Whole genome sequencing of Vibrio fischeri strain litR+6
Genomic DNA (gDNA) was extracted from the enriched strains following pellicle enrichment using the Quick-DNA Miniprep Plus Kit (Zymo Research). The resulting gDNA was sequenced by SeqCoast Genomics (Portsmouth, NH, USA). Briefly, samples were prepared for whole genome sequencing on the Illumina NextSeq2000 using the Illumina DNA Prep tagmentation kit. Sequencing was performed using a 300-cycle flow cell kit for 2x150 bp paired reads. PhiX control (1-2%) was spiked into the run for optimal base calling. DRAGEN v3.10.11 was used to demultiplex and trim reads and run analytics. Fastqc metrics were used for quality control (Wingett and Andrews 2018). Variant calling was done using the Breseq software v0.37.0. Reads were mapped to the V. fischeri ES114 reference genome sequences NC_006840.2, NC_006841.2, and NC_006842.1 and mutations were identified (Deatherage and Barrick 2014; Langmead and Salzberg 2012).
SUB15192683
litR-6