6 research outputs found

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

    No full text
    <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.

    No full text
    <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

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

    No full text
    <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 5.10<sup>5</sup> steps for burnin followed by 1.5 × 10<sup>6</sup> iterations with a thinning interval of 10 steps. Strains appear in the same order as in the ClonalFrame coalescent.</p

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

    No full text
    <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
    corecore