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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