Lactobacillus plantarum ATCC 8014 genome sequencing - SRA

SRX682141: Lactobacillus plantarum ATCC 8014 genome sequencing
1 ILLUMINA (Illumina MiSeq) run: 2.8M spots, 1.4G bases, 758.2Mb downloads

Design: 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.

Submitted by: Massey University

Study: Lactobacillus plantarum ATCC 8014 WT Genome sequencing, assembly and annotation

PRJNA247443 • SRP045513 • All experiments • All runs

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The genome of Glycocin F resistant Lactobacillus plantarum ATCC 8014 WT was sequenced by the Illumina MiSeq™ System. De-novo assembly was completed using Velvet and the contigs annotated by PROKKA (http://www.vicbioinformatics.com/).

Sample: Laboratory wildtype Lactobacillus plantarum ATCC 8014 strain

SAMN02777132 • SRS685295 • All experiments • All runs

Organism: Lactiplantibacillus plantarum

Library:

Name: Illumina TruSeq

Instrument: Illumina MiSeq

Strategy: WGS

Source: GENOMIC

Selection: RANDOM

Layout: PAIRED

Spot descriptor:

1 forward251 reverse

Pipeline: show...hide...

Program	Version
Burrows-Wheller-Aligner	0.7.10
fastx-clipper	1.1.2-318

Runs: 1 run, 2.8M spots, 1.4G bases, 758.2Mb

Run	# of Spots	# of Bases	Size	Published
SRR1552613	2,776,720	1.4G	758.2Mb	2014-10-30

ID:: 955051

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