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Table 4 Pathotype-specific putative pseudogenes, genic frameshifts and truncations

From: Comparative genomics of 43 strains of Xanthomonas citri pv. citri reveals the evolutionary events giving rise to pathotypes with different host ranges

Pathotype

Gene

Description

Native coordinates

Alignment coordinates

Gene fragment 1

Gene fragment 2

Note

A

 

methyltransferase domain

60851-61836

61748-62734

XANAC_0061

XAC0050

Putative ψ

LacZ

beta-galactosidase

838208-841101

850951-853845

XAC0707

XAC0708

Putative ψ

 

putative secreted protein

986002-986826

999771-1000595

XAC0825

XANAC_0965

Putative ψ

oppD/yliA

ABC transporter

1021079-1022728

1034920-1036570

XAC0859

XAC0860

Putative ψ

araJ

MFS transporter

3326112-3327329

3414846-3416063

XAC2837

XAC2836

Putative ψ

rarD

Permease – chloramphenicol resistence

4693056-4693966

4830382-4831292

XAC4000

XAC4001

Putative ψ

catB

catalase

4719198-4720710

4856716-4858239

XAC4029

XAC4030

Putative ψ

A*

 

PbsX Transcription Factor

614013-614472

630726-631530

XAC71A_130207

XAC71A_130208

Putative ψ

 

acyl-CoA synthetase

1041072-1042552

1063009-1064489

XAC71A_170122

XAC71A_170123

Putative ψ

  

1622056-1625651

1640494-1644089

XAC71A_280103

XAC71A_280104

Putative ψ

  

1860274-1860803

1904352-1904881

XAC71A_310052

XAC71A_310053

Putative ψ

rpfB

acyl-CoA synthetase

2187629-2189311

2300143-2301825

XAC71A_390075

XAC71A_390076

Putative ψ

  

2269033-2269866

2382037-2382870

XAC71A_410007

XAC71A_410008

Putative ψ

 

GGDEF family protein

2286218-2289170

2399383-2402335

XAC71A_410020

XAC71A_410021

Putative ψ

comA

competence protein

2447016-2449565

2572127-2574695

XAC71A_450029

XAC71A_450030

Putative ψ

XACSR11

carboxypeptidase

3101427-3102721

3299904-3301198

XAC71A_660002

XAC71A_660003

Putative ψ

xopN

type III effector

3293500-3295557

3508783-3510840

XAC71A_730134

 

Putative ψ, truncated 3′

yagT

putative oxidoreductase, 2Fe-2S subunit

3420879-3421529

3641125-3641775

XAC71A_740038

XAC71A_740039

Putative ψ

yodB

Cytochrome B561

3563369-3564046

3785148-3785825

XAC71A_750009

 

frameshift, longer 3′

xopL

type III effector

3641485-3643372

3864216-3866109

XAC71A_760048

XAC71A_760049

Putative ψ

rimK

Ribosomal protein S6 modification protein

3847131-3848050

4111446-4112365

XAC71A_840004

XAC71A_840005

Putative ψ

  

3998076-3997795

4263201-4262920

XAC71A_880069

 

Putative ψ, truncated 5′

Aw

  

59860-61116

60605-61861

XAC3218_20024

XAC3218_20025

Putative ψ

adh

alcohol dehydrogenase

247107-247385

256015-256293

XAC3218_100056

 

Putative ψ, truncated 3′

yojM

superoxide dismutase-like

256565-257695

265546-267635

XAC3218_110001

XAC3218_110002

Putative ψ

  

3010085-3008397

3123577-3121889

XAC3218_630012

 

longer

 

LysR Transcription Factor

4453733-4452393

4671211-4669871

XAC3218_910186

 

longer

 

exported

4957802-4960197

5228371-5230773

XAC3218_960285

XAC3218_960286

Putative ψ

  

4962702-4964291

5233406-5234995

XAC3218_970002

XAC3218_970003

Putative ψ

ttcA

2-thiocytidine biosynthesis protein TtcA

4988408-4989507

5261994-5263093

XAC3218_990014

XAC3218_990015

Putative ψ

xylB

xylulose B

5015663-5013780

5290774-5288891

XAC3218_990034

 

longer