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Arang Rhie, Shane McCarthy, Olivier D. Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano‐Silva, William Chow, Arkarachai Fungtammasan, Juwan Kim and 119 more
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 Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries.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.
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Rhie, A., McCarthy, S., Fedrigo, O. D., 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. S., Bista, I., Smith, M., … Jarvis, E. D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737–746. https://doi.org/10.1038/s41586-021-03451-0
Rhie, Arang, et al. "Towards complete and error-free genome assemblies of all vertebrate species." Nature, vol. 592, no. 7856, 2021, pp. 737–746, https://doi.org/10.1038/s41586-021-03451-0.
Rhie, Arang, Shane McCarthy, Olivier D. Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, Marcela Uliano‐Silva, et al. "Towards complete and error-free genome assemblies of all vertebrate species." Nature 592, no. 7856 (2021): 737–746. https://doi.org/10.1038/s41586-021-03451-0.
Rhie A., McCarthy S., Fedrigo O. D. [и др.] Towards complete and error-free genome assemblies of all vertebrate species // Nature. — 2021. — Vol. 592, № 7856. — P. 737–746. — URL: https://doi.org/10.1038/s41586-021-03451-0
@article{rhie2021towards,
title = {{Towards complete and error-free genome assemblies of all vertebrate species}},
author = {Arang Rhie and Shane McCarthy and Olivier D. Fedrigo and Joana Damas and Giulio Formenti and Sergey Koren and Marcela Uliano‐Silva and William Chow and Arkarachai Fungtammasan and Juwan Kim and Chul Lee and Byung June Ko and Mark Chaisson and Gregory L. Gedman and Lindsey J. Cantin and Françoise Thibaud‐Nissen and Leanne S. Haggerty and Iliana Bista and Michelle Smith and Bettina Haase and Jacquelyn Mountcastle and Sylke Winkler and Sadye Paez and Jason Travis Howard and Sonja C. Vernes and Tanya M. Lama and Frank Grützner and Wesley C. Warren and Christopher N. Balakrishnan and David W. Burt and Julia M. George and Matthew T. Biegler and David Iorns and Andrew Digby and Daryl Eason and Bruce C. Robertson and Taylor Edwards and Mark Wilkinson and George F. Turner and Axel Meyer and Andreas F. Kautt and Paolo Franchini and H. William Detrich and Hannes Svardal and Maximilian Wagner and Gavin J. P. Naylor and Martin Pippel and Milan Malinsky and Mark Mooney and Maria Simbirsky and Brett T. Hannigan and Trevor Pesout and Marlys L. Houck and Ann C. Misuraca and Sarah B. Kingan and Richard J. Hall and Zev N. Kronenberg and Ivan Sović and Christopher Dunn and Zemin Ning and Alex R. Hastie and Joyce Lee and Siddarth Selvaraj and Richard Edward Green and Nicholas H. Putnam and Ivo Glynne Gut and Jay Ghurye and Erik P. Garrison and Ying Sims and Joanna Collins and Sarah E. Pelan and James Torrance and Alan Tracey and Jonathan M. D. Wood and Robel E. Dagnew and Dengfeng Guan and Sarah E. London and David F. Clayton and Claudio V. Mello and Samantha R. Friedrich and Peter V. Lovell and Ekaterina Osipova and Farooq O. Al-Ajli and Simona Secomandi and Heebal Kim and Constantina Theofanopoulou and Michael Hiller and Yang Zhou and Robert S. Harris and Kateryna D. Makova and Paul Medvedev and Jinna Hoffman and Patrick Masterson and Karen Clark and Fergal J. Martin and Kevin Howe and Kevin Howe and Paul Flicek and Brian P. Walenz and Woori Kwak and Hiram Clawson and Mark Diekhans and Luis R Nassar and Benedict Paten and Robert H. S. Kraus and Andrew J. Crawford and Marcus Thomas P. Gilbert and Guojie Zhang and Byrappa Venkatesh and Robert W. Murphy and Klaus‐Peter Koepfli and Beth Shapiro and Warren E. Johnson and Federica Di Palma and Tomàs Marquès‐Bonet and Emma C. Teeling and Tandy Warnow and Jennifer Marshall Graves and Oliver A. Ryder and David H. Haussler and Stephen J. O’Brien and Jonas Korlach and Harris A. Lewin and Kerstin Howe and Kerstin Howe and Eugene Wimberly Myers and Richard Michael Durbin and Adam M. Phillippy and Erich David Jarvis},
