# Experimental Evolution of Magnetic Nanoparticle Resistance in _Escherichia coli_
## 3 Results
### Whole Genome  
The genomic variants found in the FeNP are listed in Table 3a-c. Descriptions of these genes are given in Table 4a-c. The genomic variants for the controls are provided in Appendix B Tables A3 and A4. The controls showed no hard selective sweeps. Furthermore, genomic variants for the ancestral population are not reported here as these are given in our prior research [41; 42]. The ancestral variants were filtered out of all variant calls in the FeNP and Control populations. At 25 days, three of the five FeNP replicates (FeNP\({}_{1}\), FeNP\({}_{2}\), and FeNP\({}_{5}\)) displayed a hard selective sweep for non-synonymous (NS) substitutions in the RNA polymerase subunit \(\beta^{\prime}\) (_rpoC_) gene. Significant polymorphisms in RNA polymerase subunit \(\alpha\) (_rpoA_) were observed in FeNP\({}_{3}\) and FeNP\({}_{5}\) (f = 0.503 and 0.665, respectively). FeNP\({}_{4}\) was the only population displaying no hard selective sweeps but had significant polymorphisms in the flagellar hook protein (_flgE_) and NADH: ubiquinone oxidoreductase, chain G (_muoG_) genes (f = 0.295, 0.439 respectively). Significant polymorphisms (f > 0.250) were observed in all replicates (Table 3b). FeNP\({}_{1}\) showed NS polymorphisms in porphyrinogen oxidase, cytoplasmic (_yfeX_), and putative metal-dependent hydrolase (_ygjP_). FeNP\({}_{2}\) had NS polymorphisms in hydroxyacylglutathione hydrolase (_glb_) and a synonymous substitution in the glutamate/aspartate: proton symporter (_glbP_). Synonymous substitutions may result from linkage to a NS beneficial mutation, or they can result from favorable selection due to codon bias. FeNP\({}_{3}\) had NS polymorphisms in RNA polymerase \(\alpha\) subunit (_rpoA_) and a synonymous variant in chromate reductase, Class I, flavoprotein (_chrR_). FeNP\({}_{4}\) in flagellar hook protein (_fggE_) and NADH ubiquinone oxidoreductase, chain G (_muoG_). Finally, FeNP\({}_{5}\) also showed a significant NS polymorphism in RNA polymerase, \(\alpha\) subunit (_rpoA_). Minor polymorphisms are listed in Table 3c. The controls displayed significant NS polymorphisms in RNA polymerase subunits \(\beta\) and \(\beta^{\prime}\). These are often associated with adaptation to minimal medium such as DMB. The _rpoB_ H526Y variant has been repeatability observed arising in our control populations in several of our past studies [41; 42]. Figure 4: **Bacteria cell width and length distribution**. Box plots of _E. coli_ MG1655 mean cell width and length for FeNP compared to controls and ancestors is shown. The sample size was N = 20 cells per replicate population measures in the FeNP and control populations for a total of 100 cells per selection treatment. Sample size for ancestors was 15 for each replicate, for a total of 75 cells. \begin{table}
\begin{tabular}{c c c} \hline  & **(a)** \\ \hline
**Gene** & **Position** & **Description** \\ \hline rpoC\(\rightarrow\) & 4,186,578 \& 4,187,214 & RNA polymerase, beta prime subunit \\ \hline \end{tabular}
\end{table} 
Table 4: **(a)** Position and description of selective sweeps in FeNP-resistant populations at day 25. **(b)** Position and description of significant polymorphisms in FeNP-resistant populations at day 28. **(c)** Position and description of minor polymorphisms in FeNP-resistant populations at day 25.