Skip to main content

Table 2 Identification and classification of strains based on WC-MALDI-TOF MS and on phylogenetic analysis of housekeeping genes sequences

From: Diversity of pathogenic Pseudomonas isolated from citrus in Tunisia

Straina

WC-MALDI-TOF-MSb

Sequences identity

Final identi-fication

P. s. phylo-groupf

Box-PCR profileg

Best match with

Score valued

ctsorrpoD gene sequence

Concanated gene sequencee

Closest type strain

%

Closest type strain

%

BE12A

P. congelans

2.09

P. congelans(rpoD)

98.0

P. congelans

99.1

P. congelans

PG02c

NA

BE1

P. syringae

2.06

P. syringae (rpoD)

99.7

P. syringae

99.6

P. syringae

PG02b

P1

BE3

P. syringae

2.01

P. syringae (rpoD)

99.8

P. syringae

99.6

P. syringae

PG02b

P2

Iy3DA

P. syringae

1.75

P. syringae (rpoD)

99.5

NA

 

P. syringae

PG02b

NA

Iy3EA

P. syringae

1.98

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

NA

Iy3GB

P. syringae

1.83

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

NA

Iy5HA

P. syringae

2.33

P. syringae (rpoD)

99.7

P. syringae

99.2

P. syringae

PG02b

NA

IyGA

P. syringae

1.93

P. syringae (rpoD)

99.5

NA

 

P. syringae

PG02b

NA

IyGC

P. syringae

2.36

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

P2

KB49

P. cannabina/P. syringae

1.99/1.87

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

P2

KC19

P. syringae

2.11

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

NA

KC29B2

P. syringae

1.84

P. syringae (rpoD)

99.5

NA

 

P. syringae

PG02b

P2

KC46

P. syringae

2.01

P. syringae (rpoD)

99.5

NA

 

P. syringae

PG02b

NA

KC54

P. syringae

1.94

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

P5

KC55

P. syringae

2.13

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

NA

KC82

P. syringae

1.99

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

NA

TRR12

P. syringae

2.06

P. syringae (rpoD)

99.8

P. syringae

99.6

P. syringae

PG02b

P2

TRR15

P. syringae

2.15

P. syringae (rpoD)

99.9

NA

 

P. syringae

PG02b

P2

TRR9

P. syringae

2.02

P. syringae (rpoD)

99.8

P. syringae

99.6

P. syringae

PG02b

P2

MTR3B

P. congelans

2.12

P. congelans(rpoD)

98.2

NA

 

P. congelans

PG02c

P7

E10AA

P. syringae

1.92

P. syringae (rpoD)

99.7

NA

 

P. syringae

PG02b

P4

E10CA

P. syringae

2.42

P. syringae (rpoD)

99.8

NA

 

P. syringae

PG02b

P2

E10CB2

P. syringae

2.45

P. syringae (rpoD)

99.7

P. syringae

99.2

P. syringae

PG02b

P2

E11

P. syringae

2.19

P. syringae (rpoD)

99.5

P. syringae

99.5

P. syringae

PG02b

NA

E12A

P. syringae

2.17

P. syringae (rpoD)

99.7

P. syringae

99.6

P. syringae

PG02b

NA

E91

P. syringae

2.21

P. syringae(rpoD)

99.5

NA

 

P. syringae

PG02b

P3

E93A

P. syringae

2.46

P. syringae(rpoD)

97.9

NA

 

P. syringae

PG02b

P6

E9A

P. syringae

2.43

P. syringae(rpoD)

99.7

NA

 

P. syringae

PG02b

NA

EL1A

P. syringae

2.11

P. syringae(rpoD)

99.4

P. syringae

99.1

P. syringae

PG02b

NA

EL2

P. syringae

1.97

P. syringae(rpoD)

99.5

P. syringae

99.3

P. syringae

PG02b

NA

M5*

NAc

NA

P. syringae(cts)

 

NA

 

P. syringae

PG02b

P8

M29*

NA

NA

NA

 

NA

 

P. syringae

PG02b

P8

M30*

NA

NA

NA

 

NA

 

P. syringae

PG02b

P8

M32*

NA

NA

NA

 

NA

 

P. syringae

PG02b

P8

M47*

NA

NA

P. syringae(cts)

 

NA

 

P. syringae

PG02b

P8

V2A2F14*

NA

NA

P. cerasi(cts)

 

NA

NA

P. cerasi

PG02a

NA

V2A2F15*

NA

NA

P. cerasi(cts)

 

NA

 

P. cerasi

PG02a

NA

V2A2F27*

NA

NA

P. cerasi(cts)

 

NA

 

P. cerasi

PG02a

NA

V2A2F45*

NA

NA

P. cerasi(cts)

 

NA

 

P. cerasi

PG02a

NA

V2A2F52*

NA

NA

P. cerasi(cts)

 

NA

 

P. cerasi

PG02a

NA

V2A2F79*

NA

NA

P. cerasi(cts)

 

NA

NA

P. cerasi

PG02a

NA

  1. aStrainwith * werelostduringthestudy and were no longeravailable to do alltests
  2. b Biotyper-indoor DB
  3. c NA, Not Analysed
  4. d Score value between 2.0 and 2.3 indicates a secure identification at the genus level, but not at the species level; a value equal orhigher than 2.3 indicates a secure species identification; values lower than 2.0 indicates probably identification at the genus level
  5. e Concatenated gene sequences: partialsequences of rrs (16S rRNA), gyrBand rpoDgenes wereconcatenatedbeforephylogeneticanalysis
  6. f P. s. phylogroup, P. syringaephylogroup were assigned following Berge et al. (2014)
  7. g Box-PCR profile of strains were visually compared. Strains sharing the same Box-PCR profile were considered very close and are supposed to belong to the same species and phylogroup (see Additional file 1: Figure S1 to see P1 to P7)