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1. The complete sequence of a human Y chromosome

Author

Arang Rhie, Sergey Nurk, Monika Cechova, Savannah J. Hoyt, Dylan J. Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Mikko Rautiainen, Ivan A. Alexandrov, Jamie Allen, Mobin Asri, Andrey V. Bzikadze, Nae-Chyun Chen, Chen-Shan Chin, Mark Diekhans, Paul Flicek, Giulio Formenti, Arkarachai Fungtammasan, Carlos Garcia Giron, Erik Garrison, Ariel Gershman, Jennifer Gerton, Patrick G.S. Grady, Andrea Guarracino, Leanne Haggerty, Reza Halabian, Nancy F. Hansen, Robert Harris, Gabrielle A. Hartley, William T. Harvey, Marina Haukness, Jakob Heinz, Thibaut Hourlier, Robert M. Hubley, Sarah E. Hunt, Stephen Hwang, Miten Jain, Rupesh K. Kesharwani, Alexandra P. Lewis, Heng Li, Glennis A. Logsdon, Julian K. Lucas, Wojciech Makalowski, Christopher Markovic, Fergal J. Martin, Ann M. Mc Cartney, Rajiv C. McCoy, Jennifer McDaniel, Brandy M. McNulty, Paul Medvedev, Alla Mikheenko, Katherine M. Munson, Terence D. Murphy, Hugh E. Olsen, Nathan D. Olson, Luis F. Paulin, David Porubsky, Tamara Potapova, Fedor Ryabov, Steven L. Salzberg, Michael E.G. Sauria, Fritz J. Sedlazeck, Kishwar Shafin, Valery A. Shepelev, Alaina Shumate, Jessica M. Storer, Likhitha Surapaneni, Angela M. Taravella Oill, Françoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Allison C. Watwood, Matthias H. Weissensteiner, Aaron M. Wenger, Melissa A. Wilson, Samantha Zarate, Yiming Zhu, Justin M. Zook, Evan E. Eichler, Rachel O’Neill, Michael C. Schatz, Karen H. Miga, Kateryna D. Makova, and Adam M. Phillippy

Abstract

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029 base pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, revealing the complete ampliconic structures ofTSPY, DAZ, andRBMY; 42 additional protein-coding genes, mostly from theTSPYgene family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a prior assembly of the CHM13 genome and mapped available population variation, clinical variants, and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Published
2022
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2. The complete sequence of a human Y chromosome

Author

Rhie, Arang, primary, Nurk, Sergey, additional, Cechova, Monika, additional, Hoyt, Savannah J., additional, Taylor, Dylan J., additional, Altemose, Nicolas, additional, Hook, Paul W., additional, Koren, Sergey, additional, Rautiainen, Mikko, additional, Alexandrov, Ivan A., additional, Allen, Jamie, additional, Asri, Mobin, additional, Bzikadze, Andrey V., additional, Chen, Nae-Chyun, additional, Chin, Chen-Shan, additional, Diekhans, Mark, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Fungtammasan, Arkarachai, additional, Garcia Giron, Carlos, additional, Garrison, Erik, additional, Gershman, Ariel, additional, Gerton, Jennifer L., additional, Grady, Patrick G.S., additional, Guarracino, Andrea, additional, Haggerty, Leanne, additional, Halabian, Reza, additional, Hansen, Nancy F., additional, Harris, Robert, additional, Hartley, Gabrielle A., additional, Harvey, William T., additional, Haukness, Marina, additional, Heinz, Jakob, additional, Hourlier, Thibaut, additional, Hubley, Robert M., additional, Hunt, Sarah E., additional, Hwang, Stephen, additional, Jain, Miten, additional, Kesharwani, Rupesh K., additional, Lewis, Alexandra P., additional, Li, Heng, additional, Logsdon, Glennis A., additional, Lucas, Julian K., additional, Makalowski, Wojciech, additional, Markovic, Christopher, additional, Martin, Fergal J., additional, Mc Cartney, Ann M., additional, McCoy, Rajiv C., additional, McDaniel, Jennifer, additional, McNulty, Brandy M., additional, Medvedev, Paul, additional, Mikheenko, Alla, additional, Munson, Katherine M., additional, Murphy, Terence D., additional, Olsen, Hugh E., additional, Olson, Nathan D., additional, Paulin, Luis F., additional, Porubsky, David, additional, Potapova, Tamara, additional, Ryabov, Fedor, additional, Salzberg, Steven L., additional, Sauria, Michael E.G., additional, Sedlazeck, Fritz J., additional, Shafin, Kishwar, additional, Shepelev, Valery A., additional, Shumate, Alaina, additional, Storer, Jessica M., additional, Surapaneni, Likhitha, additional, Taravella Oill, Angela M., additional, Thibaud-Nissen, Françoise, additional, Timp, Winston, additional, Tomaszkiewicz, Marta, additional, Vollger, Mitchell R., additional, Walenz, Brian P., additional, Watwood, Allison C., additional, Weissensteiner, Matthias H., additional, Wenger, Aaron M., additional, Wilson, Melissa A., additional, Zarate, Samantha, additional, Zhu, Yiming, additional, Zook, Justin M., additional, Eichler, Evan E., additional, O’Neill, Rachel J., additional, Schatz, Michael C., additional, Miga, Karen H., additional, Makova, Kateryna D., additional, and Phillippy, Adam M., additional

Published
2022
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3. Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Author

Simona Secomandi, Guido Roberto Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders Pape Møller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer-Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Françoise Thibaud-Nissen, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, and Giulio Formenti

Abstract

Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.

