title: Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome.
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.
authors.affiliation: Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, Wisconsin, USA.
authors.forename: Derek M
authors.identifier: http://orcid.org/0000-0003-2223-9285
authors.initials: DM
authors.lastname: Bickhart
authors.affiliation: Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Rosen
authors.affiliation: Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
authors.forename: Sergey
authors.initials: S
authors.lastname: Koren
authors.affiliation: Department of Biology, Virginia State University, Petersburg, Virginia, USA.
authors.forename: Brian L
authors.initials: BL
authors.lastname: Sayre
authors.affiliation: BioNano Genomics, San Diego, California, USA.
authors.forename: Alex R
authors.initials: AR
authors.lastname: Hastie
authors.affiliation: BioNano Genomics, San Diego, California, USA.
authors.forename: Saki
authors.initials: S
authors.lastname: Chan
authors.affiliation: BioNano Genomics, San Diego, California, USA.
authors.forename: Joyce
authors.identifier: http://orcid.org/0000-0002-3492-1102
authors.initials: J
authors.lastname: Lee
authors.affiliation: BioNano Genomics, San Diego, California, USA.
authors.forename: Ernest T
authors.initials: ET
authors.lastname: Lam
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
authors.forename: Ivan
authors.initials: I
authors.lastname: Liachko
authors.affiliation: Phase Genomics, Seattle, Washington, USA.
authors.forename: Shawn T
authors.initials: ST
authors.lastname: Sullivan
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Burton
authors.affiliation: Department of Animal Science, Cornell University, Ithaca, New York, USA.
authors.forename: Heather J
authors.identifier: http://orcid.org/0000-0001-8299-0447
authors.initials: HJ
authors.lastname: Huson
authors.affiliation: Department of Animal Science, Cornell University, Ithaca, New York, USA.
authors.forename: John C
authors.initials: JC
authors.lastname: Nystrom
authors.affiliation: US Meat Animal Research Center, ARS USDA, Clay Center, Nebraska, USA.
authors.forename: Christy M
authors.initials: CM
authors.lastname: Kelley
authors.affiliation: Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
authors.forename: Jana L
authors.initials: JL
authors.lastname: Hutchison
authors.affiliation: 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.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: South China Agricultural University, Tianhe, Guangzhou, China.
authors.forename: Jiajie
authors.initials: J
authors.lastname: Sun
authors.affiliation: Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA)-Animal Production Research Centre, Rome, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Crisà
authors.affiliation: Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA.
authors.forename: F Abel
authors.identifier: http://orcid.org/0000-0001-8645-553X
authors.initials: FA
authors.lastname: Ponce de León
authors.affiliation: Livestock Viral Diseases Programme, The Pirbright Institute, Woking, UK.
authors.forename: John C
authors.identifier: http://orcid.org/0000-0003-2057-1831
authors.initials: JC
authors.lastname: Schwartz
authors.affiliation: Livestock Viral Diseases Programme, The Pirbright Institute, Woking, UK.
authors.forename: John A
authors.initials: JA
authors.lastname: Hammond
authors.affiliation: Warmwater Aquaculture Research Unit, ARS USDA, Stoneville, Mississippi, USA.
authors.forename: Geoffrey C
authors.initials: GC
authors.lastname: Waldbieser
authors.affiliation: Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
authors.forename: Steven G
authors.initials: SG
authors.lastname: Schroeder
authors.affiliation: Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
authors.forename: George E
authors.initials: GE
authors.lastname: Liu
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
authors.forename: Maitreya J
authors.identifier: http://orcid.org/0000-0001-9944-2666
authors.initials: MJ
authors.lastname: Dunham
authors.affiliation: Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.|Howard Hughes Medical Institute, Seattle, Washington, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: Recombinetics, Inc., St. Paul, Minnesota, USA.
authors.forename: Tad S
authors.initials: TS
authors.lastname: Sonstegard
authors.affiliation: Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Phillippy
authors.affiliation: Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
authors.forename: Curtis P
authors.initials: CP
authors.lastname: Van Tassell
authors.affiliation: US Meat Animal Research Center, ARS USDA, Clay Center, Nebraska, USA.
authors.forename: Timothy P L
authors.initials: TP
authors.lastname: Smith
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D002875:Chromosomes / Q000235:genetics; D016678:Genome / Q000235:genetics*; D006041:Goats / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics
chemical_list: D002843:Chromatin