Dramatic improvement in genome assembly achieved using doubled-haploid genomes

Hong Zhang, Engkong Tan, Yutaka Suzuki, Yusuke Hirose, Shigeharu Kinoshita, Hideyuki Okano, Jun Kudo, Atsushi Shimizu, Kazuyoshi Saito, Shugo Watabe, Shuichi Asakawa

Research output: Contribution to journalArticle

15 Citations (Scopus)

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.

Original languageEnglish
Article number6780
JournalScientific Reports
Volume4
DOIs
Publication statusPublished - 2014 Oct 27

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Haploidy
Genome
Takifugu

ASJC Scopus subject areas

  • General
  • Medicine(all)

Cite this

Zhang, H., Tan, E., Suzuki, Y., Hirose, Y., Kinoshita, S., Okano, H., ... Asakawa, S. (2014). Dramatic improvement in genome assembly achieved using doubled-haploid genomes. Scientific Reports, 4, [6780]. https://doi.org/10.1038/srep06780

Dramatic improvement in genome assembly achieved using doubled-haploid genomes. / Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudo, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi.

In: Scientific Reports, Vol. 4, 6780, 27.10.2014.

Research output: Contribution to journalArticle

Zhang, H, Tan, E, Suzuki, Y, Hirose, Y, Kinoshita, S, Okano, H, Kudo, J, Shimizu, A, Saito, K, Watabe, S & Asakawa, S 2014, 'Dramatic improvement in genome assembly achieved using doubled-haploid genomes', Scientific Reports, vol. 4, 6780. https://doi.org/10.1038/srep06780
Zhang, Hong ; Tan, Engkong ; Suzuki, Yutaka ; Hirose, Yusuke ; Kinoshita, Shigeharu ; Okano, Hideyuki ; Kudo, Jun ; Shimizu, Atsushi ; Saito, Kazuyoshi ; Watabe, Shugo ; Asakawa, Shuichi. / Dramatic improvement in genome assembly achieved using doubled-haploid genomes. In: Scientific Reports. 2014 ; Vol. 4.
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