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Open Access Highly Accessed Research article

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data

Yukari Nishito1, Yasunori Osana2, Tsuyoshi Hachiya1, Kris Popendorf1, Atsushi Toyoda3, Asao Fujiyama4, Mitsuhiro Itaya5 and Yasubumi Sakakibara1*

Author affiliations

1 Department of Biosciences and Informatics, Keio University, Hiyoshi, Kohoku-ku, Yokohama, Japan

2 Department of Computer and Information Science, Seikei University, Musashino, Tokyo, Japan

3 Center for Genetic Resource Information, National Institute of Genetics, Shizouka, Japan

4 Principles of Informatics Research Division, National Institute of Informatics, Tokyo, Japan

5 Institute for Advanced Biosciences, Keio University, Minato, Tokyo, Japan

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Citation and License

BMC Genomics 2010, 11:243  doi:10.1186/1471-2164-11-243

Published: 16 April 2010

Abstract

Background

Bacillus 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.

Results

We 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 γ-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.

Conclusions

The 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/ webcite.