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

  1. Rhie, Arang ORCID logo
  2. McCarthy, Shane A.
  3. Fedrigo, Olivier ORCID logo
  4. Damas, Joana
  5. Formenti, Giulio ORCID logo
  6. Koren, Sergey ORCID logo
  7. Uliano da Silva, Marcela ORCID logo
  8. Chow, William
  9. Fungtammasan, Arkarachai
  10. Kim, Juwan
  11. Lee, Chul
  12. Ko, Byung June
  13. Chaisson, Mark
  14. Gedman, Gregory L.
  15. Cantin, Lindsey J.
  16. Thibaud-Nissen, Françoise ORCID logo
  17. Haggerty, Leanne
  18. Bista, Iliana
  19. Smith, Michelle
  20. Haase, Bettina
  21. Mountcastle, Jacquelyn ORCID logo
  22. Winkler, Sylke ORCID logo
  23. Paez, Sadye
  24. Howard, Jason
  25. Vernes, Sonja ORCID logo
  26. Lama, Tanya M.
  27. Grutzner, Frank ORCID logo
  28. Warren, Wesley C.
  29. Balakrishnan, Christopher ORCID logo
  30. Burt, David ORCID logo
  31. George, Julia ORCID logo
  32. Biegler, Matthew T.
  33. Iorns, David
  34. Digby, Andrew ORCID logo
  35. Eason, Daryl
  36. Robertson, Bruce ORCID logo
  37. Edwards, Taylor ORCID logo
  38. Wilkinson, Mark
  39. Turner, George
  40. Meyer, Axel ORCID logo
  41. Kautt, Andreas ORCID logo
  42. Franchini, Paolo ORCID logo
  43. Detrich, H William ORCID logo
  44. Svardal, Hannes
  45. Wagner, Maximilian
  46. Naylor, Gavin J. P.
  47. Pippel, Martin ORCID logo
  48. Malinsky, Milan ORCID logo
  49. Mooney, Mark
  50. Simbirsky, Maria
  51. Hannigan, Brett T.
  52. Pesout, Trevor
  53. Houck, Marlys
  54. Misuraca, Ann
  55. Kingan, Sarah ORCID logo
  56. Hall, Richard ORCID logo
  57. Kronenberg, Zev
  58. Sović, Ivan
  59. Dunn, Christopher ORCID logo
  60. Ning, Zemin
  61. Hastie, Alex
  62. Lee, Joyce ORCID logo
  63. Selvaraj, Siddarth
  64. Green, Richard E.
  65. Putnam, Nicholas ORCID logo
  66. Gut, Ivo ORCID logo
  67. Ghurye, Jay
  68. Garrison, Erik
  69. Sims, Ying
  70. Collins, Joanna
  71. Pelan, Sarah
  72. Torrance, James
  73. Tracey, Alan ORCID logo
  74. Wood, Jonathan
  75. Dagnew, Robel E.
  76. GUAN, DENGFENG ORCID logo
  77. London, Sarah ORCID logo
  78. Clayton, David ORCID logo
  79. Mello, Claudio ORCID logo
  80. Friedrich, Samantha ORCID logo
  81. Lovell, Peter V.
  82. Osipova, Ekaterina ORCID logo
  83. Al-Ajli, Farooq ORCID logo
  84. Secomandi, Simona ORCID logo
  85. Kim, Heebal ORCID logo
  86. Theofanopoulou, Constantina ORCID logo
  87. Hiller, Michael
  88. Zhou, Yang ORCID logo
  89. Harris, Robert S.
  90. Makova, Kateryna D.
  91. Medvedev, Paul
  92. Hoffman, Jinna
  93. Masterson, Patrick
  94. Clark, Karen
  95. Martin, Fergal ORCID logo
  96. Howe, Kevin
  97. Flicek, Paul ORCID logo
  98. Walenz, Brian ORCID logo
  99. Kwak, Woori
  100. Clawson, Hiram
  101. Diekhans, Mark ORCID logo
  102. Nassar, Luis
  103. Paten, Benedict ORCID logo
  104. Kraus, Robert H. S.
  105. Crawford, Andrew J. ORCID logo
  106. Gilbert, Marcus ORCID logo
  107. Zhang, Guojie ORCID logo
  108. Venkatesh, Byrappa ORCID logo
  109. Murphy, Robert W.
  110. Koepfli, Klaus-Peter
  111. Shapiro, Beth ORCID logo
  112. Johnson, Warren ORCID logo
  113. Di Palma, Federica
  114. Marques-Bonet, Tomas ORCID logo
  115. Teeling, Emma ORCID logo
  116. Warnow, Tandy
  117. Graves, Jennifer Marshall
  118. Ryder, Oliver ORCID logo
  119. Haussler, David ORCID logo
  120. O’Brien, Stephen J.
  121. , Jonas ORCID logo
  122. Lewin, Harris ORCID logo
  123. Howe, Kerstin ORCID logo
  124. Myers, Eugene ORCID logo
  125. Durbin, Richard ORCID logo
  126. Phillippy, Adam ORCID logo
  127. Jarvis, Erich ORCID logo

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1000 Titel
  • Towards complete and error-free genome assemblies of all vertebrate species
