current academic or industry affiliation
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jay Ghurye
47Dovetail Genomics, Santa Cruz, California, USA
49Department of Computer Science, University of Maryland College Park, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erik Garrison
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Erik Garrison
Ying Sims
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ying Sims
Joanna Collins
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joanna Collins
Sarah Pelan
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sarah Pelan
James Torrance
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for James Torrance
Alan Tracey
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alan Tracey
Jonathan Wood
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jonathan Wood
Dengfeng Guan
2Department of Genetics, University of Cambridge, Cambridge, UK
50School of Computer Science and Technology, Center for Bioinformatics, Harbin Institute of Technology, Harbin, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Dengfeng Guan
Sarah E. London
51Department of Psychology, Institute for Mind and Biology, University of Chicago, Chicago, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sarah E. London
David F. Clayton
24School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for David F. Clayton
Claudio V. Mello
52Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Claudio V. Mello
Samantha R. Friedrich
52Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Samantha R. Friedrich
Peter V. Lovell
52Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Peter V. Lovell
Ekaterina Osipova
14Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
38Center for Systems Biology, Dresden, Germany
53Max Planck Institute for the Physics of Complex Systems, Dresden Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Farooq O. Al-Ajli
54Monash University Malaysia Genomics Facility, School of Science, Selangor Darul Ehsan, Malaysia
55Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Selangor Darul Ehsan, Malaysia
56Qatar Falcon Genome Project, Al-Gannas Qatari Society, Doha, State of Qatar
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Farooq O. Al-Ajli
Simona Secomandi
57Department of Biosciences, University of Milan, Milan, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Simona Secomandi
Heebal Kim
12Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
13Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
58C&K Genomics, Seoul, Republic of Korea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Constantina Theofanopoulou
6Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Constantina Theofanopoulou
Yang Zhou
59Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
60China National Genebank, BGI-Shenzhen, Shenzhen, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yang Zhou
Robert S. Harris
61Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kateryna D. Makova
61Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA
62Center for Medical Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
63Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kateryna D. Makova
Paul Medvedev
62Center for Medical Genomics, Pennsylvania State University, University Park, Pennsylvania, USA
63Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, USA
64Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
65Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Paul Medvedev
Jinna Hoffman
10National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patrick Masterson
10National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Karen Clark
10National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fergal Martin
11European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Fergal Martin
Kevin Howe
11European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kevin Howe
Paul Flicek
11European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Paul Flicek
Brian P. Walenz
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Brian P. Walenz
Woori Kwak
58C&K Genomics, Seoul, Republic of Korea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Woori Kwak
Hiram Clawson
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mark Diekhans
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mark Diekhans
Luis Nassar
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Benedict Paten
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Benedict Paten
Robert H.S. Kraus
31Department of Biology, University of Konstanz, Konstanz, Germany
66Department of Migration, Max Planck Institute of Animal Behavior, Radolfzell, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Robert H.S. Kraus
Harris Lewin
5The Genome Center, University of California Davis, California, USA
67Department of Evolution and Ecology, University of California Davis, California, USA
68John Muir Institute for the Environment, University of California Davis, California, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Harris Lewin
Andrew J. Crawford
69Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrew J. Crawford
M. Thomas P. Gilbert
70Center for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
71University Museum, Trondheim, Norway
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for M. Thomas P. Gilbert
Guojie Zhang
59Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
60China National Genebank, BGI-Shenzhen, Shenzhen, China
72State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
73Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Guojie Zhang
Byrappa Venkatesh
74Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Robert W. Murphy
75Centre for Biodiversity, Royal Ontario Museum, Toronto, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Robert W. Murphy
Klaus-Peter Koepfli
76Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, D.C., USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Klaus-Peter Koepfli
Beth Shapiro
77Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, USA
78Howard Hughes Medical Institute, Chevy Chase, Maryland USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Beth Shapiro
Warren E. Johnson
76Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, D.C., USA
79The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, USA
80Walter Reed Army Institute of Research, Silver Spring, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Warren E. Johnson
Federica Di Palma
81Department of Biological Sciences, University of East Anglia, Earlham Institute, Norwich, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tomas Margues-Bonet
82Universitat Pompeu Fabra, Spain
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Emma C. Teeling
83School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Emma C. Teeling
Tandy Warnow
84Department of Computer Science, The University of Illinois at Urbana-Champaign, Urbana, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tandy Warnow
Jennifer Marshall Graves
85School of Life science, La Trobe University, Melbourne, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jennifer Marshall Graves
Oliver A. Ryder
42San Diego Zoo Global, Escondido, CA, USA
86Dept. of Evolution, Behavior, and Ecology, University of California, San Diego
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Oliver A. Ryder
David Hausler
41UC Santa Cruz, Genomics Insitute, University of California, Santa Cruz, California, USA
78Howard Hughes Medical Institute, Chevy Chase, Maryland USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for David Hausler
Stephen J. O’Brien
87Laboratory of Genomics Diversity-Center for Computer Technologies, ITMO University, St. Petersburg, Russian Federation
88Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Kerstin Howe
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kerstin Howe
  • For correspondence: ejarvis@rockefeller.edu adam.phillippy@nih.gov rd109@cam.ac.uk gene@mpi-cbg.de kj2@sanger.ac.uk
Eugene W. Myers
14Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
38Center for Systems Biology, Dresden, Germany
39Zoological Institute, University of Basel, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Eugene W. Myers
  • For correspondence: ejarvis@rockefeller.edu adam.phillippy@nih.gov rd109@cam.ac.uk gene@mpi-cbg.de kj2@sanger.ac.uk
Richard Durbin
2Department of Genetics, University of Cambridge, Cambridge, UK
3Wellcome Sanger Institute, Hinxton, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Richard Durbin
  • For correspondence: ejarvis@rockefeller.edu adam.phillippy@nih.gov rd109@cam.ac.uk gene@mpi-cbg.de kj2@sanger.ac.uk
Adam M. Phillippy
1Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: ejarvis@rockefeller.edu adam.phillippy@nih.gov rd109@cam.ac.uk gene@mpi-cbg.de kj2@sanger.ac.uk
Erich D. Jarvis
4Vertebrate Genome Lab, The Rockefeller University, New York City, USA
6Laboratory of Neurogenetics of Language, The Rockefeller University, New York City, USA
78Howard Hughes Medical Institute, Chevy Chase, Maryland USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Erich D. Jarvis
  • For correspondence: ejarvis@rockefeller.edu adam.phillippy@nih.gov rd109@cam.ac.uk gene@mpi-cbg.de kj2@sanger.ac.uk
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

