Dramatic improvement in genome assembly achieved using doubled-haploid genomes

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

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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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    Zhang, H., Tan, E., Suzuki, Y., Hirose, Y., Kinoshita, S., Okano, H., Kudoh, J., Shimizu, A., Saito, K., Watabe, S., & Asakawa, S. (2014). Dramatic improvement in genome assembly achieved using doubled-haploid genomes. Scientific reports, 4, [6780]. https://doi.org/10.1038/srep06780