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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.

SUBMITTER: Zhang H 

PROVIDER: S-EPMC5381364 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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

Zhang Hong H   Tan Engkong E   Suzuki Yutaka Y   Hirose Yusuke Y   Kinoshita Shigeharu S   Okano Hideyuki H   Kudoh Jun J   Shimizu Atsushi A   Saito Kazuyoshi K   Watabe Shugo S   Asakawa Shuichi S  

Scientific reports 20141027

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  ...[more]

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