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 only available for 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 the most accurate and complete reference genomes to date. Here we summarize these developments, introduce a set of quality standards, and present lessons learned from sequencing and assembling 16 species representing major vertebrate lineages (mammals, birds, reptiles, amphibians, teleost fishes and cartilaginous fishes). 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 error in assemblies. Our new assemblies identify and correct substantial errors in some of the best historical reference genomes. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an effort to generate high-quality, complete reference genomes for all ~70,000 extant vertebrate species and help enable a new era of discovery across the life sciences.

Competing Interest Statement

During the contributing period, B.T.H, M.Si., A.F. and M.Mo. were employees of DNAnexus Inc. S.B.K., R.H., Z.K., J.Ko., I.S. and C.D. are full-time employees at Pacific Biosciences, a company developing single-molecule sequencing technologies. R.D. is a scientific advisory board member of Dovetail Inc. P.Fl. is a member of the Scientific Advisory Boards of Fabric Genomics, Inc., and Eagle Genomics, Ltd. H.C. receives royalties from the sale of UCSC Genome Browser source code, LiftOver, GBiB, and GBiC licenses to commercial entities. S.K has received travel funds to speak at symposia organized by Oxford Nanopore. M.D. and L.N. receives royalties from licensing of UCSC Genome Browser. For W.E.J., the content here is not to be construed as the views of the DA or DOD.

