Draft Genome Sequence of Oceanobacillus picturae Heshi-B3, Isolated from Fermented Rice Bran in a Traditional Japanese Seafood Dish Sayuri Akuzawa,a Junko Nagaoka,a Motoki Kanekatsu,b Yu Kanesaki,c Tomonori Suzukia Department of Nutritional Science and Food Safety, Tokyo University of Agriculture, Tokyo, Japana; Department of Biological Production, Tokyo University of Agriculture and Technology, Tokyo, Japanb; NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japanc
Oceanobacillus picturae strain Heshi-B3 was isolated from rice bran in a traditional fermented seafood dish named Heshiko, which was produced in Fukui Prefecture in Japan. Here, we report the draft genome sequence of O. picturae strain Heshi B-3.
Citation Akuzawa S, Nagaoka J, Kanekatsu M, Kanesaki Y, Suzuki T. 2016. Draft genome sequence of Oceanobacillus picturae Heshi-B3, isolated from fermented rice bran in a traditional Japanese seafood dish. Genome Announc 4(1):e01621-15. doi:10.1128/genomeA.01621-15 Copyright © 2016 Akuzawa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Sayuri Akuzawa, [email protected]
, and Tomonori Suzuki, [email protected]
eshiko is one of the traditional fermented seafood dishes in Japan. It is produced by aging salted mackerel with rice bran for around 7 months. Some studies on fermented seafood have focused on the microbiological profile in rice bran and chemical changes in salted fish (1); however, they have not analyzed the genome sequence of the bacteria isolated from fermented rice bran. Here, we have newly isolated a bacterium belonging to the genus Oceanobacillus from Heshiko, and we deciphered the draft genome sequence. According to the similarity of genetic sequences, we named this strain Oceanobacillus picturae Heshi-B3. Bacterial cells were cultured in medium (1% soluble starch, 0.5% yeast extract, 0.5% peptone, 0.1% K2HPO4, 0.02% MgSO4· 7H2O, and 5% NaCl) at 30°C and were collected by centrifugation (10,000 ⫻ g, 15 min, 4°C). The cell pellet was treated with cell lysis solution (20 mg/ml lysozyme, 20 mM Tris-HCl [pH 8.0], 2 mM EDTA, 1.2% Triton X-100) for 30 min at 37°C. The bacterial genomic DNA was prepared using the DNeasy blood and tissue kit (Qiagen, Valencia, CA, USA). Five micrograms of genomic DNA dissolved in Tris-EDTA (TE) buffer was digested by a Covaris S-2 sonicator (Covaris, Woburn, MA, USA), with an average size of 500 bases. A DNA library was constructed using the NEBNext DNA library preparation kit (New England BioLabs, Ipswich, MA, USA), according to the manufacturer’s protocol. The library was sequenced by a massively parallel sequencer (MiSeq; Illumina KK, Tokyo, Japan) with a 300-base paired-end format, and finally, 2.90 Gb of sequence reads was obtained. The sequence reads were screened by a quality score higher than the Phred score of 30 and were each trimmed 10 bases from the both 5= and 3= ends. The
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trimmed reads were assembled de novo by CLC Genomics Workbench version 7.5 (Qiagen). Finally, the 92 contigs (⬎1 kb) were assembled, with a total length of 3,900,724 bp and N50 of 89,442 bp. Annotation of the contigs was performed by MiGAP (2). As a result, 9 rRNAs, 61 tRNAs, and 3,889 coding sequences (CDSs) were identified. So far, in the species of O. picturae, genomic sequences are available for only two strains, S1 (GenBank accession no. GCA_000612865.1) and Heshi-B3 (this work). Our sequencing data will largely contribute to future studies to understand the genetic variation among the species of O. picturae. Nucleotide sequence accession numbers. Original sequence reads and metadata for this project were deposited to DDBJ/ EMBL/GenBank under the accession numbers DRA003517 and PRJDB3832. Annotations and sequences of the assembled contigs are available under the accession numbers BBXV01000001 to BBXV01000092. FUNDING INFORMATION The Strategic Research Foundation at Private Universities provided funding through a MEXT-supported program under 2013–2017 (S1311017).
REFERENCES 1. Kosaka Y, Ooizumi T. 2012. Effects of microbial growth inhibition by antibiotics on the production of taste-active components during the processing of heshiko produced by aging salted mackerel with rice bran. Fish Sci 78:735–742. http://dx.doi.org/10.1007/s12562-012-0478-4. 2. Sugawara H, Ohyama A, Mori H, Kurokawa K. 2009. Microbial genome annotation pipeline (MiGAP) for diverse users, abstr S-001. Abstr 20th Int Conf Genome Informatics, Kanagawa, Japan.
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Received 26 November 2015 Accepted 11 December 2015 Published 4 February 2016