In the SSH-MAI1 libraries, we identified 22 IS elements. In Xanthomonas spp., virulence and pathogenicity islands are commonly associated with mobile genetic elements such as phages and transposons (Monteiro-Vitorello et al., 2005; Lima et al., 2008). The capacity of IS elements to control the expression of other genomic elements has been reported in bacterial pathogens (Mahillon & Chandler, 1998; Nagy & Chandler,

2004; Zerillo et learn more al., 2008). The role played by IS elements in genomic rearrangements, pathogenicity islands, and expression control of nearby genes should be further studied in the African Xoo strain. The SSH Xoo MAI1 nonredundant set of sequences was searched, using blast against several Xanthomonas genomes available (Table S1 and Fig. 2). In silico analysis revealed that 10 Xoo MAI1 sequences (FI978086, FI978097, FI978101, FI978130, FI978141, FI978168, FI978177, FI978191, FI978193, and FI978197) were not present in the Xanthomonas genomes analyzed including the African Xoo genome BAI3, therefore suggesting that these genes might be present only in the Xoo African strain MAI1 (Fig. 2 and Table S1). Of these 10 fragments, one (FI978197) was tested by Southern blot analysis and found to be specific to Xoo strain MAI1 (Table 1). Validation of the other nine is needed to confirm these fragments as being

Xoo MAI1 specific. All these SSH sequences show similarity to genes encoding unknown proteins (Table S1). Nine SSH sequences (FI978092, FI978100, FI978112, FI978118, FI978126, FI978163, FI978167, FI978185, and M1B1BA10) were present in both African Xoo strains MAI1 (from

Mali) Roxadustat molecular weight and BAI3 (from Burkina), but not in the other genomes of Xanthomonas analyzed (Table S1 and Fig. 2). Two were validated by Southern blot (FI978100 and FI978167) and found to be specific to African Xoo strains representative from Burkina, Mali, and Niger (Table 1). Five sequences were present in Xoo strains, but were absent in Xoc BLS256 (FI978109, FI978127, FI978135, FI978182, and FI978187) (Table S1). Controlling Baricitinib Xoo and Xoc requires the development of tools that will allow the accurate identification of strains at the pathovar level. Both Xoc and Xoo are known to be present in the same fields in Mali (Gonzalez et al., 2007). These two phytopathogenic bacteria are closely related and, hence, difficult to rapidly differentiate genetically and phenotypically. From our study, we identified Xoo MAI1 SSH fragments not present in Xoc BLS256 and Xoc strains from Mali. Their presence or absence needs to be studied in a larger collection of Xoc in Mali to determine whether these fragments would be useful for discriminating Xoo from the closely related Xoc. Recently, a computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to identify unique regions for the development of highly specific diagnostic markers.