Footnotes

  • ↵+ Co-first authors: rhiea{at}nih.gov; sam68{at}cam.ac.uk; ofedrigo{at}mail.rockefeller.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted May 23, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Towards complete and error-free genome assemblies of all vertebrate species
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher Balakrishnan, Dave Burt, Julia M. George, Mathew Biegler, David Iorns, Andrew Digby, Daryl Eason, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H William Detrich III, Hannes Svardal, Maximilian Wagner, Gavin J.P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Jonas Korlach, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, 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, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H.S. Kraus, Harris Lewin, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Margues-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Hausler, Stephen J. O’Brien, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis
bioRxiv 2020.05.22.110833; doi: https://doi.org/10.1101/2020.05.22.110833
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie, Shane A. McCarthy, Olivier Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano-Silva, William Chow, Arkarachai Fungtammasan, Gregory L. Gedman, Lindsey J. Cantin, Francoise Thibaud-Nissen, Leanne Haggerty, Chul Lee, Byung June Ko, Juwan Kim, Iliana Bista, Michelle Smith, Bettina Haase, Jacquelyn Mountcastle, Sylke Winkler, Sadye Paez, Jason Howard, Sonja C. Vernes, Tanya M. Lama, Frank Grutzner, Wesley C. Warren, Christopher Balakrishnan, Dave Burt, Julia M. George, Mathew Biegler, David Iorns, Andrew Digby, Daryl Eason, Taylor Edwards, Mark Wilkinson, George Turner, Axel Meyer, Andreas F. Kautt, Paolo Franchini, H William Detrich III, Hannes Svardal, Maximilian Wagner, Gavin J.P. Naylor, Martin Pippel, Milan Malinsky, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout, Marlys Houck, Ann Misuraca, Sarah B. Kingan, Richard Hall, Zev Kronenberg, Jonas Korlach, Ivan Sović, Christopher Dunn, Zemin Ning, Alex Hastie, Joyce Lee, Siddarth Selvaraj, Richard E. Green, Nicholas H. Putnam, Jay Ghurye, Erik Garrison, Ying Sims, Joanna Collins, Sarah Pelan, James Torrance, Alan Tracey, Jonathan Wood, 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, Yang Zhou, Robert S. Harris, Kateryna D. Makova, Paul Medvedev, Jinna Hoffman, Patrick Masterson, Karen Clark, Fergal Martin, Kevin Howe, Paul Flicek, Brian P. Walenz, Woori Kwak, Hiram Clawson, Mark Diekhans, Luis Nassar, Benedict Paten, Robert H.S. Kraus, Harris Lewin, Andrew J. Crawford, M. Thomas P. Gilbert, Guojie Zhang, Byrappa Venkatesh, Robert W. Murphy, Klaus-Peter Koepfli, Beth Shapiro, Warren E. Johnson, Federica Di Palma, Tomas Margues-Bonet, Emma C. Teeling, Tandy Warnow, Jennifer Marshall Graves, Oliver A. Ryder, David Hausler, Stephen J. O’Brien, Kerstin Howe, Eugene W. Myers, Richard Durbin, Adam M. Phillippy, Erich D. Jarvis
bioRxiv 2020.05.22.110833; doi: https://doi.org/10.1101/2020.05.22.110833

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4380)
  • Biochemistry (9571)
  • Bioengineering (7084)
  • Bioinformatics (24832)
  • Biophysics (12595)
  • Cancer Biology (9949)
  • Cell Biology (14344)
  • Clinical Trials (138)
  • Developmental Biology (7943)
  • Ecology (12095)
  • Epidemiology (2067)
  • Evolutionary Biology (15980)
  • Genetics (10915)
  • Genomics (14730)
  • Immunology (9862)
  • Microbiology (23636)
  • Molecular Biology (9472)
  • Neuroscience (50824)
  • Paleontology (369)
  • Pathology (1538)
  • Pharmacology and Toxicology (2678)
  • Physiology (4009)
  • Plant Biology (8653)
  • Scientific Communication and Education (1508)
  • Synthetic Biology (2389)
  • Systems Biology (6422)
  • Zoology (1345)