Putative pathogenicity elements identified in the genome of <i>Xam</i> CIO151.

1<p>Number indicates CDS identified by key word searches in iANT.</p

Circular representation of the genome sequence of <i>Xam</i> CIO151.

<p>From outside to inside: first circle in blue indicates CDS predicted in the positive strands for the scaffolds classified as probable chromosomal regions. Second circle in red indicates the CDS predicted in the negative strand. Red spots in the black third circle indicate the region identified with atypical nucleotide composition. The fourth circle indicates the deviation pattern from the average G+C content. Inner circle shows GC skew values, positive values are shown in purple and negative values are shown in orange. Numbers correspond to scaffold IDs.</p

Phylogeny of conserved effectors in the genus <i>Xanthomonas</i>.

<p>Phylogenetic tree of concatenated conserved effector protein sequences of AvrBs2, XopK, XopL, XopN, XopQ XopR families and the Hpa1 protein, obtained with a Bayesian approach. Numbers on branches indicate Bayesian support values. Length of branches indicates the number of amino acid substitutions per site.</p

Comparison of the genomic structure of <i>Xam</i> CIO151 with that of closely related members from the genus <i>Xanthomonas</i>.

<p>Scaffolds of <i>Xam</i> CIO151 were ordered based on the alignment with the complete genome sequence of <i>X. euvesicatoria</i>, <b><i>Xeu</i></b>, and then genome comparisons were performed using MUMmer (<b>A</b>). Alignment of ordered scaffolds of <i>Xam</i> CIO151 with the complete genome sequences of <i>X. axonopodis</i> pv. citri str. 306, <b><i>Xac</i></b> (<b>B</b>); <i>X. campestris</i> pv. campestris str. 8004, <b><i>Xcc</i></b> (<b>C</b>); <i>X. albilineans</i>, <b><i>Xal</i></b> (<b>D</b>); and <i>Xanthomonas oryzae</i> pv. <i>oryzae</i> PXO99^A, <b><i>Xoo</i></b> (<b>E</b>) chromosomes. Scaffolds classified as parts of the chromosome of <i>Xam</i> CIO151 are shown in the y-axis. Red dots represent conserved segments while blue dots represent inverted regions.</p

Characteristics of VNTR loci for 65 <i>Xam</i> draft genome sequences.

1<p>: Repeat unit sizes are given in bp.</p>2 and 3<p>: Minimal and maximal numbers of repeats (only those in integer numbers) are given.</p>4<p>Number of samples with a complete VNTR locus in the draft genome sequence is given.</p>5<p>Number of different VNTR patterns (haplotypes) is given.</p>6<p>Hunter-Gaston discriminatory index (HGDI) scores are given.</p

Organization of pathogenicity-related gene clusters in the <i>Xam</i> CIO151 genome.

<p>Open arrows with labels indicate genes with assigned functions, black arrows indicate genes with early stop codons, open arrows without labels indicate conserved hypothetical proteins and grey arrows indicate non-conserved hypothetical proteins. Graphs above clusters show the G+C content and deviations from the average value. <b>A</b>. Xanthomonadin gene cluster; * indicates genes related to <i>pigB</i> genomic region and ** indicates genes reported as important for cluster functionality. Abbreviations used are: <b>H</b> = halogenase (xanmn_chr15_0075), <b>BP</b> = xanthomonadin biosynthesis protein (xanmn_chr15_0079), <b>E = </b>xanthomonadin exporter (xanmn_chr15_0373), <b>PSP</b> = putative secreted protein (xanmn_chr15_0080), <b>BACPD</b> = xanthomonadin biosynthesis acyl carrier protein dehydratase (xanmn_chr15_0082), <b>BA</b> = putative xanthomonadin biosynthesis acyltransferase (xanmn_chr15_0081 and xanmn_chr15_0083), <b>BMP</b> = putative xanthomonadin biosynthesis membrane protein (xanmn_chr15_0084), <b>ACP</b> = acyl carrier protein (xanmn_chr15_0085), <b>XanB1</b> = putative reductase/halogenase (xanmn_chr15_0086), <b>XanB2</b> = putative pteridine-dependent deoxygenase like protein (xanmn_chr15_0087), <b>AMP-l</b> = AMP-ligase (xanmn_chr15_0088), <b>DP</b> = dipeptidyl peptidase (xanmn_chr15_0090). <b>B</b>. Cluster implicated in xanthan production (<i>gum</i>). <b>C</b>. Regulation of pathogenicity factors (<i>rpf</i>) cluster. <b>D</b>. Type III secretion system (<b>T3SS</b>) cluster.</p

General features of the genome of <i>Xam</i> CIO151.

<p>General features of the genome of <i>Xam</i> CIO151.</p

Molecular analysis of selected VNTR loci of <i>Xam</i>.

<p>PCR amplicons of VNTR loci of <i>Xam</i> were separated by agarose gel electrophoresis. A, XaG1_02 (362 bp); B, XaG1_29 (251 bp); C, XaG1_58 (192 bp); D, XaG2_50 (119 bp); E, XaG1_12 (111 bp). For comparison, expected sizes for <i>Xam</i> strain CIO151 are given in brackets.</p