Lactobacillus plantarum ATCC LP8_1L genome sequencing
L. plantarum subsp. plantarum ATCC 14917 or L. plantarum ATCC 8014 cell-embedded MRS agar plates containing 100 nM glycocin F were made. From log phase cultures of L. plantarum ATCC 8014 and L. plantarum subsp. plantarum ATCC 14917, aliquots containing 1.61 x 107 and 2.0 x 107 CFU respectively were diluted into 20 mL of molten (40°C) MRS agar containing 100 nM glycocin F and incubated for 48 hours at 30°C. Surface colonies were streaked on to MRS agar plates that contained 100 nM glycocin F. These were re-streaked once more onto MRS agar plates that contained 100 nM glycocin F and incubated overnight at 30°C. Final isolated colonies were used to inoculate 10 mL of MRS broth containing 100 nM glycocin F which were incubated at 30°C overnight. Genomic DNA from the glycocin F-resistant mutants and their respective glycocin F sensitive wild type strains were sequenced using the Illumina® MiSeq™ system. The mutants were selected for genome sequencing based on the findings of glycocin F solid plate and liquid culture sensitivity assays; from each strain, two high level glycocin F resistant mutants and one low level glycocin F resistant mutant were selected: LP1_2H, LP1_3L and LP1_4H from L. plantarum subsp. plantarum ATCC 14917 mutants, and LP8_1L, LP8_4H and LP8_5H from L. plantarum ATCC 8014 mutants.     The raw sequenced reads were processed through an established quality control pipeline by the MGS: First the raw sequencing reads were mapped to the Enterobacteria λ phiX174 sensu lato genome (GenBank accession number NC_001422) using the Burrows-Wheller-Aligner software (BWA) (Li and Durbin, 2009), and any reads that mapped were removed from the BWA SAM output file. This SAM file was subsequently converted into a fastq file using the Picard suite ‘SamToFastq.jar’ tool (http://picard.sourceforge.net/index.shtml). The resultant fastq file was processed with the ‘fastx-clipper’ script, from the ea-utils suite (https://code.google.com/p/ea-utils/) to remove contaminating TruSeq™ Universal Adapter (Illumina®; San Diego, CA, USA) sequences. The final 'forward and reverse fastq files' were subjected to further quality control before downstream de novo assembly.