Table 2.

P. aeruginosa genes identified as non-synonymously mutated in at least three independent longitudinal studies

The characteristics of the 13 studies used for the intragenic regions are listed in Table 1.

				Longitudinal studies
Gene name	PAO1 locus	Product	Positive selection	No.	Reference
gyrB	PA0004	DNA gyrase subunit B	Yes	8	[6, 7, 9, 11, 14–16, 18]
pvdS	PA2426	Sigma factor	No	8	[6, 7, 9, 10, 13, 16–18]
mexA	PA0425	RND multidrug efflux membrane fusion protein MexA precursor	No	6	[6, 7, 15–18]
mexY	PA2018	Multidrug efflux protein	No	6	[6–8, 10, 13, 14, 17]
mexZ	PA2020	Transcriptional regulator of multidrug efflux pump	Yes	6	[6, 9, 13, 16–18]
gyrA	PA3168	DNA gyrase subunit A	No	6	[9, 10, 13, 14, 16–18]
ftsI	PA4418	Penicillin-binding protein 3	No	6	[8–10, 13–15, 17]
mexB	PA0426	RND multidrug efflux transporter	No	6	[6, 7, 14, 16–18]
oprD	PA0958	Basic amino acid, basic peptide and imipenem outer-membrane porin	No	6	[9, 10, 14–17]
migA	PA0705	α-1,6-Rhamnosyltransferase	No	5	[7, 9, 12–15]
algU	PA0762	RNA polymerase sigma factor	Yes	5	[9, 13, 14, 16–18]
lasR	PA1430	Transcriptional regulator of QS	Yes	5	[6, 9, 16–18]
pmrB	PA4777	Two-component regulator system signal sensor kinase	No	5	[7, 10, 11, 13–15]
mucA	PA0763	Anti-sigma factor	Yes	5	[6, 13, 16–18]
algG	PA3545	Alginate-C5-mannuronan-epimerase	No	5	[7, 9, 12, 13, 17]
mexS	PA2491	Probable oxidoreductase	Yes	4	[6, 15–17]
mexT	PA2492	Transcriptional regulator of multidrug efflux pump	No	4	[6, 10, 12, 15]
rpoB	PA4270	DNA-directed RNA polymerase β chain	No	4	[6, 7, 13, 14, 17]
chpA	PA0413	Component of chemotactic signal transduction system	No	4	[7, 10, 11, 17]
wbpM	PA3141	Nucleotide sugar epimerase/dehydratase	No	4	[9, 10, 16, 17]
fusA1	PA4266	Elongation factor G	Yes	4	[8, 9, 12, 17]
rpoN	PA4462	RNA polymerase C-54 factor	Yes	4	[6, 13, 15, 18]
pagL	PA4661	Lipid A 3-O-deacylase	Yes	4	[9, 12, 13, 17]
retS	PA4856	Regulator of exopolysaccharide and type III secretion	No	4	[7, 10, 16, 18]
rpoC	PA4269	DNA-directed RNA polymerase subunit β	No	3	[7, 13, 14, 17]
exsA	PA1713	Transcriptional regulator of T3SS	No	3	[6, 7, 12]
ampC	PA4110	β-Lactamase/d-alanine carboxypeptidase	Yes	3	[8, 9, 13, 14]
atsA	PA0183	Arylsulfatase	No	3	[7, 10, 13]
pilJ	PA0411	Twitching motility protein	Yes	3	[9, 13, 17]
xdhB	PA1523	Xanthine dehydrogenase	No	3	[7, 8, 10]
dnaX	PA1532	DNA polymerase subunits γ and τ	No	3	[6, 10, 16]
pcoA	PA2065	Copper resistance protein A precursor	No	3	[7, 10, 16]
pvdL	PA2424	Non-ribosomal peptide synthase, pyoverdine biosynthesis	No	3	[9–11]
clpA	PA2620	ATP-binding protease component	Yes	3	[9, 13, 17]
pelA	PA3064	Glycohydrolase involved in Pel biosynthesis	No	3	[10, 14, 16]
hasR	PA3408	Haem uptake outer-membrane receptor precursor	No	3	[7, 10, 17]
wspA	PA3708	Chemotaxis transducer	No	3	[10, 16, 17]
PA3728	PA3728	ATPase	Yes	3	[8, 13, 17]
purL	PA3763	Phosphoribosylformylglycinamidine synthase	Yes	3	[8, 13, 17]
bfmS	PA4102	Histidine kinase sensor	No	3	[9, 12, 15]
recC	PA4285	Exodeoxyribonuclease V subunit γ	No	3	[7, 8, 10]
ampD	PA4522	N-Acetyl-anhydromuranmyl-l-alanine amidase	No	3	[6, 7, 17]
nfxB	PA4600	Transcriptional regulator	Yes	3	[16–18]
phuR	PA4710	Putative haem/haemoglobin uptake outer-membrane receptor	No	3	[7, 15, 17]
cbrA	PA4725	Two-component sensor CbrA	No	3	[10, 11, 17]
cbrB	PA4726	Two-component response regulator CbrB	No	3	[7, 9, 13]
folP	PA4750	Dihydropteroate synthase	No	3	[7, 10, 15]
spoT	PA5338	Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolase	Yes	3	[9, 13, 17]