Published
2022
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4. Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Author

Secomandi, Simona, primary, Gallo, Guido Roberto, additional, Sozzoni, Marcella, additional, Iannucci, Alessio, additional, Galati, Elena, additional, Abueg, Linelle, additional, Balacco, Jennifer, additional, Caprioli, Manuela, additional, Chow, William, additional, Ciofi, Claudio, additional, Collins, Joanna, additional, Fedrigo, Olivier, additional, Ferretti, Luca, additional, Fungtammasan, Arkarachai, additional, Haase, Bettina, additional, Howe, Kerstin, additional, Kwak, Woori, additional, Lombardo, Gianluca, additional, Masterson, Patrick, additional, Messina, Graziella, additional, Møller, Anders Pape, additional, Mountcastle, Jacquelyn, additional, Mousseau, Timothy A., additional, Ferrer-Obiol, Joan, additional, Olivieri, Anna, additional, Rhie, Arang, additional, Rubolini, Diego, additional, Saclier, Marielle, additional, Stanyon, Roscoe, additional, Stucki, David, additional, Thibaud-Nissen, Françoise, additional, Torrance, James, additional, Torroni, Antonio, additional, Weber, Kristina, additional, Ambrosini, Roberto, additional, Bonisoli-Alquati, Andrea, additional, Jarvis, Erich D., additional, Gianfranceschi, Luca, additional, and Formenti, Giulio, additional

Published
2022
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5. Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

Author

Karen H. Miga, Christopher E. Mason, Aaron M. Wenger, Arkarachai Fungtammasan, Yiming Zhu, Nathan D. Olson, Justin M. Zook, David Jáspez, Sayed Mohammad Ebrahim Sahraeian, Haoyu Cheng, William J Rowell, Chunlin Xiao, Giuseppe Narzisi, Lindsay Harris, Aishwarya Pisupati, Justin Wagner, Byunggil Yoo, Wayne E. Clarke, Joyce V. Lee, Fritz J. Sedlazeck, Chen-Shan Chin, Richa Gupta, Yih-Chii Hwang, Alaina Shumate, José M. Lorenzo-Salazar, Jesse Farek, Carlos Flores, Jennifer McDaniel, Uday Shanker Evani, Heng Li, Stephen E Lincoln, Danny E. Miller, Luis A. Rubio-Rodríguez, Medhat Mahmoud, Adrián Muñoz-Barrera, Ziad Khan, and Mark T. W. Ebbert

Subjects
Benchmark (computing), Variation (game tree), Computational biology, Biology, Indel, Gene, Genome, Method development, DNA sequencing
Abstract

The repetitive nature and complexity of multiple medically important genes make them intractable to accurate analysis, despite the maturity of short-read sequencing, resulting in a gap in clinical applications of genome sequencing. The Genome in a Bottle Consortium has provided benchmark variant sets, but these excluded some medically relevant genes due to their repetitiveness or polymorphic complexity. In this study, we characterize 273 of these 395 challenging autosomal genes that have multiple implications for medical sequencing. This extended, curated benchmark reports over 17,000 SNVs, 3,600 INDELs, and 200 SVs each for GRCh37 and GRCh38 across HG002. We show that false duplications in either GRCh37 or GRCh38 result in reference-specific, missed variants for short- and long-read technologies in medically important genes including CBS, CRYAA, and KCNE1. Our proposed solution improves variant recall in these genes from 8% to 100%. This benchmark will significantly improve the comprehensive characterization of these medically relevant genes and guide new method development.

Published
2021
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6. The complete sequence of a human genome

Author

Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G.S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Yumi Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, and Adam M. Phillippy

Subjects
Complete sequence, Heterochromatin, Genomics, Human genome, Preprint, Computational biology, Biology
Abstract

In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics. While these drafts and the updates that followed effectively covered the euchromatic fraction of the genome, the heterochromatin and many other complex regions were left unfinished or erroneous. Addressing this remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium has finished the first truly complete 3.055 billion base pair (bp) sequence of a human genome, representing the largest improvement to the human reference genome since its initial release. The new T2T-CHM13 reference includes gapless assemblies for all 22 autosomes plus Chromosome X, corrects numerous errors, and introduces nearly 200 million bp of novel sequence containing 2,226 paralogous gene copies, 115 of which are predicted to be protein coding. The newly completed regions include all centromeric satellite arrays and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies for the first time.

