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Sci Rep. 2014 Oct 27;4:6780. doi: 10.1038/srep06780.

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

Author information

1
Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
2
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
3
Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.
4
Laboratory of Gene Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.
5
Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa-gun, Iwate 028-3694, Japan.
6
Akita Prefectural Institute of Fisheries, Oga, Akita 010-0531, Japan.
7
School of Marine Bioscience, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.

Abstract

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

PMID:
25345569
PMCID:
PMC5381364
DOI:
10.1038/srep06780
[Indexed for MEDLINE]
Free PMC Article

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