Whole Genome Sequencing of Bacterial Strains

Whole genome sequencing libraries for strains H98, ID76, ID77 and ID112 were prepared using the Illumina Nextera Flex DNA kit with custom index primers. Sequencing fragment libraries were then pooled and size-selected using the SPRI-Select magnetic beads (Beckman Coulter) and the pooled library was then quality checked and quantified with a Agilent Bioanalyzer 2100 using the DNA HS kit (Agilent). Sequencing of was performed using an Illumina MiSeq with a 300-cycle micro flow cell with V2 chemistry. Sequence data were de-multiplexed using Phylosift^{65 (link)} and trimmed using Trimmomatic with default settings^{66 (link)}. A draft H98 genome was assembled using the A5 miseq assembler (version 20150522)^{67 (link)}, and then the trimmed reads for the three ΔftsZ strains were aligned to the draft H98 genome using bwa^{68 (link)}. Variant calling was done using bcftools mpileup and call^{69 (link)}. Any single nucleotide polymorphisms (SNPs) that had a quality score of less than 20 or were located within contigs of less than 1000 bp were discarded. Non-synonymous variants in coding regions or any variants in intergenic regions were then identified in ID76, ID77 and ID112 compared to the H98 draft reference genome (Supplementary Table 5).