Published
2021
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7. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Author

Cartney, Ann M. Mc, primary, Shafin, Kishwar, additional, Alonge, Michael, additional, Bzikadze, Andrey V., additional, Formenti, Giulio, additional, Fungtammasan, Arkarachai, additional, Howe, Kerstin, additional, Jain, Chirag, additional, Koren, Sergey, additional, Logsdon, Glennis A., additional, Miga, Karen H., additional, Mikheenko, Alla, additional, Paten, Benedict, additional, Shumate, Alaina, additional, Soto, Daniela C., additional, Sović, Ivan, additional, Wood, Jonathan MD, additional, Zook, Justin M., additional, Phillippy, Adam M., additional, and Rhie, Arang, additional

Published
2021
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8. Towards a Comprehensive Variation Benchmark for Challenging Medically-Relevant Autosomal Genes

Author

Wagner, Justin, primary, Olson, Nathan D, additional, Harris, Lindsay, additional, McDaniel, Jennifer, additional, Cheng, Haoyu, additional, Fungtammasan, Arkarachai, additional, Hwang, Yih-Chii, additional, Gupta, Richa, additional, Wenger, Aaron M, additional, Rowell, William J, additional, Khan, Ziad M, additional, Farek, Jesse, additional, Zhu, Yiming, additional, Pisupati, Aishwarya, additional, Mahmoud, Medhat, additional, Xiao, Chunlin, additional, Yoo, Byunggil, additional, Sahraeian, Sayed Mohammad Ebrahim, additional, Miller, Danny E., additional, Jáspez, David, additional, Lorenzo-Salazar, José M., additional, Muñoz-Barrera, Adrián, additional, Rubio-Rodríguez, Luis A., additional, Flores, Carlos, additional, Narzisi, Giuseppe, additional, Evani, Uday Shanker, additional, Clarke, Wayne E., additional, Lee, Joyce, additional, Mason, Christopher E., additional, Lincoln, Stephen E., additional, Miga, Karen H., additional, Ebbert, Mark T. W., additional, Shumate, Alaina, additional, Li, Heng, additional, Chin, Chen-Shan, additional, Zook, Justin M, additional, and Sedlazeck, Fritz J, additional

Published
2021
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9. Benchmarking challenging small variants with linked and long reads

Author

Justin Wagner, Nathan D Olson, Lindsay Harris, Jennifer McDaniel, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stankovic, Vladimir Kovacevic, Byunggil Yoo, Neil Miller, Jeffrey A. Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne Clarke, Uday S. Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Peter Ebert, Tobias Marschall, Peter Lansdorp, Vincent Hanlon, Carl-Adam Mattsson, Alvaro Martinez Barrio, Ian T Fiddes, Chunlin Xiao, Arkarachai Fungtammasan, Chen-Shan Chin, Aaron M Wenger, William J Rowell, Fritz J Sedlazeck, Andrew Carroll, Marc Salit, and Justin M Zook

Subjects
Structural variation, Computer science, Centromere, Benchmark (computing), PMS2, Computational biology, Benchmarking, Copy-number variation, Indel, Genome, Gene, Segmental duplication
Abstract

Genome in a Bottle (GIAB) benchmarks have been widely used to help validate clinical sequencing pipelines and develop new variant calling and sequencing methods. Here we use accurate long and linked reads to expand the prior benchmark to include difficult-to-map regions and segmental duplications that are not readily accessible to short reads. Our new benchmark adds more than 300,000 SNVs, 50,000 indels, and 16 % new exonic variants, many in challenging, clinically relevant genes not previously covered (e.g., PMS2). We increase coverage of the autosomal GRCh38 assembly from 85 % to 92 %, while excluding problematic regions for benchmarking small variants (e.g., copy number variants and assembly errors) that should not have been in the previous version. Our new benchmark reliably identifies both false positives and false negatives across multiple short-, linked-, and long-read based variant calling methods. As an example of its utility, this benchmark identifies eight times more false negatives in a short read variant call set relative to our previous benchmark, mostly in difficult-to-map regions. To enable robust small variant benchmarking, we still exclude 3.6% of GRCh37 and 5.0% of GRCh38 in (1) highly repetitive regions such as large, highly similar segmental duplications and the centromere not accessible to our data and (2) regions where our sample is highly divergent from the reference due to large indels, structural variation, copy number variation, and/or errors in the reference (e.g., some KIR genes that have duplications in HG002). We have demonstrated the utility of this benchmark to assess performance in more challenging regions, which enables benchmarking in more difficult genes and continued technology and bioinformatics development. The v4.2.1 benchmarks are available under ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/.

