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PMID: 28263316 Published · ppublish English Journal Article

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.

Nature genetics ·Vol. 49 ·No. 4 ·2017-04-00 ·Pages 643-650

Bickhart DM, Rosen BD, Koren S, Sayre BL, Hastie AR, Chan S, Lee J, Lam ET, Liachko I, Sullivan ST, Burton JN, Huson HJ, Nystrom JC, Kelley CM, Hutchison JL, Zhou Y, Sun J, Crisà A, Ponce de León FA, Schwartz JC, Hammond JA, Waldbieser GC, Schroeder SG, Liu GE, Dunham MJ, Shendure J, Sonstegard TS, Phillippy AM, Van Tassell CP, Smith TP

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 what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

MeSH Terms
Animals Chromatin/genetics Chromosomes/genetics Genome/genetics Goats/genetics High-Throughput Nucleotide Sequencing/methods Repetitive Sequences, Nucleic Acid/genetics
Chemicals
Chromatin
Authors & Affiliations
30 authors, click to expand affiliations / ORCID
Bickhart Derek M ORCID
Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, Wisconsin, USA.
Rosen Benjamin D
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
Koren Sergey
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
Sayre Brian L
Department of Biology, Virginia State University, Petersburg, Virginia, USA.
Hastie Alex R
BioNano Genomics, San Diego, California, USA.
Chan Saki
BioNano Genomics, San Diego, California, USA.
Lee Joyce ORCID
BioNano Genomics, San Diego, California, USA.
Lam Ernest T
BioNano Genomics, San Diego, California, USA.
Liachko Ivan
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Sullivan Shawn T
Phase Genomics, Seattle, Washington, USA.
Burton Joshua N
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Huson Heather J ORCID
Department of Animal Science, Cornell University, Ithaca, New York, USA.
Nystrom John C
Department of Animal Science, Cornell University, Ithaca, New York, USA.
Kelley Christy M
US Meat Animal Research Center, ARS USDA, Clay Center, Nebraska, USA.
Hutchison Jana L
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
Zhou Yang
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA. | Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
Sun Jiajie
South China Agricultural University, Tianhe, Guangzhou, China.
Crisà Alessandra
Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA)-Animal Production Research Centre, Rome, Italy.
Ponce de León F Abel ORCID
Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA.
Schwartz John C ORCID
Livestock Viral Diseases Programme, The Pirbright Institute, Woking, UK.
Hammond John A
Livestock Viral Diseases Programme, The Pirbright Institute, Woking, UK.
Waldbieser Geoffrey C
Warmwater Aquaculture Research Unit, ARS USDA, Stoneville, Mississippi, USA.
Schroeder Steven G
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
Liu George E
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
Dunham Maitreya J ORCID
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
Shendure Jay
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA. | Howard Hughes Medical Institute, Seattle, Washington, USA.
Sonstegard Tad S
Recombinetics, Inc., St. Paul, Minnesota, USA.
Phillippy Adam M
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
Van Tassell Curtis P
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
Smith Timothy P L
US Meat Animal Research Center, ARS USDA, Clay Center, Nebraska, USA.
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.3802
Published
2017-04-00
Epub
2017-00-06
Pages
643-650
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC5909822
Subset
IM
Grants
NIGMS NIH HHS · P41 GM103533 · United States
NHGRI NIH HHS · R01 HG006283 · United States
External Links
PubMed source DOI: 10.1038/ng.3802 PMC Full Text View journal details
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