TABLE 1.

Genes where insertions are specifically lost or enriched in the radD strain after evolution in MH or TOB

Decrease or increasee and antibiotic	Gene ID		Role	Fold change for T16 vs T0 (P value) for strain:
	Locus tag	Name		MH radD straina	MH WTb	TOB radD strainc	TOB WTd
Decrease
No antibiotic	VC1835	pal	Outer membrane integrity	No reads (0)	−1.8
	VC1837*	tolA	Outer membrane integrity	No reads (0)	8.3
	VC1838	tolR	Outer membrane integrity	No reads (0)	5.9
	VC1839	tolQ	Outer membrane integrity	No reads (0)	−1.2
	VC2291	ngrE	Iron and oxidative stress	No reads (0)	6.2
	VC2292	ngrD	Iron and oxidative stress	No reads (0)	1.1
	VC2293	ngrC	Iron and oxidative stress	No reads (0)	1.2
	VC2294	nqrB	Iron and oxidative stress	No reads (0)	5.1
	VCA0897	pgl	Pentose phosphate pathway	−26.3 (0.009)	2.1
	VCA0609		Unknown	−23.4 (1.60E−15)	2.9
	VCA0634		Putative tRNA modification	−9.3 (0.011)	1.5
	VC2517		Putative ABC-type transport	−6.7 (1.00E−08)	1.5
	VC2234*	rnhA	RNase H1, R-loop degradation	−5.9 (0.014)	−1.7
	VC1575		Unknown	−4.1 (4.50E−07)	−1.7
TOB, 50% MIC	VC1948		Unknown	1.6	−1.5	−30.9 (0.001)	−1.2
	VC0678	hlyU	Transcriptional regulator	−2.9	−3.2	−16.8 (0.001)	1.3
	ncRNA235		Noncoding RNA	−1.3	2	−16.2 (0.006)	−1.8
	VC2392*	mutT	Nucleotide detoxification	1	−1.8	−13.6 (8.70E−05)	−2.4
	VC2234*	rnhA	R-loop degradation	−5.9	−1.7	−13.5 (0.002)	−1.6
	VCA0569	vxrE	Unknown	−1.8	1.8	−10.3 (1.90E−04)	1.2
	VC2718	bioH	Metabolism	1.9	1.2	−8.7 (1.50E−04)	−2.2
	VC1759		Prophage integrase	−1.1	1.3	−8 (0.001)	1.6
	VCA0032		Unknown	−2.8	−1.4	−5.6 (2.20E−04)	−1.5
	VCA0741		Unknown	1.8	2.2	−5 (0.008)	−1.3
	VCA0654	scrR	Carbohydrate metabolism	−1.6	2.1	−4.9 (5.80E−05)	−1.2
	VC0099	glpG	Protease	1.3	−1.6	−4.8 (3.70E−06)	−1.5
	VC1824		Carbohydrate metabolism	−1.3	−1.7	−4.5 (0.004)	−1.1
	VCA0608	yjjG	Nucleotide detoxification	−1.2	2.1	−4.2 (1.90E−05)	−1
	VCA0501		Unknown	1.3	1.5	−4.1 (2.60E−11)	1.9
Increase
No antibiotic	VC0887*	yqcC	Pseudouridine synthase (Hyp)	8.3 (0.045)	2.9
	VC0330	rsd	Putative transcription factor	6.5 (0.003)	1.1
	VC1167	tdk	Pyrimidine metabolism	4.7 (7.20E−09)	2.7
TOB, 50% MIC	VC1262		Putative methyltransferase	−1.1	1.3	6.4 (3.00E−05)	1.7
	VC1150		Unknown	2.4	1.2	4.8 (1.00E−04)	2.1

^aAverage insertions detected in MH radD strain at T₁₆ compared to radD strain at T₀; all numbers express fold changes.

^bInsertions in MH WT at T₁₆ compared to WT T₀.

^cAverage insertions detected in TOB radD strain at T₁₆ compared to radD strain at T₀.

^dAverage insertions detected in TOB WT at T₁₆ compared to WT T₀. Genes with at least 4-fold changes are shown. Deletions for genes marked with an asterisk were constructed in V. cholerae WT and radD strains.

^eIn radD strain but not WT at time T₁₆.