Inferences on transfer of VA genes possibly involved in host specificity.

<p>The repertoires of 107 genes encoding MCPs, sensors, adhesins, and T3Es were previously determined for each strain of the collection <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone.0058474-Hajri1" target="_blank">[27]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone.0058474-MhedbiHajri1" target="_blank">[28]</a>. Using a parsimony approach implemented in Mesquite 2.5 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone.0058474-Maddison1" target="_blank">[61]</a>, repertoires of genes at nodes of the ClonalFrame genealogy were inferred. Comparison of repertoires at ancestral nodes provided hypotheses on horizontal transfers concomitant to migration events identified in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058474#pone-0058474-g002" target="_blank">Figure 2</a>. Populations 9.1 to 9.6 refer to genetic groups in <i>X. axonopodis</i> and A1 to A5 refer to ancestral populations. Four of the migration events detected by IMa2 may be associated to transfers of genes encoding MCP (<i>xac3768, xcv1954</i>), adhesins (<i>fhaB1</i>, <i>fhaB2</i>), sensors (<i>xac0852</i>, <i>xac2152, xac2155, xac3050</i>, <i>xac3498</i>, <i>xac4062</i>), and T3Es (<i>avrXccA2</i>, <i>xopC1, xopE1, xopF2, xopJ5, xopL, xopP, xopAJ, xopAF</i>).</p

List of <i>X. axonopodis</i> strains used in the study.

<p>CFBP (French Collection of Plant Pathogenic Bacteria) code for strain (Strain code) except * which were provided by O. Pruvost, Cirad, Reunion Island, France and ** code of the reference strains whose genome are publicly available. All strains were provided by the CFBP. Genetic group number (Group) from Rademaker <i>et al</i>. (2005); not available (n a).</p

Mutation rate per gene and per year inferred from EBSP analysis in BEAST for each of the six housekeeping genes in each of the six groups within <i>X. axonopodis</i>.

<p>Mutation rate per gene and per year inferred from EBSP analysis in BEAST for each of the six housekeeping genes in each of the six groups within <i>X. axonopodis</i>.</p

Primers characteristics.

<p>Primers characteristics.</p

Evolutionary history set in IMa2 of 131 strains of <i>X. axonopodis</i> belonging to 25 pathovars.

<p>Divergence time estimates are given in kyr at the left (in black). Plain gray double arrows indicate 95% Confidence Interval. Values in light gray r indicate lower and upper limits of 95% highest posterior density on divergence times. Directions of migration are represented by dotted grey arrows; numerical values represent the effective number of migrants. Only migrations significantly different from zero are represented (p<0.05). Populations 9.1 to 9.6 refer to genetic groups in <i>X. axonopodis</i> and A1 to A5 refer to ancestral populations.</p

Genetic structure of <i>X. axonopodis</i>.

<p>(a) Majority-rule consensus genealogy inferred by ClonalFrame. Captions 9.1 to 9.6 refer to genetic groups within <i>X. axonopodis</i>. Populations A1 to A5 represent ancestral populations. Parameters were estimated from the sampling of 100 000 iterations of 131 strains typed on 94 non-recombinant loci. Red branches indicate significant occurrence of recombination (p>0.9). Despite being grouped in the same rake, strains may contain different closely related haplotypes. Limit of node age was set at 1.2 in coalescence unit. (b) Cluster analysis using STRUCTURE 2.3 with Linkage model. Four clustering are shown here for K = 2, 4, 5, 6, 21, 22 and. For each K, 30 independent runs were performed and analyzed using CLUMPP with 10,000 permutations. For each run, we used ten independent chains assuming different starting points, and for each chain 5.10⁵ steps for burnin followed by 1.5 × 10⁶ iterations with a thinning interval of 10 steps. Strains appear in the same order as in the ClonalFrame coalescent.</p

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

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

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

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