Published
2020
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10. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats

Author

Sylke Winkler, Daniel Fordham, Marcela Uliano-Silva, Samara Brown, Emma Betteridge, James Torrance, David S. Horner, Shane A. McCarthy, Jennifer Balacco, Alan Tracey, Simon Mayes, Farooq O. Al-Ajli, Matteo Chiara, Sergey Koren, Edward L. Braun, Michelle Smith, Jason Skelton, Arang Rhie, Richard Durbin, Alessandro Achilli, Craig Corton, Vania Costa, Iliana Bista, Bettina Haase, Peter Houde, Olivier Fedrigo, Marco Rosario Capodiferro, Erich D. Jarvis, Woori Kwak, Jonas Korlach, Jacquelyn Mountcastle, Giulio Formenti, Karen Oliver, Jonathan Wood, Kerstin Howe, Jale Dolucan, Eugene W. Myers, Roberto Ambrosini, Arkarachai Fungtammasan, and Adam M. Phillippy

Subjects
Novel gene, Mitochondrial DNA, Fully automated, biology, biology.animal, Sequence assembly, Vertebrate, Tissue type, Computational biology, Genome, Gene
Abstract

Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. As part of the Vertebrate Genomes Project (VGP) we have developed mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (>10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline led to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We have observed that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we have identified errors, missing sequences, and incomplete genes in those references, particularly in repeat regions. Our assemblies have also identified novel gene region duplications, shedding new light on mitochondrial genome evolution and organization.

Published
2020
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11. Towards complete and error-free genome assemblies of all vertebrate species

Author

Claudio V. Mello, H. William Detrich, Oliver A. Ryder, George F. Turner, Robert H. S. Kraus, Daryl Eason, Sergey Koren, Stephen J. O'Brien, Ivan Sović, Tandy Warnow, Dave W Burt, Martin Pippel, Mark Diekhans, Jonathan Wood, Sylke Winkler, Joana Damas, Benedict Paten, Shane A. McCarthy, Gregory Gedman, M. Thomas P. Gilbert, David F. Clayton, Erich D. Jarvis, Frank Grützner, Richard E. Green, Andrew J. Crawford, Federica Di Palma, Jason T. Howard, Fergal J. Martin, Brett T. Hannigan, Samantha R. Friedrich, Emma C. Teeling, David Iorns, Woori Kwak, Maximilian Wagner, Iliana Bista, Hiram Clawson, Milan Malinsky, Peter V. Lovell, Gavin J. P. Naylor, Robert S. Harris, Ekaterina Osipova, Sadye Paez, Christopher N. Balakrishnan, Eugene W. Myers, Byrappa Venkatesh, Brian P. Walenz, Warren E. Johnson, Nicholas H. Putnam, Harris A. Lewin, Hannes Svardal, Leanne Haggerty, Andreas F. Kautt, Tomas Marques-Bonet, Luis R Nassar, Maria Simbirsky, Christopher Dunn, William Chow, Marlys L. Houck, Paolo Franchini, Joanna Collins, Jinna Hoffman, Sonja C. Vernes, Alan Tracey, Siddarth Selvaraj, Sarah E. London, Ann C Misuraca, Heebal Kim, Byung June Ko, Trevor Pesout, Françoise Thibaud-Nissen, Jimin George, Jennifer A. Marshall Graves, Arang Rhie, Ying Sims, Mark Wilkinson, Robert W. Murphy, Dengfeng Guan, Axel Meyer, Richard Durbin, Arkarachai Fungtammasan, Sarah Pelan, Lindsey J. Cantin, Erik Garrison, Kerstin Howe, Farooq O. Al-Ajli, Zev N. Kronenberg, Michelle Smith, Paul Flicek, James Torrance, Guojie Zhang, J. H. Kim, Richard Hall, Tanya M. Lama, David Haussler, Matthew T. Biegler, Klaus-Peter Koepfli, Beth Shapiro, Bettina Haase, Andrew Digby, Wesley C. Warren, Alex Hastie, Adam M. Phillippy, Paul Medvedev, Marcela Uliano-Silva, Mark Mooney, Constantina Theofanopoulou, Karen Clark, Chul Hee Lee, Zemin Ning, Olivier Fedrigo, Taylor Edwards, Simona Secomandi, Joyce V. Lee, Jonas Korlach, Patrick Masterson, Jay Ghurye, Jacquelyn Mountcastle, Giulio Formenti, Yang Zhou, Kevin L. Howe, Sarah B. Kingan, and Kateryna D. Makova

Subjects
Biodiversity conservation, Extant taxon, biology, Evolutionary biology, biology.animal, Vertebrate, Genomics, Sources of error, Genome, Reference genome
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.

Published
2020
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12. The complete sequence of a human genome

