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Table 2 The distribution of genes/clusters related to virulence among 84 Pectobacterium genomes

From: Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle

Gene/cluster

Locus tag

Pectobacterium

Reference Dickeya strainsa

Pc (n = 56)

Pa (n = 10)

Pp (n = 6)

CPm (n = 8)

Ppo (n = 4)

D. zeae Ech 586

D. dadanti 3937

D. paradisiaca Ech703

Pcb (n = 29)

Pcc (n = 9)

Pco (n = 15)

Pca (n = 3)

Cellulases (PCWDEs)

 celV/celB

BCS7_11780/BCS7_07535

29

9

15

3

10

6

8

4

–

–

–

 putative cellulase

BCS7_10680

29

9

15

3

10

6

8

4

Dd586_2061

Dda3937_00081

–

Oligogalacturonide (PCWDEs)

 ogl

BCS7_09745

29

9

15

3

10

6

8

4

Dd586_1940

Dda3937_03686

Dd703_2056

Pectate_lyase (PCWDEs)

 pelX/pelB/pelW

BCS7_21380/BCS7_11020/BCS7_09865

29

9

15

3

10

6

8

4

Dd586_4161/Dd586_3789/Dd586_1962

Dda3937_00143/Dda3937_04192/Dda3937_03361

Dd703_3996/Dd703_0352/Dd703_2033

 pel

BCS7_14745

29

9

15

3

10

0

8

4

–

–

–

 pelA

BCS7_11155

29

9

15

3

10

0

8

3

Dd586_3083

Dda3937_03370

Dd703_2763

 pelL/pelZ

BCS7_08875/BCS7_19275

29

9

15

3

10

6

8

4

Dd586_1488/Dd586_3790

Dda3937_02794/Dda3937_04191

Dd703_1887/Dd703_0351

 pel1/pel2/pel3

BCS7_19260-BCS7_19270

29

9

15

3

10

6

8

4

–

–

–

 pelI

BCS7_05195

29

9

15

3

10

6

8

4

Dd586_2937

Dda3937_00058

–

Pectin acetylesterase (PCWDEs)

 paeX/paeY

BCS7_09835/BCS7_15435

29

9

15

3

10

6

8

4

Dd586_1956/Dd586_3086

Dda3937_03363/Dda3937_03373

Dd703_2039/Dd703_2765

Pectin lyase

 pnl

BCS7_06950

29

9

15

3

10

6

8

4

–

Dda3937_03551

Dd703_3378

Pectin methylesterase (PCWDEs)

 pemA

BCS7_15440

29

9

15

3

10

6

8

4

Dd586_3087

Dda3937_03374

Dd703_2766

 pemB

BCS7_00330

29

9

15

3

10

6

8

4

–

Dda3937_03435

–

Polygalacturonase (PCWDEs)

 pgl

BCS7_17010

29

9

15

3

9

0

8

4

Dd586_3319

Dda3937_00206

Dd703_0972

 pehX

BCS7_14740

29

9

15

3

10

6

8

4

Dd586_3904

Dda3937_00261

Dd703_0200

 pehN

BCS7_05675

29

9

15

3

10

6

8

4

–

Dda3937_04155

–

 pehA

BCS7_05200

29

9

15

3

10

6

8

4

–

–

–

Rhamnogalacturonate lyase (PCWDEs)

