Table 1 Whole genome sequencing data for evolved (T18) P. aeruginosa populations compared to the starting planktonic culture strain (T0).

From: In vitro evolution of Pseudomonas aeruginosa AA2 biofilms in the presence of cystic fibrosis lung microbiome members

Sample name

Gene name

PA number

Mutation type

Nucleotides

Position

(contig) nt

Amino acids affected

Relative abundance (%)

T18 L1 C

lasR

PA1430

Del

ΔG

(2) 294159

K182RfsX27*a

100

pqsR

PA1003

In

In

+A

transposase

(11) 20879

(11) 20654

L98FfsX34

H173transpos*b

81

5

gntR

PA4132

SNP

SNP

SNP

C → G

A → C

G → A

(34) 41825

(34) 41176

(34) 40992

Y349X

D133A

V72M

41

4

2

mexL

PA3678

SNP

G → A

(12) 221690

A26T

23

sahH

PA0432

SNP

G → A

(1) 95660

297 nt upstream*c

99

pilA

PA4525

Del

CTACCA

(6) 118729

T154_T155del

97

T18 L1 M

lasR

PA1430

Del

ΔG

(2) 294159

K182RfsX27

100

pqsR

PA1003

Del

In

Del

ΔTTGAT + A

ΔCGAGCTGACCGC

(11) 20762

(11) 20879

(11) 21061

I136AfsX208

L98FfsX34

A34_S37del*d

69

11

7

sahH

PA0432

SNP

G → A

(1) 95660

297 nt upstream

56

pilA

PA4525

Del

CTACCA

(6) 118729

T154_T155del

92

T18 L2 C

lasR

PA1430

In

+A

(2) 294001

S129KfsX104

94

pqsR

PA1003

SNP

C → T

(11) 20505

D223H

38

mexL

PA3678

duplication

SNP

SNP

35 nt

T → G

C → A

(12) 222153

(12) 221786

(12) 222105

E192GfsX0

F58T

A164D

24

17

12

sahH

PA0432

Del

ΔG

(1) 95633

271 nt upstream

32

pilA

PA4525

Del

CTACCA

(6) 118729

T154_T155del

98

T18 L2 M

lasR

PA1430

In

Del

+A

ΔG

(2) 294001

(2) 294159

K182RfsX27

59

31

pqsR

PA1003

SNP

A → T

(11) 21047

L42Q

59

pqsA-phnA

PA0996-PA1001

Del

Δ(4618 nt)

(11) 13454–18072

V306(pqsA)_S2(phnA)

del fsX69*e

10

mexL

PA3678

SNP

G → C

(12) 221695

K27N

23

pilA

PA4525

Del

CTACCA

(6) 118729

T154_T155del

49

T18 L3 C

lasR

PA1430

In

Del

+A

ΔG

(2) 294001

(2) 294159

S129KfsX104

K182RfsX27

89

10

pqsR

PA1003

In

SNP

+G

T → G

(11) 20642

(11) 20645

L178VfsX168

H176P

74

9

gntR

PA4132

SNP

In

In

A → C + CTG + C

(34) 41988

(34) 41357

(34) 40926

T404P

L194_L195insL*f

G52RfsX260

9

9

2

mexL

PA3678

SNP

SNP

SNP

T → G

G → A

G → T

(12) 222042

(12) 221744

(12) 221842

M143R

A44T

Q76H

46

9

6

sahH

PA0432

SNP

G → A

(1) 95660

297 nt upstream

77

pilA

PA4525

Del

CTACCA

(6) 118729

T154_T155del

87

T18 L3 M

lasR

PA1430

Del

In

ΔG + A

(2) 294159

(2) 294001

K182RfsX27

S129KfsX104

89

12

pqsR

PA1003

In

Del

transposase

ΔAG

(11) 21137

(11) 20400

F12transpos

Y258TfsX131

33

5

sahH

PA0432

SNP

G → A

(1) 95660

297 nt upstream

10

pilA

PA4525

Del

CTACCA

(6) 118729

T154_T155del

93

  1. In: insertion (+), Del: deletion (Δ), SNP: single nucleotide polymorphism (→). nt: nucleotide. QS: quorum sensing. T18: timepoint 18 (final evolved population). L1, L2, L3: lineage 1, 2, 3. C: control (=evolution in the absence of the microbiome), M: microbiome (=evolution in the presence of the microbiome). PA number: Pseudomonas aeruginosa PAO1 homologue number. This table lists genes that were mutated in at least one sample at a frequency above 35%.
  2. *aK182RfsX27: K at position 182 is the first amino acid residue affected, it is changed to R followed by a frameshift of 27 codons in total, including the next stop codon.
  3. *bH173transpos: the codon H at position 173 is interrupted by a transposase.
  4. *cThe mutations relating to sahH are located in the intergenic region upstream of the start of the gene.
  5. *dA34_S37del: the amino acids 34 to 37 are deleted.
  6. *eV306(pqsA)_S2(phnA)del fsX69: the deletion affects V in position 306 of pqsA to S in position 2 of phnA, followed by a frameshift of 69 codons including the stop codon.
  7. *fL194_L195insL: L is inserted between position 194 and 195.
Back to article page