Author

Nurk, Sergey, primary, Koren, Sergey, additional, Rhie, Arang, additional, Rautiainen, Mikko, additional, Bzikadze, Andrey V., additional, Mikheenko, Alla, additional, Vollger, Mitchell R., additional, Altemose, Nicolas, additional, Uralsky, Lev, additional, Gershman, Ariel, additional, Aganezov, Sergey, additional, Hoyt, Savannah J., additional, Diekhans, Mark, additional, Logsdon, Glennis A., additional, Alonge, Michael, additional, Antonarakis, Stylianos E., additional, Borchers, Matthew, additional, Bouffard, Gerard G., additional, Brooks, Shelise Y., additional, Caldas, Gina V., additional, Cheng, Haoyu, additional, Chin, Chen-Shan, additional, Chow, William, additional, de Lima, Leonardo G., additional, Dishuck, Philip C., additional, Durbin, Richard, additional, Dvorkina, Tatiana, additional, Fiddes, Ian T., additional, Formenti, Giulio, additional, Fulton, Robert S., additional, Fungtammasan, Arkarachai, additional, Garrison, Erik, additional, Grady, Patrick G.S., additional, Graves-Lindsay, Tina A., additional, Hall, Ira M., additional, Hansen, Nancy F., additional, Hartley, Gabrielle A., additional, Haukness, Marina, additional, Howe, Kerstin, additional, Hunkapiller, Michael W., additional, Jain, Chirag, additional, Jain, Miten, additional, Jarvis, Erich D., additional, Kerpedjiev, Peter, additional, Kirsche, Melanie, additional, Kolmogorov, Mikhail, additional, Korlach, Jonas, additional, Kremitzki, Milinn, additional, Li, Heng, additional, Maduro, Valerie V., additional, Marschall, Tobias, additional, McCartney, Ann M., additional, McDaniel, Jennifer, additional, Miller, Danny E., additional, Mullikin, James C., additional, Myers, Eugene W., additional, Olson, Nathan D., additional, Paten, Benedict, additional, Peluso, Paul, additional, Pevzner, Pavel A., additional, Porubsky, David, additional, Potapova, Tamara, additional, Rogaev, Evgeny I., additional, Rosenfeld, Jeffrey A., additional, Salzberg, Steven L., additional, Schneider, Valerie A., additional, Sedlazeck, Fritz J., additional, Shafin, Kishwar, additional, Shew, Colin J., additional, Shumate, Alaina, additional, Sims, Yumi, additional, Smit, Arian F. A., additional, Soto, Daniela C., additional, Sović, Ivan, additional, Storer, Jessica M., additional, Streets, Aaron, additional, Sullivan, Beth A., additional, Thibaud-Nissen, Françoise, additional, Torrance, James, additional, Wagner, Justin, additional, Walenz, Brian P., additional, Wenger, Aaron, additional, Wood, Jonathan M. D., additional, Xiao, Chunlin, additional, Yan, Stephanie M., additional, Young, Alice C., additional, Zarate, Samantha, additional, Surti, Urvashi, additional, McCoy, Rajiv C., additional, Dennis, Megan Y., additional, Alexandrov, Ivan A., additional, Gerton, Jennifer L., additional, O’Neill, Rachel J., additional, Timp, Winston, additional, Zook, Justin M., additional, Schatz, Michael C., additional, Eichler, Evan E., additional, Miga, Karen H., additional, and Phillippy, Adam M., additional

Published
2021
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13. Benchmarking challenging small variants with linked and long reads

Author

Wagner, Justin, primary, Olson, Nathan D, additional, Harris, Lindsay, additional, McDaniel, Jennifer, additional, Khan, Ziad, additional, Farek, Jesse, additional, Mahmoud, Medhat, additional, Stankovic, Ana, additional, Kovacevic, Vladimir, additional, Yoo, Byunggil, additional, Miller, Neil, additional, Rosenfeld, Jeffrey A., additional, Ni, Bohan, additional, Zarate, Samantha, additional, Kirsche, Melanie, additional, Aganezov, Sergey, additional, Schatz, Michael, additional, Narzisi, Giuseppe, additional, Byrska-Bishop, Marta, additional, Clarke, Wayne, additional, Evani, Uday S., additional, Markello, Charles, additional, Shafin, Kishwar, additional, Zhou, Xin, additional, Sidow, Arend, additional, Bansal, Vikas, additional, Ebert, Peter, additional, Marschall, Tobias, additional, Lansdorp, Peter, additional, Hanlon, Vincent, additional, Mattsson, Carl-Adam, additional, Barrio, Alvaro Martinez, additional, Fiddes, Ian T, additional, Xiao, Chunlin, additional, Fungtammasan, Arkarachai, additional, Chin, Chen-Shan, additional, Wenger, Aaron M, additional, Rowell, William J, additional, Sedlazeck, Fritz J, additional, Carroll, Andrew, additional, Salit, Marc, additional, and Zook, Justin M, additional

Published
2020
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14. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A., primary, Archer, Frederick I., additional, Avila, Catherine D., additional, Balacco, Jennifer R., additional, Bukhman, Yury V., additional, Chow, William, additional, Fedrigo, Olivier, additional, Formenti, Giulio, additional, Fronczek, Julie A., additional, Fungtammasan, Arkarachai, additional, Gulland, Frances M.D., additional, Haase, Bettina, additional, Heide-Jorgensen, Mads Peter, additional, Houck, Marlys L., additional, Howe, Kerstin, additional, Misuraca, Ann C., additional, Mountcastle, Jacquelyn, additional, Musser, Whitney, additional, Paez, Sadye, additional, Pelan, Sarah, additional, Phillippy, Adam, additional, Rhie, Arang, additional, Robinson, Jacqueline, additional, Rojas-Bracho, Lorenzo, additional, Rowles, Teri K., additional, Ryder, Oliver A., additional, Smith, Cynthia R., additional, Stevenson, Sacha, additional, Taylor, Barbara L., additional, Teilmann, Jonas, additional, Torrance, James, additional, Wells, Randall S., additional, Westgate, Andrew, additional, and Jarvis, Erich D., additional

