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Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes

Derek M. Bickhart, Benjamin D. Rosen, Sergey Koren, Brian L. Sayre, Alex R. Hastie, Saki Chan, Joyce Lee, Ernest T. Lam, Ivan Liachko, Shawn T. Sullivan, Joshua N. Burton, Heather J. Huson, Christy M. Kelley, Jana L. Hutchison, Yang Zhou, Jiajie Sun, Alessandra Crisà, F. Abel Ponce De León, John C. Schwartz, John A. Hammond, Geoffrey C. Waldbieser, Steven G. Schroeder, George E. Liu, Maitreya J. Dunham, Jay Shendure, Tad S. Sonstegard, Adam M. Phillippy, Curtis P. Van Tassell, Timothy P.L. Smith
doi: https://doi.org/10.1101/064352
Derek M. Bickhart
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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Benjamin D. Rosen
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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Sergey Koren
2National Human Genome Research Institute, Bethesda, USA 21702
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Brian L. Sayre
3Department of Biology, Virginia State University, Petersburg, Virginia, USA 23806
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Alex R. Hastie
4BioNano Genomics, San Diego, California, USA 92121
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Saki Chan
4BioNano Genomics, San Diego, California, USA 92121
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Joyce Lee
4BioNano Genomics, San Diego, California, USA 92121
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Ernest T. Lam
4BioNano Genomics, San Diego, California, USA 92121
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Ivan Liachko
5Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
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Shawn T. Sullivan
6Phase Genomics, 4000 Mason Road, Suite 225, Seattle, WA 98195
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Joshua N. Burton
5Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
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Heather J. Huson
7Department of Animal Science, Cornell University, Ithaca, New York, USA 14853,
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Christy M. Kelley
8Genetics, Breeding and Animal Health Research, ARS USDA, Clay Center, Nebraska, USA 68933
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Jana L. Hutchison
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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Yang Zhou
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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Jiajie Sun
9South China Agricultural University, 483 Wushan Rd, Tianhe, Guangzhou, Guangdong, China
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Alessandra Crisà
10CRA Agricultural Research Council, Research Centre for Meat Production and Genetic Improvement, Rome, Italy
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F. Abel Ponce De León
11Department of Animal Science, University of Minnesota, St. Paul, MN, USA 55108
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John C. Schwartz
12Livestock Viral Disease Programme, The Pirbright Institute, Woking, GU24 0NF, UK
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John A. Hammond
12Livestock Viral Disease Programme, The Pirbright Institute, Woking, GU24 0NF, UK
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Geoffrey C. Waldbieser
13Warmwater Aquaculture Research Unit, ARS USDA, Stoneville, Mississippi, USA 38776
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Steven G. Schroeder
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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George E. Liu
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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Maitreya J. Dunham
5Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
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Jay Shendure
5Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195
14Howard Hughes Medical Institute, Seattle WA 98195
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Tad S. Sonstegard
15Recombinetics, Inc. 1246 University Ave W #301, St. Paul, MN 55104
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Adam M. Phillippy
2National Human Genome Research Institute, Bethesda, USA 21702
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Curtis P. Van Tassell
1Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA 20705
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Timothy P.L. Smith
8Genetics, Breeding and Animal Health Research, ARS USDA, Clay Center, Nebraska, USA 68933
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Abstract

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.

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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.
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Posted July 18, 2016.
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Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes
Derek M. Bickhart, Benjamin D. Rosen, Sergey Koren, Brian L. Sayre, Alex R. Hastie, Saki Chan, Joyce Lee, Ernest T. Lam, Ivan Liachko, Shawn T. Sullivan, Joshua N. Burton, Heather J. Huson, Christy M. Kelley, Jana L. Hutchison, Yang Zhou, Jiajie Sun, Alessandra Crisà, F. Abel Ponce De León, John C. Schwartz, John A. Hammond, Geoffrey C. Waldbieser, Steven G. Schroeder, George E. Liu, Maitreya J. Dunham, Jay Shendure, Tad S. Sonstegard, Adam M. Phillippy, Curtis P. Van Tassell, Timothy P.L. Smith
bioRxiv 064352; doi: https://doi.org/10.1101/064352
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Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes
Derek M. Bickhart, Benjamin D. Rosen, Sergey Koren, Brian L. Sayre, Alex R. Hastie, Saki Chan, Joyce Lee, Ernest T. Lam, Ivan Liachko, Shawn T. Sullivan, Joshua N. Burton, Heather J. Huson, Christy M. Kelley, Jana L. Hutchison, Yang Zhou, Jiajie Sun, Alessandra Crisà, F. Abel Ponce De León, John C. Schwartz, John A. Hammond, Geoffrey C. Waldbieser, Steven G. Schroeder, George E. Liu, Maitreya J. Dunham, Jay Shendure, Tad S. Sonstegard, Adam M. Phillippy, Curtis P. Van Tassell, Timothy P.L. Smith
bioRxiv 064352; doi: https://doi.org/10.1101/064352

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