 rhiE

BCS7_03460

29

9

15

3

10

6

7

4

Dd586_2097

Dda3937_01465

–

Pilus assembly proteins

 pilA

BCS7_01135

1

0

15

0

0

0

0

0

–

–

–

 cpaABCDEF

BCS7_01140-BCS7_01165

1

0

15

0

0

0

0

0

–

–

–

 tadBCDE

BCS7_01170-BCS7_01185

1

0

15

0

0

0

0

0

–

–

–

 -

BCS7_01190-BCS7_01230

1

0

15

0

0

0

0

0

–

–

–

 papA

BASYS00091

28

9

0

3

10

1

8

3

–

–

–

 papC

BASYS00090

28

9

0

3

10

5

8

3

–

–

–

 papD

BASYS00089

28

9

0

3

10

6

8

3

–

–

–

 fhaB

BASYS01817

29

9

15

3

0

0

8

4

–

–

–

Siderophore synthetase

 entB

BASYS04531

29

9

15

3

10

0

8

4

Dd586_2819

Dda3937_02432

Dd703_1488

 foxA

BASYS03462

29

9

15

3

10

0

8

4

–

–

Dd703_0458

 iucABCD

W5S_0838-W5S_0841

0

0

0

0

0

6

0

0

–

–

–

 -

W5S_0842

0

0

0

0

10

6

0

0

–

–

–

 -/entS/ fepD/fepG

W5S_3869-W5S_3872

0

0

0

0

0

6

0

0

Dd586_2808-Dd586_2811

Dda3937_03032-Dda3937_03035

Dd703_1499-Dd703_1496

 fepC

W5S_3873

29

9

15

3

10

6

8

4

Dd586_2812

Dda3937_03036

Dd703_1495

 -/mbtH/−/−

W5S_3874-W5S_3877

0

0

0

0

0

6

0

0

Dd586_2813-Dd586_2816

Dda3937_03038-Dda3937_03042

Dd703_1494-Dd703_1491

 -

W5S_3878

0

0

0

0

0

6

0

0

–

–

–

 fyuA/−

BASYS00782/BASYS00783

28

9

0

3

0

0

8

3

–

–

–

 -

BASYS00784

28

5

0

3

0

0

1

0

–

–

–

 pchR/msbA

BASYS00785/BASYS00786

28

9

0

3

0

0

8

3

–

–

–

 ygaD

BASYS00787

28

9

0

3

0

0

8

4

–

–

–

 fecABCDE

BASYS00244-BASYS00240

27

4

0

3

10

0

8

3

–

–

–

 nosA

BCS7_07445

0

0

15

3

10

6

8

0

–

–

–

Synthesis of LPS

 rfaD/waaFb/waaC

W5S_4520-W5S_4523

29

9

15

3

10

6

8

4

Dd586_0164-Dd586_0162

Dda3937_02041-Dda3937_02039

Dd703_0173-Dd703_0171

 waaL1

W5S_4524

18

6

15

3

10

6

2

2

–

–

–

 waaL2

W5S_4526

0

0

0

0

7

2

0

0

–

–

–

 waaQ/waaG

W5S_4527/W5S_4528

18

6

15

3

10

6

2

2

–

–

–

 waaI

W5S_4529

18

6

10

3

10

6

2

2

–

–

–

 waaJ

W5S_4530

3

3

3

0

7

2

1

0

–

–

–

 -

W5S_4532

7

0

0

0

0

2

0

0

–

–

–

 waaX

W5S_4533

0

0

0

0

7

2

0

0

–

–

–

 kdtX

W5S_4534

26

6

5

3

7

2

7

3

Dd586_0155

Dda3937_02032

Dd703_0164

 -

W5S_4535

6

4

5

0

7

2

1

0

–

–

–

 kdtA/kdtB

W5S_4536/W5S_4537

29

9

15

3

10

6

8

4

Dd586_0156/Dd586_0154

Dda3937_02033/Dda3937_02031

Dd703_0165/Dd703_0163

 rfbP

ECA1420

4

2

8

0

10

2

0

1

–

–

–

 rfbI/rfbF/rfbG/rfbH

ECA1421-ECA1424

0

0

1

0

9

0

1

0

–

–

–

 hpcH/−/−/nahO/nahM/−/rfbX/−

ECA1425-ECA1432

0

0

0

0

9

0

0

0

–

–

–

 -

ECA1433

0

0

0

0

9

0

0

0

Dd586_0507

–

–

 −/rfc/rfbU

ECA1434-ECA1436

0

0

0

0

9

0

0

0

–

–

–

 rfbN

ECA1437

1

2

6

0

9

0

0

1

Dd586_1241

Dda3937_03925

–

 rfbM

ECA1438

15

3

3

0

9

0

6

1

Dd586_1250

Dda3937_00442

Dd703_3281

 rfbK

ECA1439

12

3

2

0

9

0

6

1

Dd586_1251

Dda3937_00443

Dd703_3280

 rfbD/rfbC

ECA1440/ECA1441

18

6

15

3

10

6

2

3

Dd586_1246/Dd586_1245

Dda3937_03921/Dda3937_03922

Dd703_3287/Dd703_3288

 rfbA

ECA1442

28

9

15

3

10

6

8

4

Dd586_1244

Dda3937_03923

Dd703_3286

Synthesis of ECA

 wecG/wzyE/wecF/wzxE/rffA/rffC/rffG/wecC/wecB

BASYS03691-BASYS03699

29

9

15

3

10

6

8

4

Dd586_3890-Dd586_3897

Dda3937_00277-Dda3937_00270

Dd703_0212-Dd703_0205

 wecA/wzzE

BASYS03700/BASYS03701

29

9

15

3

10

6

8

4

Dd586_3898/Dd586_3899