Published
2020
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15. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, primary, McCarthy, Shane A., additional, Fedrigo, Olivier, additional, Damas, Joana, additional, Formenti, Giulio, additional, Koren, Sergey, additional, Uliano-Silva, Marcela, additional, Chow, William, additional, Fungtammasan, Arkarachai, additional, Gedman, Gregory L., additional, Cantin, Lindsey J., additional, Thibaud-Nissen, Francoise, additional, Haggerty, Leanne, additional, Lee, Chul, additional, Ko, Byung June, additional, Kim, Juwan, additional, Bista, Iliana, additional, Smith, Michelle, additional, Haase, Bettina, additional, Mountcastle, Jacquelyn, additional, Winkler, Sylke, additional, Paez, Sadye, additional, Howard, Jason, additional, Vernes, Sonja C., additional, Lama, Tanya M., additional, Grutzner, Frank, additional, Warren, Wesley C., additional, Balakrishnan, Christopher, additional, Burt, Dave, additional, George, Julia M., additional, Biegler, Mathew, additional, Iorns, David, additional, Digby, Andrew, additional, Eason, Daryl, additional, Edwards, Taylor, additional, Wilkinson, Mark, additional, Turner, George, additional, Meyer, Axel, additional, Kautt, Andreas F., additional, Franchini, Paolo, additional, Detrich, H William, additional, Svardal, Hannes, additional, Wagner, Maximilian, additional, Naylor, Gavin J.P., additional, Pippel, Martin, additional, Malinsky, Milan, additional, Mooney, Mark, additional, Simbirsky, Maria, additional, Hannigan, Brett T., additional, Pesout, Trevor, additional, Houck, Marlys, additional, Misuraca, Ann, additional, Kingan, Sarah B., additional, Hall, Richard, additional, Kronenberg, Zev, additional, Korlach, Jonas, additional, Sović, Ivan, additional, Dunn, Christopher, additional, Ning, Zemin, additional, Hastie, Alex, additional, Lee, Joyce, additional, Selvaraj, Siddarth, additional, Green, Richard E., additional, Putnam, Nicholas H., additional, Ghurye, Jay, additional, Garrison, Erik, additional, Sims, Ying, additional, Collins, Joanna, additional, Pelan, Sarah, additional, Torrance, James, additional, Tracey, Alan, additional, Wood, Jonathan, additional, Guan, Dengfeng, additional, London, Sarah E., additional, Clayton, David F., additional, Mello, Claudio V., additional, Friedrich, Samantha R., additional, Lovell, Peter V., additional, Osipova, Ekaterina, additional, Al-Ajli, Farooq O., additional, Secomandi, Simona, additional, Kim, Heebal, additional, Theofanopoulou, Constantina, additional, Zhou, Yang, additional, Harris, Robert S., additional, Makova, Kateryna D., additional, Medvedev, Paul, additional, Hoffman, Jinna, additional, Masterson, Patrick, additional, Clark, Karen, additional, Martin, Fergal, additional, Howe, Kevin, additional, Flicek, Paul, additional, Walenz, Brian P., additional, Kwak, Woori, additional, Clawson, Hiram, additional, Diekhans, Mark, additional, Nassar, Luis, additional, Paten, Benedict, additional, Kraus, Robert H.S., additional, Lewin, Harris, additional, Crawford, Andrew J., additional, Gilbert, M. Thomas P., additional, Zhang, Guojie, additional, Venkatesh, Byrappa, additional, Murphy, Robert W., additional, Koepfli, Klaus-Peter, additional, Shapiro, Beth, additional, Johnson, Warren E., additional, Di Palma, Federica, additional, Margues-Bonet, Tomas, additional, Teeling, Emma C., additional, Warnow, Tandy, additional, Graves, Jennifer Marshall, additional, Ryder, Oliver A., additional, Hausler, David, additional, O’Brien, Stephen J., additional, Howe, Kerstin, additional, Myers, Eugene W., additional, Durbin, Richard, additional, Phillippy, Adam M., additional, and Jarvis, Erich D., additional

Published
2020
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16. A Diploid Assembly-based Benchmark for Variants in the Major Histocompatibility Complex

Author

Erik Garrison, Chen-Shan Chin, Shilpa Garg, Qiandong Zeng, Justin Wagner, Alexander T. Dilthey, Arkarachai Fungtammasan, Tobias Marschall, Mikko Rautiainen, and Justin M. Zook

Subjects
Personal Genome Project, Contig, Computer science, Haplotype, Benchmark (computing), Human genome, Computational biology, Human leukocyte antigen, Genome, Reference genome
Abstract

