Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads

Mayumi Kamada, Sumitaka Hase, Kengo Sato, Atsushi Toyoda, Asao Fujiyama, Yasubumi Sakakibara

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

De novo microbial genome sequencing reached a turning point with third-generation sequencing (TGS) platforms, and several microbial genomes have been improved by TGS long reads. Bacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and it has a function in the production of the traditional Japanese fermented food "natto." The B. subtilis natto BEST195 genome was previously sequenced with short reads, but it included some incomplete regions. We resequenced the BEST195 genome using a PacBio RS sequencer, and we successfully obtained a complete genome sequence from one scaffold without any gaps, and we also applied Illumina MiSeq short reads to enhance quality. Compared with the previous BEST195 draft genome and Marburg 168 genome, we found that incomplete regions in the previous genome sequence were attributed to GC-bias and repetitive sequences, and we also identified some novel genes that are found only in the new genome.

Original languageEnglish
Article numbere109999
JournalPLoS One
Volume9
Issue number10
DOIs
Publication statusPublished - 2014 Oct 16

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natto
Bacilli
Bacillus subtilis
Genes
Genome
genome
Microbial Genome
Soy Foods
Nucleic Acid Repetitive Sequences
fermented foods
repetitive sequences
production functions
Scaffolds
Food

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads. / Kamada, Mayumi; Hase, Sumitaka; Sato, Kengo; Toyoda, Atsushi; Fujiyama, Asao; Sakakibara, Yasubumi.

In: PLoS One, Vol. 9, No. 10, e109999, 16.10.2014.

Research output: Contribution to journalArticle

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