1000 Autor/in
  1. Rhie, Arang |
  2. McCarthy, Shane A. |
  3. Fedrigo, Olivier |
  4. Damas, Joana |
  5. Formenti, Giulio |
  6. Koren, Sergey |
  7. Uliano da Silva, Marcela |
  8. Chow, William |
  9. Fungtammasan, Arkarachai |
  10. Kim, Juwan |
  11. Lee, Chul |
  12. Ko, Byung June |
  13. Chaisson, Mark |
  14. Gedman, Gregory L. |
  15. Cantin, Lindsey J. |
  16. Thibaud-Nissen, Françoise |
  17. Haggerty, Leanne |
  18. Bista, Iliana |
  19. Smith, Michelle |
  20. Haase, Bettina |
  21. Mountcastle, Jacquelyn |
  22. Winkler, Sylke |
  23. Paez, Sadye |
  24. Howard, Jason |
  25. Vernes, Sonja |
  26. Lama, Tanya M. |
  27. Grutzner, Frank |
  28. Warren, Wesley C. |
  29. Balakrishnan, Christopher |
  30. Burt, David |
  31. George, Julia |
  32. Biegler, Matthew T. |
  33. Iorns, David |
  34. Digby, Andrew |
  35. Eason, Daryl |
  36. Robertson, Bruce |
  37. Edwards, Taylor |
  38. Wilkinson, Mark |
  39. Turner, George |
  40. Meyer, Axel |
  41. Kautt, Andreas |
  42. Franchini, Paolo |
  43. Detrich, H William |
  44. Svardal, Hannes |
  45. Wagner, Maximilian |
  46. Naylor, Gavin J. P. |
  47. Pippel, Martin |
  48. Malinsky, Milan |
  49. Mooney, Mark |
  50. Simbirsky, Maria |
  51. Hannigan, Brett T. |
  52. Pesout, Trevor |
  53. Houck, Marlys |
  54. Misuraca, Ann |
  55. Kingan, Sarah |
  56. Hall, Richard |
  57. Kronenberg, Zev |
  58. Sović, Ivan |
  59. Dunn, Christopher |
  60. Ning, Zemin |
  61. Hastie, Alex |
  62. Lee, Joyce |
  63. Selvaraj, Siddarth |
  64. Green, Richard E. |
  65. Putnam, Nicholas |
  66. Gut, Ivo |
  67. Ghurye, Jay |
  68. Garrison, Erik |
  69. Sims, Ying |
  70. Collins, Joanna |
  71. Pelan, Sarah |
  72. Torrance, James |
  73. Tracey, Alan |
  74. Wood, Jonathan |
  75. Dagnew, Robel E. |
  76. GUAN, DENGFENG |
  77. London, Sarah |
  78. Clayton, David |
  79. Mello, Claudio |
  80. Friedrich, Samantha |
  81. Lovell, Peter V. |
  82. Osipova, Ekaterina |
  83. Al-Ajli, Farooq |
  84. Secomandi, Simona |
  85. Kim, Heebal |
  86. Theofanopoulou, Constantina |
  87. Hiller, Michael |
  88. Zhou, Yang |
  89. Harris, Robert S. |
  90. Makova, Kateryna D. |
  91. Medvedev, Paul |
  92. Hoffman, Jinna |
  93. Masterson, Patrick |
  94. Clark, Karen |
  95. Martin, Fergal |
  96. Howe, Kevin |
  97. Flicek, Paul |
  98. Walenz, Brian |
  99. Kwak, Woori |
  100. Clawson, Hiram |
  101. Diekhans, Mark |
  102. Nassar, Luis |
  103. Paten, Benedict |
  104. Kraus, Robert H. S. |
  105. Crawford, Andrew J. |
  106. Gilbert, Marcus |
  107. Zhang, Guojie |
  108. Venkatesh, Byrappa |
  109. Murphy, Robert W. |
  110. Koepfli, Klaus-Peter |
  111. Shapiro, Beth |
  112. Johnson, Warren |
  113. Di Palma, Federica |
  114. Marques-Bonet, Tomas |
  115. Teeling, Emma |
  116. Warnow, Tandy |
  117. Graves, Jennifer Marshall |
  118. Ryder, Oliver |
  119. Haussler, David |
  120. O’Brien, Stephen J. |
  121. , Jonas |
  122. Lewin, Harris |
  123. Howe, Kerstin |
  124. Myers, Eugene |
  125. Durbin, Richard |
  126. Phillippy, Adam |
  127. Jarvis, Erich |
1000 Erscheinungsjahr 2021
1000 LeibnizOpen
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2021-04-28
1000 Erschienen in
1000 Quellenangabe
  • 592(7856):737-746
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2021
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1038/s41586-021-03451-0 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8081667/ |
1000 Ergänzendes Material
  • https://www.nature.com/articles/s41586-021-03451-0#Sec57 |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • 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.
