Figure 3

Chromosome maps of mutations discovered through whole genome resequencing of isobutanol tolerant clones. Genome resequencing of clones G3.2 and G3.6 (from G3 end population), X3.5 (from X3 end population), and G3.266.7 (from G3 lineage, generation 266) was done using the Illumina Solexa platform. SNPs (single nucleotide polymorphisms) and short indels (nucleotide insertions or deletions) were detected by mapping reads were onto the reference E. coli EcNR1 genome sequence. Structural Variation (SV) breakpoints were detected by de novo assembly of unmapped reads for single-end sequence data or with BreakDancer v0.0.1 for paired-end sequence data. (A) Chromosome map of mutations detected in X3.5; (B) Chromosome map of overlapping mutations in G3.2/G3.6 and G3.266.7. Mutations in G3.2/G3.6 are shown on the outer ring, while mutations in G3.266.7 are shown on the inner ring. All mutations in G3.266.7 except for the gltB-yhcE 10 kb deletion and ycfK 1688 bp deletion are on the same line of descent as G3.2 and G3.6 clones.