Comparative genomics is a powerful tool for exploring the genetic features of related bacteria, including diversity, population characteristics, evolution, mobile genetic elements, and horizontal gene transfer. Variations among Xoo strains were documented recently by whole-genome analysis of the Japanese strain MAFF311018 (Ochiai et al., 2005), the Korean strain KACC10331 (Lee et al., 2005), and the Philippine strain PXO99A (Salzberg et al., 2008), together with the Xoc strain BLS256 (http://cmr.jcvi.org/tigr-scripts/CMR/cmrHomePage.cgi).
selleck chemicals These two bacteria, Xoo and Xoc, constitute an excellent comparative model for understanding the determinants of strain specificity, as well as host and tissue specificity in plant–bacteria interactions (Lu et al., 2008). Two main characteristics distinguish the Xoo genome from other Xanthomonas: a higher abundance of IS elements and the prevalence of transcription activator-like Nintedanib chemical structure (tal) effector genes of the avrBs3/pthA family (Ochiai et al., 2005; Nino-Liu et al., 2006). Pathogenicity assays and molecular analyses were conducted on a collection of African Xoo strains (Gonzalez et al., 2007). The genetic tools used showed that the African Xoo strains were genetically different from the Asian ones and more closely related to the Asian Xoc. A specific and intriguing feature of African strains is
a smaller number of tal effector genes and IS elements in their genome (Gonzalez et al., 2007). New races among African Xoo strains were described. Nothing is known of the specificity
and genetic determinants governing pathogenicity in African Xoo strains. One of our objectives was to identify the specific genetic characteristics of the African Xoo strains. Given that sequencing learn more the genome of each strain analyzed is still not feasible, an alternative approach is to use suppression-subtractive hybridization (SSH). SSH is a powerful method that has been widely used in bacterial genome analysis to discover new epidemiological markers, virulence factors, or host-specificity determinants (Winstanley, 2002; Harakava & Gabriel, 2003; Bernier & Sokol, 2005; Guo et al., 2006; Triplett et al., 2006; Alavi et al., 2008). We developed SSH libraries using the African Xoo MAI1 strain. This strain belongs to race A3, which is only present so far in Mali and is avirulent on all the Xa genes tested (Gonzalez et al., 2007). Xoo MAI1 was used as a tester and the Philippine Xoo strain PXO86 and Xoc strain BLS256 as drivers. The sequences generated were used to perform a comparative analysis with the Xanthomonas genomes available. All these analyses allowed us to identify DNA sequences specific to Xoo MAI1. The 11 bacterial strains used in this study are listed in Table 1, including those used for SSH libraries (Xoo strain PXO86, Xoc strain BLS256, both from the Philippines, and Xoo strain MAI1). Two enriched libraries were constructed for the Xoo strain MAI1.