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. 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1000 Label
1000 Förderer
  1. National Institutes of Health |
  2. Ministry of Health and Welfare |
  3. Wellcome Trust |
  4. European Molecular Biology Laboratory |
  5. Howard Hughes Medical Institute |
  6. Rockefeller University |
  7. Robert and Rosabel Osborne Endowment |
  8. H2020 Marie Skłodowska-Curie Actions |
  9. Ministry of Oceans and Fisheries |
  10. Alfred P. Sloan Foundation |
  11. Max-Planck-Gesellschaft |
  12. Human Frontier Science Program |
  13. Maine Department of Inland Fisheries and Wildlife |
  14. Walter Reed Army Institute of Research |
  15. National Science Foundation |
  16. Science Exchange Inc. (Palo Alto, CA) |
  17. Northeastern University |
  18. Lenfest Ocean Program |
  19. Bundesministerium für Bildung und Forschung |
  20. European Molecular Biology Organization |
  21. National Key Research and Development Program of China |
  22. Al-Gannas Qatari Society |
  23. The Cultural Village Foundation-Katara, Doha, State of Qatar |
  24. Monash University Malaysia |
  25. Hessisches Ministerium für Wissenschaft und Kunst |
  26. Ministerium für Wissenschaft, Forschung und Kunst Baden-Württemberg |
  27. Universities of the State of Baden-Württemberg, Germany |
  28. Biomedical Research Council of A*STAR, Singapore |
  29. Ministerio de Economía y Competitividad |
  30. Federación Española de Enfermedades Raras |
  31. Unidad de Excelencia María de Maeztu, AEI |
  32. Howard Hughes International Early Career award |
  33. Secretaria d’Universitats i Recerca |
  34. Generalitat de Catalunya |
  35. European Research Council |
  36. Irish Research Council |
  37. Danmarks Grundforskningsfond |
  38. Australian Research Council |
1000 Fördernummer
  1. 1ZIAHG200398; R44HG008118; R21 DC014432/DC/NIDCD; R01GM130691; 5U41HG002371-19; U41HG007234; R01HG010485; 5U41HG002371-19
  2. HI17C2098
  3. WT207492; WT206194; WT108749/Z/15/Z; WT218328/B/19/Z; 108749/Z/15/Z
  4. -
  5. -
  6. -
  7. -
  8. 750747; 864203
  9. 20180430
  10. FG-2020-12932
  11. -
  12. RGP0058/2016; RGP0030/2015
  13. F11AF01099
  14. -
  15. 1457541; 1456612; OPP-0132032; PLR-1444167; OPP-1955368; 1458652
  16. -
  17. -
  18. 30884
  19. 01IS18026C
  20. ALTF 456-2016
  21. 2017YFC1201201; 2018YFC0910504; 2017YFC0907503
  22. -
  23. -
  24. -
  25. -
  26. -
  27. bwHPC-C5
  28. -
  29. BFU2017-86471-P
  30. BFU2017-86471-P
  31. CEX2018-000792-M
  32. -
  33. GRC 2017 SGR 880
  34. GRC 2017 SGR 880
  35. ERC-2012-StG311000; 681396
  36. -
  37. DNRF143
  38. CEO561477
1000 Förderprogramm
  1. Intramural Research Program of the NHGRI; Intramural Research Program of the NLM; S. Selvaraj
  2. Korea Health Technology R&D Project
  3. -
  4. -
  5. -
  6. -
  7. -
  8. -
  9. Marine Biotechnology Program
  10. -
  11. -
  12. -
  13. -
  14. National Research Council Research Associateship Award
  15. ICEFISH 2004 Cruise
  16. -
  17. -
  18. -
  19. -
  20. -
  21. -
  22. -
  23. -
  24. -
  25. LOEWE-Centre for Translational Biodiversity Genomics (TBG)
  26. -
  27. -
  28. -
  29. -
  30. -
  31. -
  32. -
  33. -
  34. CERCA Programme
  35. Consolidator Award -Extinction Genomics
  36. Laureate Award
  37. -
  38. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer National Institutes of Health |
    1000 Förderprogramm Intramural Research Program of the NHGRI; Intramural Research Program of the NLM; S. Selvaraj
    1000 Fördernummer 1ZIAHG200398; R44HG008118; R21 DC014432/DC/NIDCD; R01GM130691; 5U41HG002371-19; U41HG007234; R01HG010485; 5U41HG002371-19
  2. 1000 joinedFunding-child
    1000 Förderer Ministry of Health and Welfare |
    1000 Förderprogramm Korea Health Technology R&D Project
    1000 Fördernummer HI17C2098
  3. 1000 joinedFunding-child
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1000 Erstellt am 2022-08-08T14:44:59.217+0200
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