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J Bacteriol. May 2012; 194(9): 2371–2372.
PMCID: PMC3347058

Complete Genome Sequence of Klebsiella oxytoca KCTC 1686, Used in Production of 2,3-Butanediol

Abstract

Here we report the full genome sequence of Klebsiella oxytoca KCTC 1686, which is used in production of 2,3-butanediol. The KCTC 1686 strain contains 5,974,109 bp with G+C content of 56.05 mol% and contains 5,488 protein-coding genes and 110 structural RNAs.

GENOME ANNOUNCEMENT

Klebsiella oxytoca (formerly Klebsiella pneumoniae or Aerobacter aerogenes), which is a Gram-negative, rod-shaped bacterium, metabolizes a wide variety of sugars present in hemicelluloses and cellulose hydrolysates (9, 12). K. oxytoca is used in production of 2,3-butylene glycol and 2,3-butanediol from xylose (4, 5). Many studies of 2,3-butanediol production using K. oxytoca have been recently reported (6, 7, 11). In order to understand these unique properties on the genomic level, K. oxytoca KCTC 1686 was obtained from the Korean Collection for Type Culture (Daejun, South Korea). Whole-genome sequencing was performed. Other collection numbers are ATCC 8724 and NRRL B-199.

Genomic DNA isolated from an overnight culture of K. oxytoca strain KCTC 1686 by the use of a DNeasy blood and tissue kit (Qiagen) was sequenced by 454 GS FLX Titanium pyrosequencing (Roche), following the manufacturer's instructions, with 25× coverage (8). The 491,471 reads generated, with a length of 127,991,134 bp, were then assembled using GS De Novo assembler (version 2.3; Roche). The N50 contig was 223,060 bp, and the largest contig assembled was 466,071 bp. This assembly generated 61 large (>500 bp) contigs, with a length of 6,102,926 bp. The 471,296 reads (95.59% of the total) were assembled into 12 scaffolds composed of 96 contigs, with a length of 6,122,793 bp. The N50 scaffold was 3,470,062 bp, and the average length of the scaffolds was 510,232 bp.

The order of scaffolds was determined by a similarity search among published references and confirmed by a PCR size check. Gaps both within and between scaffolds can be closed by long-range PCR (using MG Taq-HF DNA polymerase; Macrogen, Seoul, South Korea) and subsequent Sanger sequencing using an ABI 3730XL capillary sequencer. The sequences from ABI 3730XL sequencing and scaffolds were completely assembled into one circular genome by the use of Phred/Phrap/Consed software (1, 2, 3) and annotated with Prokaryote Genomes Automatic Annotation Pipeline (PGAAP) software (10).

The complete genome is composed of a circular chromosome of 5,974,109 bp (56.05% G+C content), including 5,488 coding genes, 85 tRNAs, and 25 rRNAs. A total of 4,385 coding genes (79.90% of the total) have putative functions assigned on the basis of annotation. A KCTC 1686 transcriptome experiment was performed using a Roche/FLX system to improve its genome annotation. Although a small amount of non-rRNA sequences were obtained from transcriptome analysis, 13,041 reads (86.17%) of the total of 15,134 mapped non-rRNA reads were mapped to 2,435 predicted coding genes.

This is the first genome sequence of the K. oxytoca species, which should provide the basis for a better understanding of the genetic background for further study. A more detailed analysis of a full-genome comparison of the available Klebsiella strains is to be included in a further publication on transcriptome analysis.

Nucleotide sequence accession number.

The genome sequence of K. oxytoca KCTC 1686 has been deposited in NCBI GenBank under accession number CP003218.

ACKNOWLEDGMENT

This work was supported by the Industrial Strategic technology development program (10035147, Development of 2,3-butanediol and derivative production technology for C-Zero bio-platform industry) funded by the Ministry of Knowledge Economy (MKE), Republic of Korea.

REFERENCES

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