Complete Genome Sequence of Leuconostoc mesenteroides subsp. mesenteroides Strain J18, Isolated from Kimchi

Abstract

Leuconostoc mesenteroides subsp. mesenteroides is one of the most predominant lactic acid bacterial groups during kimchi fermentation. Here, we report the complete genome sequence of L. mesenteroides subsp. mesenteroides J18, which was isolated from kimchi. The genome of the strain consists of a 1,896,561-bp chromosome and five plasmids.

GENOME ANNOUNCEMENT

Kimchi, a traditional Korean fermented food, is made by fermentation of vegetables such as Chinese cabbage and radish with assorted seasoning mixtures containing ingredients such as red pepper powder, garlic, ginger, green onion, and fermented seafood (jeotgal). Taxonomic studies using conventional and molecular methods have shown that various lactic acid bacterium (LAB) species, such as Leuconostoc mesenteroides, Lactobacillus sakei, and Weissella koreensis, are likely to be key players responsible for kimchi fermentation (1, 6, 9). Members of the genus Leuconostoc are heterofermentative LAB that are typically dominant during the early and mid-phases of kimchi fermentation (2, 6) and are known to be among the LAB that determine kimchi's flavors (7, 10, 12). A strain of L. mesenteroides subsp. mesenteroides, designated J18, was isolated from baechu (Chinese cabbage) kimchi fermented at 4°C. Here, we report the complete genome sequence and annotation of L. mesenteroides subsp. mesenteroides J18.

The whole genome of strain J18 was sequenced at Chunlab (Republic of Korea). About 39.38 Mb (∼19.5-fold coverage) with 203,962 paired-end reads containing 8-kb inserts and about 2,171.1 Mb (∼1,076.7-fold coverage) with 25,902,870 paired-end reads containing 100-bp inserts were generated from the 454 GS FLX Titanium system (Roche) and a model IIx Illumina genome analyzer, respectively. The resulting complete sequences were assembled into seven large scaffolds, including 26 contigs, using the GS Assembler 2.3 (Roche) and the CLC Genomics Workbench 4.5.1 (CLC bio) software programs. All the intrascaffold and interscaffold gaps were closed by sequencing of PCR products. The Phred/Phrap/Consed software programs (3, 4, 5) were used for sequence assembly and quality assessment. The final whole-genome sequence was further validated by Sanger sequencing of uncertain regions such as mononucleotide runs and low-quality/depth segments. The complete sequence was submitted to the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP) for annotation. The tRNA and rRNA genes were annotated using the tRNAscan-SE (11) and RNAmmer (8) software programs, respectively. The genome of L. mesenteroides subsp. mesenteroides J18 is composed of one circular chromosomal genome of 1,896,561 bp (37.77% G+C content) and five circular plasmids (pKLE01, 37,252 bp; pKLE02, 35,425 bp; KLE03, 24,548 bp; pKLE04, 19,293 bp; and pKLE05, 3,347 bp) (Table 1). The entire genome (2,016,426 bp) contains 1,942 predicted protein-coding sequences, i.e., 1,803 coding sequences with an average gene length of 930 bp and a coding intensity of 88.38% on the chromosome and 43, 46, 29, 19, and 2 coding sequences on plasmids pKLE01 to -5, respectively, as well as four complete rRNA operons and 71 tRNA genes coding 20 amino acids on the chromosome. The G+C content of the chromosome is 37.77%, while those of the five plasmids are in the range of 34.85 to 38.78% (Table 1).

Table 1.

Sequence features of 5 plasmids in the Leuconostoc mesenteroides subsp. mesenteroides strain J18 genome

Plasmid name	Size (bp)	No. of coding gene sequences	Avg gene length (bp)	Coding density (%)	G+C content (%)	GenBank accession no.
pKLE01	37,252	43	691	78.2	34.85	CP003102
pKLE02	35,425	46	468	60.7	35.15	CP003103
pKLE03	24,548	29	641	75.7	38.28	CP003104
pKLE04	19,293	19	877	86.4	35.16	CP003105
pKLE05	3,347	2	1,515	90.5	38.78	CP003106

Nucleotide sequence accession numbers.

The genome information for the chromosome of Leuconostoc mesenteroides subsp. mesenteroides strain J18 was deposited in NCBI under GenBank accession number CP003101, and the accession numbers for the plasmids are listed in Table 1.