3.2 Comparative genomic analysis of E. coliBQ<A1> and B3<T7> derivatives
To search for genetic factors involved in the ability to maintain a high growth rate under production conditions, we sequenced the genomes of 11 B3<T7-GFP> and 2 BQ<A1-GFP> derivatives (Table 1) and 3 B3<T7-Fab> and 4 BQ<A1-Fab> derivatives (Table 2). We found one to three mutations (SNPs or indels) per genome, corresponding to the mutation rate for E. coli of approximately 1 × 10-3 per generation for cells cultured under standard laboratory conditions.[40] Notably, the spontaneous mutation rate is stress-dependent [41]and mutants that result in an increased growth rate under production conditions are more likely to be selected. We applied read mapping and ade novo assembly approach to examine SNPs and short indels, as well as detect larger deletions or subpopulations of genomes.