Additional file 1 of The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility

Additional file 1: Table S1. TBLASTN and BLASTP of homologous structural genes of Pseudomonas aeruginosa T6SS selected. Homologous structural genes of Pseudomonas aeruginosa T6SS selected by TBLASTN (Altschul et al., 1997) against the genomes of Xanthomonas citri subsp. citri str. 306 (Xcc), Xanthomonas euvesicatoria str. 85–10 (Xeu) and Xanthomonas phaseoli pv. manihotis str. CIO151 (Xpm). Similarity of structural genes of Pseudomonas aeruginosa T6SS selected by BLASTP against the genomes of Xanthomonas oryzae pv. oryzae str. PXO 099 (Xoo), Xanthomonas campestris pv. campestris str. ATCC 33913 (Xcac) and Xanthomonas albilineans GPE PC73 (Xalb). Colors follow the same guidelines as in Fig. 1. Table S2. Bacterial strains and plasmids used in this study. Derivative strains of Xanthomonas phaseoli pv. manihotis str. CIO151 (Xpm) with knockouts in T6SS genes. Table S3. List of primers used in this study. Table S4. Analysis of Xanthomonas genomes with or without T6SS genes. Results of BLASTP and ORTHOMCL analyses show that the reconstructed T6SS clusters in Xanthomonas contain between twelve and sixteen genes. Table S5. Structural genes of type VI secretion system of Xanthomonas. Distribution of type VI secretion system gene clusters in 14 strains of Xanthomonas. For each strain of Xanthomonas, the genes found in T6SS are divided by clusters (I, II and II) and are shown with gene, protein and product sizes. Table S6. Results of the search for T6SS-encoding genes in the genomes of Xanthomonas perforans (Xp 91–118), Xanthomonas cassavae str. CFBP4642 and Xanthomonas axonopodis str. 29 with EDGAR 2.0. EDGAR displays the orthologous genes in each genome. For each gene, the nomenclature and annotation are denoted. Table S7. Localization, protein family and motif prediction of T6SS proteins in Xpm. The core proteins of T6SS were subjected to in silico analyses for subcellular localization using PSORT, prediction of transmembrane domains (TMpred), domain prediction (INTERPRO, CDD and PRODOM) and protein families (Pfam) and motifs (Motif finder and MOTIF search). The colors follow the same guidelines as in Fig. 1. Table S8. Insertion sequences in the T6SS. The clusters of the T6SS of Xeu, Xcc3 and Xpm were examined for IS families and groups, defined in the database ISfinder [31].