TABLE 1

Genes in the 24 type III effector gene families were analyzed for features suggesting horizontal transfer: discrepancy in GC3 content and codon usage and genomic association with mobile elements

P. syringaeXanthomonas spp.R. solanacearumOther
FamilyNo. of
 sequencesGC3
 contentaCodon
 usageaMobile
 elementaGroupGC3
 contentaCodon
 usageaMobile
 elementaGroupGC3
 contentaCodon
 usageaMobile
 elementaGroupGC3
 contentaCodon
 usageaMobile
 elementaGroup
avrA 31/11/11/1Recent2/22/22/2Recent
avrB 54/44/44/4Recent1/11/11/1Recent
avrD1210/1010/1010/10Recent1/11/11/1ND0/1ND1/1ND
avrE 80/21/20/2AncientNDND0/5Ancient
avrF 60/20/20/2AncientNDND0/4Ancient
avrPphD 70/40/41/2Ancient0/10/1NDAncient0/10/11/1AncientNDND1/1ND
avrPphE15 5/14 5/14 4/12Intermediate0/10/11/1ND
avrPpiA1 55/55/55/5Recent
avrPpiB 33/33/33/3Recent
avrPpiG1 61/11/11/1Recent2/42/41/1Intermediate0/10/11/1ND
holPtoN 32/22/22/2Recent1/10/1NDND
holPtoQ 41/10/11/1Recent0/20/21/2Ancient0/10/10/1Ancient
holPtoR 30/10/10/1Ancient0/10/10/1Ancient0/10/10/1Ancient
holPtoW 31/11/11/1Recent0/10/10/1Ancient0/10/10/1Ancient
hopPmaB 40/10/10/1Ancient0/30/32/3Ancient
hopPmaD 30/10/1NDAncient0/10/1NDAncientNDND0/1ND
hopPmaG 70/30/30/3Ancient0/20/21/1Ancient0/10/10/1AncientNDND1/1ND
hopPmaH 90/30/30/3AncientNDNDNDND
hopPmaI 30/30/31/3Ancient
hopPmaJ 30/30/31/3Ancient
hopPmaL 83/85/85/6Intermediate
hopPtoA 50/40/40/4Ancient0/10/10/1Ancient
hrpW 50/30/30/3Ancient0/11/10/1NDNDNDNDND
hrpZ12 0/12 0/120/6Ancient
  • a The proportion of genes for which the discrepancy or linkage to mobile elements (when available) is indicated.

  • Results are given by species or genus. ND, not done.