A17, the First Sequenced Strain ofLactococcus lactis subsp.cremoris with Potential Immunomodulatory Functions
Abstract
GENOME ANNOUNCEMENT
The genome of A17 was sequenced with both MiSeq (Illumina, Inc.) and RSII (Pacific Biosciences of California, Inc.) platforms to generate 4,117,596 paired-end reads and 163,471 PacBio long reads, respectively. We trimmed Illumina paired-end reads by limiting the quality score of reads to more than 30 and removed 20 nucleotides on both ends of the reads. The filtered Illumina reads were de novo assembled (with a word size of 50 bp and a bubble size of 98 bp) with PacBio long reads as the guidance in CLC Genomics Workbench 7.04 (Qiagen) with the CLC Microbial Genome Finishing Module (Qiagen). The resulted genome assembly of A17 has 16 contigs, comprising 2,679,936 bp. The estimated G+C content of the assembled A17 genome is 35.6%. The A17 genome assembly was annotated using the NCBI prokaryotic genome annotation pipeline (PGAP) and then uploaded to NCBI GenBank. The annotation of the A17 assembly contains 2,500 genes, including 2,321 coding DNA sequences (CDS), 93 pseudogenes, 18 rRNA genes (5S, 16S, and 23S), 67 tRNA genes, one ribozyme gene (RNase P), and 63 frameshifted genes. A17 was shown to be a potential exopolysaccharide (EPS) producing bacterium with seven genes for polysaccharide metabolism found in the genome. These genes encode one polysaccharide deacetylase (JL36_00195), one polysaccharide permease (JL36_11180), one membrane protein for polysaccharide transport (JL36_07670), and 4 proteins for polysaccharide biosynthesis (JL36_05435, JL36_09505, JL36_09510, and JL36_11200). After a BLASTn search (with default parameters) against the virulence factors database (VFDB [see http://www.mgc.ac.cn/VFs/]), none of the genes in the A17 genome were found to be similar to virulence genes in VFDB.
Nucleotide sequence accession numbers.
This draft genome of
Footnotes
Citation Yang C-H, Wu C-C, Cheng W-S, Chung M-C, Tsai Y-C, Chang C-H. 2015. A17, the first sequenced strain of Lactococcus lactis subsp. cremoris with potential immunomodulatory functions. Genome Announc 3(1):e01563-14. doi:10.1128/genomeA.01563-14.
ACKNOWLEDGMENTS
This work was sponsored by grants from the Academic Technology Development Program (103-EC-17-A-17-S1-197) of the Ministry of Economic Affairs, ROC and National Core Facility Program for Biotechnology, Taiwan (High-throughput Genome Analysis Core Facility [NSC-102-2319-B-010-001] and Bioinformatics Consortium of Taiwan [MOST 103-2319-B-010-002]).
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