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Nat Genet. 2017 Apr;49(4):643-650. doi: 10.1038/ng.3802. Epub 2017 Mar 6.

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

Author information

1
Cell Wall Biology and Utilization Laboratory, ARS USDA, Madison, Wisconsin, USA.
2
Animal Genomics and Improvement Laboratory, ARS USDA, Beltsville, Maryland, USA.
3
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland, USA.
4
Department of Biology, Virginia State University, Petersburg, Virginia, USA.
5
BioNano Genomics, San Diego, California, USA.
6
Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA.
7
Phase Genomics, Seattle, Washington, USA.
8
Department of Animal Science, Cornell University, Ithaca, New York, USA.
9
US Meat Animal Research Center, ARS USDA, Clay Center, Nebraska, USA.
10
Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, China.
11
South China Agricultural University, Tianhe, Guangzhou, China.
12
Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA)-Animal Production Research Centre, Rome, Italy.
13
Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA.
14
Livestock Viral Diseases Programme, The Pirbright Institute, Woking, UK.
15
Warmwater Aquaculture Research Unit, ARS USDA, Stoneville, Mississippi, USA.
16
Howard Hughes Medical Institute, Seattle, Washington, USA.
17
Recombinetics, Inc., St. Paul, Minnesota, USA.

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.

PMID:
28263316
PMCID:
PMC5909822
DOI:
10.1038/ng.3802
[Indexed for MEDLINE]
Free PMC Article

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