Dda3937_00269/Dda3937_00268

–

Metabolic regulatory protein

 metJ

BCS7_20315

29

9

15

3

9

6

8

4

Dd586_3934

Dda3937_03887

Dd703_3792

Necrosis-inducing virulence protein

 nip

BCS7_14620

29

9

15

3

10

6

8

4

Dd586_2805

Dda3937_00483

–

Xanthomonas campestris avirulence protein

 svx

BCS7_04170

29

9

15

3

10

6

8

4

Dd586_2807

Dda3937_00480

–

Citrate transporter

 citN

BCS7_06975

29

9

15

3

10

6

8

4

–

–

–

sirB locus

 sirB1

BCS7_10775

29

9

15

3

10

6

8

4

Dd586_2024

Dda3937_00039

Dd703_1858

 sirB2

BCS7_10780

29

9

15

3

10

6

8

4

–

–

–

The 3-hydroxy-2-butanone pathway

 budR/budA

BCS7_03160/BCS7_03165

29

9

15

3

10

6

8

4

Dd586_0623/Dd586_0624

Dda3937_02312/Dda3937_02311

Dd703_3319/Dd703_3318

 budB

BCS7_03170

28

9

15

3

10

6

8

4

Dd586_0625

Dda3937_02310

Dd703_3317

 budC

BCS7_01530

29

9

15

3

10

6

8

4

Dd586_3192

Dda3937_03162

Dd703_0990

Unknown proteases

 -

BCS7_01920-BCS7_01935

6

0

15

3

10

0

4

0

Dd586_0366-Dd586_0369

–

Dd703_3577-Dd703_3574

 -

BASYS00142

21

5

0

0

10

0

8

3

–

–

–

 yedU

BASYS03033

29

9

15

3

9

0

8

4

Dd586_2787

Dda3937_02122

Dd703_0349

Regulation network

Rsm system–post-transcriptional gene regulation

 rsmA

BCS7_16095

29

9

15

3

10

6

8

4

Dd586_3183

Dda3937_03151

Dd703_0999

 rsmBc

–

29

9

15

3

10

6

8

4

1

1

0

 rsmC

BCS7_03480

29

9

15

3

10

6

7

4

Dd586_0685

Dda3937_02456

Dd703_3258

ExpI-ExpR Quorum-Sensing system

 expI/expR

BCS7_00320/BCS7_00325

29

9

15

3

10

6

8

4

Dd586_0112/Dd586_0111

Dda3937_03219/Dda3937_03218

–

KdgR repressor

 kdgR

BCS7_09750

29

9

15

3

10

6

8

4

Dd586_1941

Dda3937_03685

Dd703_2055

RdgA-RdgB regulate system of pectin lyase production

 rdgA/rdgB

BCS7_09700/BCS7_09695

29

9

15

3

10

6

8

4

–

–

–

RNA polymerase sigma factor

 rpoS

BCS7_16895

29

9

15

3

9

6

8

4

Dd586_3302

Dda3937_03911

Dd703_0872

HexA repressor of extracellular enzyme and motility

 hexA

BCS7_14160

29

9

15

3

10

6

8

4

Dd586_2749

Dda3937_00364

Dd703_2551

Response regulator

 expM

BCS7_10215

29

9

15

3

10

6

8

4

Dd586_2148

–

Dd703_1959

ExpS-ExpA two-component system

 expA

BCS7_13455

29

9

15

3

10

6

8

4

Dd586_1482

Dda3937_03960

Dd703_1450

 expS

BCS7_17085

29

9

15

3

9

6

8

4

Dd586_3330

Dda3937_00193

Dd703_0847

AepA catalytic protein

 aepA

ECA1022

15

7

0

0

10

6

5

1

–

–

–

Flagellar regulon transcriptional activators

 flhD/flhC

BCS7_13105/BCS7_13110

29

9

14

3

10

6

8

4

Dd586_1499/Dd586_1498

Dda3937_02784/Dda3937_02785

Dd703_1509/Dd703_1508

  1. The details of these virulence related genes/ RNA fragment in each strain were shown in the Additional file 1: Table S6 and Table S6–1
  2. n number of genomes tested. Numbers indicate the number of genomes that tested positive, Pcc P. carotovorum subsp. carotovorum, Pcb P. carotovorum subsp. brasiliense, Pco P. carotovorum subsp. odoriferum, Pca P. carotovorum subsp. actinidiae, Ppo P. polaris, Pp P. parmentieri, Pa, P. atrosepticum, CPm Candidatus P. maceratum
  3. aReference strains: part of data adapted from Zhou et al. (2015); bwaaF: W5S_4521, W5S_4522; crsmB, encoding a fragment of RNA acting as a global regulator of virulence, has no gene ID
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BMC Genomics

ISSN: 1471-2164

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