title: Whole genome complete resequencing of Bacillus subtilis natto by combining long reads with high-quality short reads.
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.
authors.affiliation: Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan.
authors.forename: Mayumi
authors.initials: M
authors.lastname: Kamada
authors.affiliation: Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan.
authors.forename: Sumitaka
authors.initials: S
authors.lastname: Hase
authors.affiliation: Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan.
authors.forename: Kengo
authors.initials: K
authors.lastname: Sato
authors.affiliation: Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan; Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama, Japan.
authors.forename: Yasubumi
authors.initials: Y
authors.lastname: Sakakibara
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*