Figure 2

Single-nucleotide polymorphism (SNP) variants identified by SPANDx across the genomes of seven clonal long-term E. coli in vitro passaged cultures. The number of generations is indicated in parentheses. REL606, the ancestor for these passaged cultures, was used for reference genome comparison [GenBank:NC_012967]. As confirmed by SPANDx, REL607 is known to differ from REL606 by two SNPs[18], as denoted by the red vertical lines. In contrast, the ~40 K strain REL10938 is a hypermutable strain[19] and SPANDx identified 607 SNPs separating REL10938 from REL606. Phylogenetic analysis was performed using the Ortho_SNP_matrix.nex file, an output from SPANDx that can be directly imported into PAUP* 4.0[17]. Using maximum parsimony, a highly accurate tree (consistency index = 1.0) was generated in PAUP*. SNPs were visualised with Integrative Genomics Viewer v2.3.25[20].