We develop the first human benchmark derived from a diploid assembly for the openly-consented Genome in a Bottle/Personal Genome Project Ashkenazi son (HG002). As a proof-of-principle, we focus on a medically important, highly variable, 5 million base-pair region - the Major Histocompatibility Complex (MHC). Most human genomes are characterized by aligning individual reads to the reference genome, but accurate long reads and linked reads now enable us to construct base-level accurate, phased de novo assemblies from the reads. We assemble a single haplotig (haplotype-specific contig) for each haplotype, and align reads back to each assembled haplotig to identify two regions of lower confidence. We align the haplotigs to the reference, call phased small and structural variants, and define the first small variant benchmark for the MHC, covering 21496 small variants in 4.58 million base-pairs (92 % of the MHC). The assembly-based benchmark is 99.95 % concordant with a draft mapping-based benchmark from the same long and linked reads within both benchmark regions, but covers 50 % more variants outside the mapping-based benchmark regions. The haplotigs and variant calls are completely concordant with phased clinical HLA types for HG002. This benchmark reliably identifies false positives and false negatives from mapping-based callsets, and enables performance assessment in regions with much denser, complex variation than regions covered by previous benchmarks. These methods demonstrate a path towards future diploid assembly-based benchmarks for other complex regions of the genome.

Published
2019
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17. Efficient chromosome-scale haplotype-resolved assembly of human genomes

Author

Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., and Li, Heng

Abstract

Haplotype-resolved or phased sequence assembly provides a complete picture of genomes and complex genetic variations. However, current phased assembly algorithms either fail to generate chromosome-scale phasing or require pedigree information, which limits their application. We present a method that leverages long accurate reads and long-range conformation data for single individuals to generate chromosome-scale phased assembly within a day. Applied to three public human genomes, PGP1, HG002, and NA12878, our method produced haplotype-resolved assemblies with contig NG50 up to 25 Mb and phased ∼99.5% of heterozygous sites to 98–99% accuracy, outperforming trio-based approach in terms of both contiguity and phasing completeness. We demonstrate the importance of chromosome-scale phased assemblies to discover structural variants, including thousands of new transposon insertions, and of highly polymorphic and medically important regions such as HLA and KIR. Our improved method will enable high-quality precision medicine and facilitate new studies of individual haplotype variation and population diversity.

Published
2019
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18. Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

Author

Gene Myers, Mark A. DePristo, Michael Alonge, Richard Hall, Michael W. Hunkapiller, Fritz J. Sedlazeck, Paul Peluso, Jana Ebler, Aaron M. Wenger, Pi-Chuan Chang, Sergey Koren, Alexander Kolesnikov, Medhat Mahmoud, Justin M. Zook, Yufeng Qian, Arkarachai Fungtammasan, Nathan D. Olson, Michael C. Schatz, David R. Rank, Jue Ruan, Tobias Marschall, Heng Li, William J Rowell, Chen-Shan Chin, Andrew Carroll, Adam M. Phillippy, Armin Töpfer, and Gregory T. Concepcion

Subjects
0303 health sciences, Contig, Computer science, Haplotype, Sequence assembly, Computational biology, Genome, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Human genome, Precision and recall, Indel, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

The major DNA sequencing technologies in use today produce either highly-accurate short reads or noisy long reads. We developed a protocol based on single-molecule, circular consensus sequencing (CCS) to generate highly-accurate (99.8%) long reads averaging 13.5 kb and applied it to sequence the well-characterized human HG002/NA24385. We optimized existing tools to comprehensively detect variants, achieving precision and recall above 99.91% for SNVs, 95.98% for indels, and 95.99% for structural variants. We estimate that 2,434 discordances are correctable mistakes in the high-quality Genome in a Bottle benchmark. Nearly all (99.64%) variants are phased into haplotypes, which further improves variant detection. De novo assembly produces a highly contiguous and accurate genome with contig N50 above 15 Mb and concordance of 99.998%. CCS reads match short reads for small variant detection, while enabling structural variant detection and de novo assembly at similar contiguity and markedly higher concordance than noisy long reads.

Published
2019
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19. How well can we create phased, diploid, human genomes?: An assessment of FALCON-Unzip phasing using a human trio

Author

Arkarachai Fungtammasan and Brett T. Hannigan

Subjects
Contig, Haplotype, Inheritance (genetic algorithm), food and beverages, SNP, Single-nucleotide polymorphism, Human genome, Computational biology, Biology, Genome, Personal genomics
Abstract

Long read sequencing technology has allowed researchers to create de novo assemblies with impressive continuity[1,2]. This advancement has dramatically increased the number of reference genomes available and hints at the possibility of a future where personal genomes are assembled rather than resequenced. In 2016 Pacific Biosciences released the FALCON-Unzip framework, which can provide long, phased haplotype contigs from de novo assemblies. This phased genome algorithm enhances the accuracy of highly heterozygous organisms and allows researchers to explore questions that require haplotype information such as allele-specific expression and regulation. However, validation of this technique has been limited to small genomes or inbred individuals[3].As a roadmap to personal genome assembly and phasing, we assess the phasing accuracy of FALCON-Unzip in humans using publicly available data for the Ashkenazi trio from the Genome in a Bottle Consortium[4]. To assess the accuracy of the Unzip algorithm, we assembled the genome of the son using FALCON and FALCON Unzip, genotyped publicly available short read data for the mother and the father, and observed the inheritance pattern of the parental SNPs along the phased genome of the son. We found that 72.8% of haplotype contigs share SNPs with only one parent suggesting that these contigs are correctly phased. Most mis-phased SNPs are random but present in high frequency toward the end of haplotype contigs. Approximately 20.7% of mis-phased haplotype contigs contain clusters of mis-phased SNPs, suggesting that haplotypes were mis-joined by FALCON-Unzip. Mis-joined boundaries in those contigs are located in areas of low SNP density. This research demonstrates that the FALCON-Unzip algorithm can be used to create long and accurate haplotypes for humans and identifies problematic regions that could benefit in future improvement.

