Dataset Information

Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2.

ABSTRACT: Bacillus subtilis strain natto VK161 was selected for its high production of vitamin K2 Its genome was sequenced and annotated in the Department of Energy-Joint Genome Institute (DOE-JGI) annotation pipeline. It resulted in a chromosome of 4,073,396?bp, which is composed of 4,332 protein-coding genes, 23 rRNA genes, and 77 tRNA genes.

SUBMITTER: Parks D

PROVIDER: S-EPMC6715861 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2.

Parks Dylan D Chung In-Hwa IH Lee In Kyu IK Kim Eui-Joong EJ Niraula Sarbjeet S Chang Woo-Suk WS

Microbiology resource announcements 20190829 35

Bacillus subtilis strain natto VK161 was selected for its high production of vitamin K2 Its genome was sequenced and annotated in the Department of Energy-Joint Genome Institute (DOE-JGI) annotation pipeline. It resulted in a chromosome of 4,073,396 bp, which is composed of 4,332 protein-coding genes, 23 rRNA genes, and 77 tRNA genes. ...[more]

PMID: 31467091

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Project description:BackgroundBacillus subtilis natto is closely related to the laboratory standard strain B. subtilis Marburg 168, and functions as a starter for the production of the traditional Japanese food "natto" made from soybeans. Although re-sequencing whole genomes of several laboratory domesticated B. subtilis 168 derivatives has already been attempted using short read sequencing data, the assembly of the whole genome sequence of a closely related strain, B. subtilis natto, from very short read data is more challenging, particularly with our aim to assemble one fully connected scaffold from short reads around 35 bp in length.ResultsWe applied a comparative genome assembly method, which combines de novo assembly and reference guided assembly, to one of the B. subtilis natto strains. We successfully assembled 28 scaffolds and managed to avoid substantial fragmentation. Completion of the assembly through long PCR experiments resulted in one connected scaffold for B. subtilis natto. Based on the assembled genome sequence, our orthologous gene analysis between natto BEST195 and Marburg 168 revealed that 82.4% of 4375 predicted genes in BEST195 are one-to-one orthologous to genes in 168, with two genes in-paralog, 3.2% are deleted in 168, 14.3% are inserted in BEST195, and 5.9% of genes present in 168 are deleted in BEST195. The natto genome contains the same alleles in the promoter region of degQ and the coding region of swrAA as the wild strain, RO-FF-1. These are specific for gamma-PGA production ability, which is related to natto production. Further, the B. subtilis natto strain completely lacked a polyketide synthesis operon, disrupted the plipastatin production operon, and possesses previously unidentified transposases.ConclusionsThe determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtilis natto harbors but B. subtilis 168 lacks. Multiple genome-level comparisons among five closely related Bacillus species were also carried out. The determined genome sequence of B. subtilis natto and gene annotations are available from the Natto genome browser http://natto-genome.org/.

Dataset Information

Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K2.

Publications

Genome Sequence of Bacillus subtilis natto VK161, a Novel Strain That Produces Vitamin K<sub>2</sub>.

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