Table 2 Differentially expressed genes that are specific to the African strain MAI1 of Xanthomonas oryzae pv. oryzae (Xoo) GenBank accession Library origin† Seq. no. ‡ Putative function Organism § E-value CP-868596 in vivo Size Time point|| Xanthomonas oryzae genome¶               1 3 6 MAFF 311018 KACC 10331 PXO 99A BLS 256 BAI3 Biological Process Unknown FI978294 1 1 No NSC 683864 cell line protein match (NPM) – - 1203 –     – - – -

– FI978293 1 1 NPM – - 974   + + – - – - – FI978295 1 1 NPM – - 1233     + – - – - – FI978297 1 1 NPM – - 906     + – - – - – FI978298 1 1 NPM – - 975   +   – - – - – FI978299 1 1 NPM – - 1499     + – - – - – FI978300 1 1 NPM – - 1122   –   – - – - – FI978301 1 1 NPM – - 1659   +   – - – - – FI978302 1 1 NPM – - 674 –   – - – - – - FI978303 1 1 NPM – - 1232     + – - – - – FI978101 1 1 NPM – - 409     + – - check details – - – FI978177 1 1 NPM – - 399     + – - – - – FI978197 1 1 NPM – - 248     – - – - – - FI978310 1 1 NPM – - 942     + – - – - – FI978308 1 1 NPM – - 931     + – - – - – FI978317 1 1 NPM – - 1175   +   – - – - – FI978273 1 7 NPM – - 897     + – - – - – FI978320 1 1 NPM – - 1471

    – - – - – - FI978321 1 1 NPM – - 1902     – - – - – - FI978086 1 1 NPM – - 544 –   – - – - – - FI978068 1 1 NPM – - 638 – + + – - – - – FI978327 2 1 NPM – - 876 –   – - – - – - FI978316 2 1 NPM – - 1157   + + – - – - – FI978296 2 1 NPM – - 1529 +     – - – - – FI978323 1 1 NPM – - 933     – - – - – - FI978322 2 1 NPM – - 861     + – - – - – Hypothetical protein FI978307 2 1 Hypothetical protein XCC2965 Xcc strain ATCC 33913 3.0E 12 835 –     – - – - – FI978239 1 and 2 2 Hypothetical protein XCC2966 Xcc strain ATCC 33913 7.0E 11 244 +     – - – - – Phage-related and IS elements FI978271 1 7 Gene transfer agent (GTA) like protein Parvibaculum lavamentivorans strain DS 1 8.0E 50 788   +   – - – - – Metabolism FI978324 1 1 Haemolysin III Xcc 5.0E 17 853 –     – - – - – †SSH library and/or libraries in which the clone was identified, where 1 corresponds to SSH library Xoo strain M1/PXO86,

and 2 to SSH library Xoo strain M1/Xoc BLS256. ‡Number of sequences by contig, where 1 indicates singleton. §Xcc is Xanthomonas campestris pv. campestris; Xoo is Xanthomonas oryzae pv. oryzae. ||Time point, in days after BCKDHA inoculation, where + indicates up-regulated, and – indicates down-regulated. ¶Xanthomonas oryzae genomes, where + indicates presence of gene homologues to Xoo MAI1 in the genome analysed, and – indicates absence. We selected eight genes to validate their strain specificity, using Southern blot hybridization. These included two genes encoding for hypothetical proteins (FI978063 and FI978079), three genes encoding for proteins with unknown function (FI978168, FI978197 and FI978322), a probable secretion protein (FI978093) and two transposases (FI978069 and FI978109)(Additional file 1, Table S1).