journal = {Nature},
year = {2021},
volume = {592},
number = {7856},
pages = {737--746},
doi = {10.1038/s41586-021-03451-0},
url = {https://doi.org/10.1038/s41586-021-03451-0}
}TY - JOUR AU - Rhie, Arang AU - McCarthy, Shane AU - Fedrigo, Olivier D. AU - Damas, Joana AU - Formenti, Giulio AU - Koren, Sergey AU - Uliano‐Silva, Marcela AU - Chow, William AU - Fungtammasan, Arkarachai AU - Kim, Juwan AU - Lee, Chul AU - Ko, Byung June AU - Chaisson, Mark AU - Gedman, Gregory L. AU - Cantin, Lindsey J. AU - Thibaud‐Nissen, Françoise AU - Haggerty, Leanne S. AU - Bista, Iliana AU - Smith, Michelle AU - Haase, Bettina AU - Mountcastle, Jacquelyn AU - Winkler, Sylke AU - Paez, Sadye AU - Howard, Jason Travis AU - Vernes, Sonja C. AU - Lama, Tanya M. AU - Grützner, Frank AU - Warren, Wesley C. AU - Balakrishnan, Christopher N. AU - Burt, David W. AU - George, Julia M. AU - Biegler, Matthew T. AU - Iorns, David AU - Digby, Andrew AU - Eason, Daryl AU - Robertson, Bruce C. AU - Edwards, Taylor AU - Wilkinson, Mark AU - Turner, George F. AU - Meyer, Axel AU - Kautt, Andreas F. AU - Franchini, Paolo AU - Detrich, H. William AU - Svardal, Hannes AU - Wagner, Maximilian AU - Naylor, Gavin J. P. AU - Pippel, Martin AU - Malinsky, Milan AU - Mooney, Mark AU - Simbirsky, Maria AU - Hannigan, Brett T. AU - Pesout, Trevor AU - Houck, Marlys L. AU - Misuraca, Ann C. AU - Kingan, Sarah B. AU - Hall, Richard J. AU - Kronenberg, Zev N. AU - Sović, Ivan AU - Dunn, Christopher AU - Ning, Zemin AU - Hastie, Alex R. AU - Lee, Joyce AU - Selvaraj, Siddarth AU - Green, Richard Edward AU - Putnam, Nicholas H. AU - Gut, Ivo Glynne AU - Ghurye, Jay AU - Garrison, Erik P. AU - Sims, Ying AU - Collins, Joanna AU - Pelan, Sarah E. AU - Torrance, James AU - Tracey, Alan AU - Wood, Jonathan M. D. AU - Dagnew, Robel E. AU - Guan, Dengfeng AU - London, Sarah E. AU - Clayton, David F. AU - Mello, Claudio V. AU - Friedrich, Samantha R. AU - Lovell, Peter V. AU - Osipova, Ekaterina AU - Al-Ajli, Farooq O. AU - Secomandi, Simona AU - Kim, Heebal AU - Theofanopoulou, Constantina AU - Hiller, Michael AU - Zhou, Yang AU - Harris, Robert S. AU - Makova, Kateryna D. AU - Medvedev, Paul AU - Hoffman, Jinna AU - Masterson, Patrick AU - Clark, Karen AU - Martin, Fergal J. AU - Howe, Kevin AU - Howe, Kevin AU - Flicek, Paul AU - Walenz, Brian P. AU - Kwak, Woori AU - Clawson, Hiram AU - Diekhans, Mark AU - Nassar, Luis R AU - Paten, Benedict AU - Kraus, Robert H. S. AU - Crawford, Andrew J. AU - Gilbert, Marcus Thomas P. AU - Zhang, Guojie AU - Venkatesh, Byrappa AU - Murphy, Robert W. AU - Koepfli, Klaus‐Peter AU - Shapiro, Beth AU - Johnson, Warren E. AU - Palma, Federica Di AU - Marquès‐Bonet, Tomàs AU - Teeling, Emma C. AU - Warnow, Tandy AU - Graves, Jennifer Marshall AU - Ryder, Oliver A. AU - Haussler, David H. AU - O’Brien, Stephen J. AU - Korlach, Jonas AU - Lewin, Harris A. AU - Howe, Kerstin AU - Howe, Kerstin AU - Myers, Eugene Wimberly AU - Durbin, Richard Michael AU - Phillippy, Adam M. AU - Jarvis, Erich David TI - Towards complete and error-free genome assemblies of all vertebrate species JO - Nature VL - 592 IS - 7856 SP - 737 EP - 746 PY - 2021 DA - 2021/04/28 DO - 10.1038/s41586-021-03451-0 UR - https://doi.org/10.1038/s41586-021-03451-0 ER -
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