Whole genome sequence of L. plantarum from raw milk
Genomic DNA was isolated from the plate using Exgene TM Cell SV kit (Cambio, UK) and quantified by Quant-iT BR assay kit (Invitrogen). The high-molecular weight genomic DNA was sheared using a Covaris S2 ultra sonicator system, in order to get appropriate sizes. Libraries with short inserts of 350bp for paired-end reads were prepared using Truseq Nano DNA sample prep kit. Products were quantified using the Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and the raw data were generated by an Illumina Novaseq 6000 platform (Illumina). Cluster generation was performed, PE 2 150bp cycle sequencing reads using Re-sequencing. The quality of the reads were checked using fastQC (v.0.11.7) and the low-quality base below Q20 were trimmed using Trimmomatic (v.0.36). High quality reads were then aligned to the Lactiplantibacillus plantarum using Burrows Wheeler Aligner (BWA) (v.0.7.17) with minimum seed length of 45. After the alignment of the reads to reference genome, the duplicated reads were further removed using MarkDuplicates tool in GenomeAnalysisTK (v.4.0.11.0).