Published
2018
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20. Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358

Author

Ou, Shujun, primary, Liu, Jianing, additional, Chougule, Kapeel M., additional, Fungtammasan, Arkarachai, additional, Seetharam, Arun, additional, Stein, Joshua, additional, Llaca, Victor, additional, Manchanda, Nancy, additional, Gilbert, Amanda M., additional, Wei, Xuehong, additional, Chin, Chen-Shan, additional, Hufnagel, David E., additional, Pedersen, Sarah, additional, Snodgrass, Samantha, additional, Fengler, Kevin, additional, Woodhouse, Margaret, additional, Walenz, Brian P., additional, Koren, Sergey, additional, Phillippy, Adam M., additional, Hannigan, Brett, additional, Kelly Dawe, R., additional, Hirsch, Candice N., additional, Hufford, Matthew B., additional, and Ware, Doreen, additional

Published
2019
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22. Accurate chromosome-scale haplotype-resolved assembly of human genomes

Author

Garg, Shilpa, primary, Fungtammasan, Arkarachai, additional, Carroll, Andrew, additional, Chou, Mike, additional, Schmitt, Anthony, additional, Zhou, Xiang, additional, Mac, Stephen, additional, Peluso, Paul, additional, Hatas, Emily, additional, Ghurye, Jay, additional, Maguire, Jared, additional, Mahmoud, Medhat, additional, Cheng, Haoyu, additional, Heller, David, additional, Zook, Justin M., additional, Moemke, Tobias, additional, Marschall, Tobias, additional, Sedlazeck, Fritz J., additional, Aach, John, additional, Chin, Chen-Shan, additional, Church, George M., additional, and Li, Heng, additional

Published
2019
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23. Highly-accurate long-read sequencing improves variant detection and assembly of a human genome

Author

Wenger, Aaron M., primary, Peluso, Paul, additional, Rowell, William J., additional, Chang, Pi-Chuan, additional, Hall, Richard J., additional, Concepcion, Gregory T., additional, Ebler, Jana, additional, Fungtammasan, Arkarachai, additional, Kolesnikov, Alexey, additional, Olson, Nathan D., additional, Töpfer, Armin, additional, Alonge, Michael, additional, Mahmoud, Medhat, additional, Qian, Yufeng, additional, Chin, Chen-Shan, additional, Phillippy, Adam M., additional, Schatz, Michael C., additional, Myers, Gene, additional, DePristo, Mark A., additional, Ruan, Jue, additional, Marschall, Tobias, additional, Sedlazeck, Fritz J., additional, Zook, Justin M., additional, Li, Heng, additional, Koren, Sergey, additional, Carroll, Andrew, additional, Rank, David R., additional, and Hunkapiller, Michael W., additional

Published
2019
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25. A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Author

Francesca Chiaromonte, Arkarachai Fungtammasan, Kristin A. Eckert, Kateryna D. Makova, and Erin Walsh

Subjects
Structural variation, Genetics, Chromosome Fragile Site, Evolutionary biology, Chromosomal fragile site, Chromosome instability, Alu element, Human genome, Chromosome breakage, Biology, Genome, Genetics (clinical)
Abstract

Chromosomal common fragile sites (CFSs) are unstable genomic regions that break under replication stress and are involved in structural variation. They frequently are sites of chromosomal rearrangements in cancer and of viral integration. However, CFSs are undercharacterized at the molecular level and thus difficult to predict computationally. Newly available genome-wide profiling studies provide us with an unprecedented opportunity to associate CFSs with features of their local genomic contexts. Here, we contrasted the genomic landscape of cytogenetically defined aphidicolin-induced CFSs (aCFSs) to that of nonfragile sites, using multiple logistic regression. We also analyzed aCFS breakage frequencies as a function of their genomic landscape, using standard multiple regression. We show that local genomic features are effective predictors both of regions harboring aCFSs (explaining ∼81% of the deviance in logistic regression models) and of aCFS breakage frequencies (explaining ∼45% of the variance in standard regression models). In our optimal models (based on a combination of biological interpretability and high R-squared value), aCFSs are predominantly located in G-negative chromosomal bands and away from centromeres, are enriched in Alu repeats, and have high DNA flexibility. In alternative models, CpG island density, H3K4me1 coverage, and mononucleotide microsatellite coverage are significant predictors. Also, aCFSs have high fragility when colocated with evolutionarily conserved chromosomal breakpoints. Our models are predictive of the fragility of aCFSs mapped at a higher resolution. Importantly, the genomic features we identified here as significant predictors of fragility allow us to draw valuable inferences on the molecular mechanisms underlying aCFSs.

Published
2012
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