Fig. 3. Whole-genome sequencing and reconstruction of alleles shared across populations of evolved synthetic auxotrophs.

(A) List of alleles identified through next-generation sequencing. †Sequencing results originally obtained during the project identified this EmrD allele as a 33-bp deletion, which was then reconstructed in the experiment shown in (B). However, resequencing performed at the end of the project identified the allele as a 39-bp deletion and was confirmed by Sanger sequencing. A repetitive GGCGCG nucleotide sequence corresponding to G323-A324 and G336-A337 creates ambiguity about the precise positional numbering of the deletion. However, the three possible 13–amino acid deletions (323–335, 324–336, and 325–337) result in the same final protein sequence. (B) Effect of reconstructed allele in DEP progenitor on doubling time as a function of BipA concentration, normalized to the doubling time of DEP at 100 μM BipA. Error bars represent the SD across technical triplicates within the same experiment.