Complete Genome Sequence of Leuconostoc kimchii Strain C2 ...

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Jun 30, 2011 - generated from the 454 GS FLX Titanium system, and the resulting reads were ... complete sequence was submitted to the NCBI Prokaryotic Genomes Automatic ... Mailing address: School of Biological Sci- ences, Chung-Ang ...
JOURNAL OF BACTERIOLOGY, Oct. 2011, p. 5548 0021-9193/11/$12.00 doi:10.1128/JB.05707-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved.

Vol. 193, No. 19

Complete Genome Sequence of Leuconostoc kimchii Strain C2, Isolated from Kimchi Seung Hyeon Lee, Ji Young Jung, Se Hee Lee, and Che Ok Jeon* School of Biological Sciences, Chung-Ang University, Seoul 156-756, Republic of Korea Received 30 June 2011/Accepted 18 July 2011

Leuconostoc kimchii strain C2 was isolated from fermented kimchi in Korea. Here we announce the complete genome sequence of Leuconostoc kimchii strain C2, consisting of a 1,877,174-bp chromosome with a GⴙC content of 37.9% and no plasmid and describe major findings from its annotation. and low-quality/low-depth segments. The complete sequence was submitted to the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP). The tRNA and rRNA genes were annotated using the tRNAscan-SE (8) and RNAmmer software programs (7), respectively. Strain C2 has a circular chromosomal genome of 1,877,273 bp with a G⫹C content of 37.9% and no plasmid. The genome contains 1,855 predicted protein coding sequences, 4 complete rRNA operons, and 68 tRNA genes. The coding density of the genome was 88.1%, with an average gene length of 891 bp. Nucleotide sequence accession number. The complete genome sequence of strain C2 has been deposited in GenBank under accession no. CP002898.

Kimchi is a traditional fermented food, emblematic of Korean culture, which is fermented from a variety of vegetables with seasoning ingredients, including red pepper powder, garlic, and salts, and in recent years, kimchi’s health-promoting characteristics have been recognized continually (1, 9). Generally, kimchi is classified on the basis of its main raw materials (vegetables), and its spontaneous fermentation without the use of starter cultures or sterilization of raw materials leads to the growth of various heterofermentative lactic acid bacteria (LAB) such as Leuconostoc mesenteroides, Lactobacillus sakei, and Weissella koreensis (5). Strain C2 was isolated from a fermented regional kimchi, which was made using the mixture of radish, Chinese cabbage, brown algae, and some seasoning ingredients. The genus Leuconostoc has been known as one of the predominant bacterial groups during kimchi fermentation (5). Members of the genus Leuconostoc, placed within the family Leuconostocaceae, are Gram-positive, non-spore-forming, heterofermentative, and coccoid bacteria (6). Here we report the complete genome sequence and annotation of Leuconostoc kimchii strain C2. This genomic sequence was determined using the Roche/454 technology. The total sequence (70 Mb [about 37⫻ coverage], with 1,536,491 paired-end reads containing 3-kb inserts) was generated from the 454 GS FLX Titanium system, and the resulting reads were assembled initially into five large scaffolds, including 39 contigs, using the Newbler program. All of the intrascaffold and interscaffold gaps were closed by sequencing PCR products. The Phred/Phrap/Consed software (2–4) was used for sequence assembly and quality assessment, and the final whole-genome sequence was further validated by Sanger sequencing of uncertain regions, such as mononucleotide runs

These efforts were supported by the Technology Development Program for Agriculture and Forestry (TDPAF) of the Ministry for Agriculture, Forestry and Fisheries and the Next-Generation BioGreen 21 Program (no. SSAC2011-PJ008220), Rural Development Administration, Republic of Korea. REFERENCES 1. Cheigh, H. S., and K. Y. Park. 1994. Biochemical, microbiological, and nutritional aspect of kimchi (Korean fermented vegetable products). Crit. Rev. Food Sci. Nutr. 34:175–203. 2. Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186–194. 3. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175–185. 4. Gordon, D., C. Abajian, and P. Green. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202. 5. Jung, J. Y., et al. 2011. Metagenomic analysis of kimchi, the Korean traditional fermented food. Appl. Environ. Microbiol. 77:2264–2274. 6. Kim, B., et al. 2003. Leuconostoc inhae sp. nov., a lactic acid bacterium isolated from kimchi. Int. J. Syst. Evol. Microbiol. 53:1123–1126. 7. Lagesen, K., et al. 2007. RNAmmer: consistent and rapid annotation of rRNA genes. Nucleic Acids Res. 35:3100–3108. 8. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of tRNA genes in genomic sequence. Nucleic Acids Res. 25:955– 964. 9. Song, Y. O. 2004. The functional properties of kimchi for the health benefits. J. Food Sci. Nutr. 9:27–33.

* Corresponding author. Mailing address: School of Biological Sciences, Chung-Ang University, 221, HeukSeok-Dong, Seoul 156-756, Republic of Korea. Phone: 82-2-820-5864. Fax: 82-2-821-8132. E-mail: [email protected].

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