The SSH Xoo MAI1 PLX3397 manufacturer nonredundant set of sequences was grouped into functional categories, using the Gene Ontology (GO) functional classification scheme (http://www.geneontology.org). We tested 17 clones by Southern blot analysis to verify that the DNA fragments derived from individual clones were present in the Xoo strain MAI1 and absent in the driver DNA (strains Xoo PXO86 or Xoc BLS256). Additionally, four fragments FI978105, FI978197, FI978167, and FI978100 (Table 1) were selected to screen genomic DNA from different Asian Xoo strains, African Xoo strains, African Xoc strains (MAI3 and MAI11), and one Asian Xoc strain (BLS256)

(Table 1). Briefly, for each strain, 5 μg of genomic DNA was digested with 10 U of RsaI and run on 0.8% agarose gels. The DNA was transferred to Hybond-N+ nylon membranes (Amersham Pharmacia Biotech, Little Chalfont,

UK). The insert DNA was amplified by PCR, using the nested primer 1 and nested primer 2R provided with the PCR-Select™ CX-4945 Bacterial Genome Subtraction Kit (BD Biosciences Clontech). The amplified DNA fragment was gel purified, using the QIAquick Gel Extraction Kit (Qiagen Inc., Valencia, CA). The DNA fragments were labeled with [α32P] dCTP by random priming (MegaPrime labeling kit, Amersham Biosciences Europe GmbH, Succursale France, Saclay, Orsay). Hybridization and washes were conducted according to the manufacturer’s instructions (Amersham Pharmacia Biotech). Two subtracted DNA libraries (SSH) were constructed to isolate unique DNA sequences from the African Xoo strain MAI1. The sequence lengths of the 530 sequences obtained varied between 85 and 1144 bp, with the average being 396 bp. The initial set of 530 sequences was reduced to 134 unique consensus sequences, comprising 85 contigs and 49 singletons (Supporting Information, Table S1). From the nonredundant set of sequences, 62 sequences were specifically found in the MAI1-PXO86 library and 52

in the MAI1-BLS256 library. Twenty sequences were found in both libraries (Table 2). A blastn search with the Xoo MAI1 nonredundant sequences was performed. The results are summarized in Table S1 and Fig. 1. Half of the genes identified ID-8 comprised 67 unique sequences that belonged to two categories of proteins, that is, either ‘hypothetical proteins’ or of unknown function (Fig. 1). Several fragments were homologs to known genes related to pathogenicity and more specifically to those encoding pathogenicity, that is, to type III secretion system proteins (T3SS). Most knowledge on T3SS in Xoo is based on studies of the AvrBs3/PthA bacterial effector proteins, a family of type III effectors with transcription activator-like (TAL) activity known so far (Yang & White, 2004; White & Yang, 2009). Moreover, fragments with similarity to an Avr/Pth14 protein and a TAL effector (tal-C10b) of Xoo PXO99A were also isolated. These TAL effectors have been shown to control the induction of plant genes during infection (Kay et al., 2007; White & Yang, 2009).