Fig. 5

Overview of strain generation and SNPs acquired during strain generation. The construction of TM242 equivalent strains follows a stepwise path of pyrE mutant strain (ΔpyrE), followed by ldh disruption, pdh up-regulation and pfl deletion both from NCIMB 11955 (11955ΔpyrE, LS001, LS003, LS005) and TM89 (TM003, TM004, TM005) progenitors. LS242 is the ΔpyrE-repaired strain of LS004. Strains in solid black lines were subjected to Illumina single-read sequencing and analysed by mapping the reads against the deposited genome of NCIMB 11955 (NCBI Accession Number: CP016622-CP016624) using CLCbio Genomic Workbench. Four mutations were acquired in the construction of LS004, two (1 Indel, 1 SNV) during the construction of 11955ΔpyrE and two (2 SNV) from 11955ΔpyrE to LS003. No mutation was acquired from LS003 to LS004. From TM89, a total of 11 mutations were acquired in TM004, with 5 (1 Indel, 4 SNV) during TM89ΔpyrE construction and 6 (all SNVs) from TM89ΔpyrE to TM004. A total of 9 differences were noted between TM89 and NICMB 11955 (1 Indel, 8 SNPs) with 2 further mutations found in TM242 (1 Indel, 1 SNV), resulting in a total of 11-nucleotide change compared to NCIMB 11955