title: Dramatic improvement in genome assembly achieved using doubled-haploid genomes.
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.
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: Engkong
authors.initials: E
authors.lastname: Tan
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: Yusuke
authors.initials: Y
authors.lastname: Hirose
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: Shigeharu
authors.initials: S
authors.lastname: Kinoshita
authors.affiliation: Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.
authors.forename: Hideyuki
authors.initials: H
authors.lastname: Okano
authors.affiliation: Laboratory of Gene Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.
authors.forename: Jun
authors.initials: J
authors.lastname: Kudoh
authors.affiliation: Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa-gun, Iwate 028-3694, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Shimizu
authors.affiliation: Akita Prefectural Institute of Fisheries, Oga, Akita 010-0531, Japan.
authors.forename: Kazuyoshi
authors.initials: K
authors.lastname: Saito
authors.affiliation: School of Marine Bioscience, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
authors.forename: Shugo
authors.initials: S
authors.lastname: Watabe
authors.affiliation: Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan.
authors.forename: Shuichi
authors.initials: S
authors.lastname: Asakawa
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D005260:Female; D015723:Gene Library; D016678:Genome; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006238:Haploidy; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D023741:Takifugu / Q000235:genetics