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

Primers characteristics.

<p>Primers characteristics.</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

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

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

Tree of the amino acid sequences of C-domains of strains GPE PC73, XaS3, X11-5A, BAI3, and BLS256 together with C-domains identified by Rausch et al. as starter C-domains or as dual C/E-domains (Additional file 2).

The tree was constructed using the maximum likelihood method and GTR as substitution model. Bootstrap percentages retrieved in 100 replications are shown at the main nodes. The scale bar (0.2) indicates the number of amino acid substitutions per site. C-domains belonging to the same clade as dual C/E-domains are in blue. C-domains belonging to the same clade as starter C-domains are in red. Putative starter C-domains of the loci META-A and META-C of strain GPE PC73, the contig G111 of strain XaS3 and the locus of strain BTAi similar to META-A and META-C are in green. C-domains Ax, Bx ad Cx correspond to C-domains of modules of the loci META-A, META-B and META-C of strain GPE PC73, respectively. C-domains Ox correspond to C-domains of modules of the locus META-B of strain BAI3. C-domains USxxx/x correspond to C-domains of modules of contigs of strain X11-5A. C-domains Gxxx/x correspond to C-domains of modules of contigs of strain XaS3. C-domains bradyx correspond to C-domains of the locus of Bradyrhizobium spp. strain BTAi similar to META-A and META-C (genes Bbta_6814, Bbta_6813, Bbta_6812). C-domains XOCx correspond to C-domains of the locus NRPS located in the same region as XaPPTase in strain BLS256. C-domains 0364 and 1145 correspond to C-domains of short NRPS genes XALc_0364 and XALc_1145 of strain GPE PC73, respectively. C-domain 0354XaS3 corresponds to the short NRPS gene of strain XaS3. C-domain Bbta4110 corresponds to the short NRPS gene of strain BTAi. C-domains identified by Rausch et al. [6] as starter C-domains were tagged “Starter1” to “Starter15” as follows: Starter1: Pseusyrin.NP_792633.1.m_1_leu Starter2: Pseusp.Q84BQ6.arfA_1_leu Starter3: Pseufluor.YP_259252.1.m_1_leu Starter4: Baciliche.YP_077640.1.lchAA_1_gln Starter5: Nocafarci.YP_117314.1.m_1_orn_lys_arg Starter6: Nocafarci.YP_119006.1.m_1_tyr Starter7: Nocafarci.YP_119328.1.m_1_ser Starter8: Nocafarci.YP_121279.1.m_1_ser Starter9: Strecoeli.NP_627443.1.m_1_ser Starter10: Strchrys.O68487.acmB_1_thr Starter11: Erwicarot.YP_049593.1.m_1_gln Starter12: Strprist.Q54959.snbC_1_thr Starter13: Bacisubti.NP_388230.1.srfAA_1_glu Starter14: Bacisubti.NP_389716.1.ppsA_1_glu Starter15: Baciliche.YP_090052.1.m_1_gln C-domains identified by Rausch et al. [6] as Dual C/E-domains were tagged “DualC/E1” to “DualC/E18” as follows: DualC/E1:Photlumin.NP_929905.1.m_9_thr_TO_val DualC/E2:Photlumin.NP_930489.1.m_2_val_TO_trp DualC/E3:Photlumin.NP_929905.1.m_6_bht_TO_trp DualC/E4:Bradjapon.NP_768748.1.m_3_ser_TO_phe DualC/E5:Chroviola.NP_902472.1.m_3_val_TO_ile_dual DualC/E6:Chroviola.NP_902472.1.m_1_thr_dual DualC/E7:Burkmalle.YP_106216.1.m_2_glu_TO_gly DualC/E8:Burkpseud.YP_111641.1.m_3_thr_TO_leu DualC/E9:Burkpseud.YP_111641.1.m_1_glu_gln DualC/E10:Pseusyrin.NP_792633.1.m_2_leu_TO_leu DualC/E11:Ralssolan.NP_522203.1.m_3_ser_TO_gly DualC/E12:Ralssolan.NP_522203.1.m_1_val DualC/E13:Pseufluor.YP_259253.1.m_4_leu_TO_ser DualC/E14:Pseufluor.YP_259253.1.m_2_thr_TO_ile DualC/E15:Pseusyrin.NP_792634.1.m_3_thr_TO_val DualC/E16:Pseusyrin.NP_792634.1.m_5_leu_TO_leu DualC/E17:Erwicarot.YP_049592.1.m_4_ser_TO_tyr_bht DualC/E18:Erwicarot.YP_049593.1.m_2_gln_TO_as

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