Using SSH, we had isolated three fragments encoding the factors HrpF, HrpD4-HpaA, and HrpB8 in Xoo MAI1. Essential for bacteria–host interaction are hrp genes encoding proteins involved in the T3SS, as demonstrated for various plant pathogenic bacteria by different authors (Alfano & Collmer, 2004; He et al., 2004; Büttner & Bonas, 2006). HrpF is a putative translocon protein that is essential

for pathogenicity in plant-pathogenic bacteria (Büttner et al., 2002, 2007; Meyer et al., 2006; Büttner & He, 2009). The hrp regions also contain so-called hrp-associated (hpa) genes; the hpaA and hrpB genes are encoded STI571 manufacturer by the hrpD and hrpB operons, respectively. The gene hpaA is an important virulence factor that contributes to T3SS and Kinase Inhibitor Library effector protein translocation to host cells (Lorenz et al., 2008), whereas the translated sequence derived from hrpB8 is similar to the amino acid sequence of FliR, which has been determined to be a component in the T3SS flagellar export apparatus in Salmonella typhimurium (Fan et al., 1997). We also found DNA fragments that present similarity to genes encoding RTX (repeats in toxin) toxins (FI978128 and FI978182). In Bradyrhizobium elkanii, rtx genes are involved in rhizobitoxine biosynthesis, which inhibits ethylene biosynthesis in plants (Sugawara et al., 2007). Recently,

B. elkanii rtx gene homologs were found, forming gene clusters in Xoo genomes (Ochiai et al., 2005; Sugawara et al., 2007). In the animal pathogen Kingella kingae, disruption of these genes results in the loss of toxicity (Kehl-Fie & Geme, 2007). Of the 17 clones tested, 12 were present oxyclozanide in the Xoo strain MAI1 and absent from the corresponding

driver DNA (Xoo PXO86 and/or Xoc BLS256). Of the four fragments tested against several other X. oryzae strains from different geographical origins, one (FI978197) specifically hybridized to the Xoo strain MAI1 (data not shown). Three (FI978100, FI978105, and FI978167) yielded hybridization signals with all the African Xoo strains tested, but not with the Asian Xoo and Xoc strains (data not shown and Table 1). These fragments corresponded to genes of ‘unknown function’ and may represent specific Xoo MAI1 genes (i.e. FI978197) and/or specific genes of African strains. From the 134 SSH Xoo MAI1 nonredundant sequences, 20 were found in both libraries (Table 2). blast analysis showed that eight of these fragments correspond to hypothetical and/or unknown proteins. The remaining 12 fragments were distributed across seven functional categories (Table 2). Using blastn, the genome of Xoc strain BLS256 was searched for these 20 SSH Xoo MAI1 sequences, with 16 being found in the Xoc BLS256 genome. The ratio identities/sequence size, obtained after blast search, nevertheless indicated a low identity percentage, <50% for most cases (Table 2).