List of CSEPs identified in the <i>P</i>. <i>xanthii</i> epiphytic secretome and orthologues present in the genome of <i>B</i>. <i>graminis</i> f. sp. <i>hordei</i>.

<p>List of CSEPs identified in the <i>P</i>. <i>xanthii</i> epiphytic secretome and orthologues present in the genome of <i>B</i>. <i>graminis</i> f. sp. <i>hordei</i>.</p

N-terminal amino acid Y/F/WxC motif and natural selection in <i>P</i>. <i>xanthii</i> CSEPs.

<p>The N-terminal amino acid motif Y/F/WxC was screened manually within the pool of CSEPs, and only the motif WxC was observed following the secretion signal. Alignments were performed with ClustalW2, and the sequence logo was represented using the Seq2Logo online server (<a href="http://www.cbs.dtu.dk/biotools/Seq2Logo/" target="_blank">www.cbs.dtu.dk/biotools/Seq2Logo/</a>).</p

The most expressed GO categories in the epiphytic transcriptome of <i>P</i>. <i>xanthii</i>.

<p>Representation of the number of average reads within the most expressed GO categories in the <i>P</i>. <i>xanthii</i> epiphytic cDNA library. For each category, the number of genes within the group of Top50 most expressed transcripts is shown on the right side of the bars. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163379#pone.0163379.s004" target="_blank">S2 Table</a> for details on Top50 most expressed genes.</p

Pie chart representing the functional annotation of predicted proteins from the epiphytic transcriptome of <i>P</i>. <i>xanthii</i>.

<p>The diagram displays the relative abundance of <i>C</i>. <i>albicans</i> GOSlim categories among the 6,645 annotated predicted proteins. All data were submitted to the NCBI database under the accession GEUO00000000.</p

Summary statistics of the annotation process of the <i>P</i>. <i>xanthii</i> epiphytic transcriptome.

<p>Summary statistics of the annotation process of the <i>P</i>. <i>xanthii</i> epiphytic transcriptome.</p

Expression of selected <i>P</i>. <i>xanthii</i> CSEP genes in a time-course experiment.

<p>Total RNA was isolated from zucchini cotyledons infected with <i>P</i>. <i>xanthii</i> at different time points, and the relative expression of five putative effector-genes (<i>CSEP01</i>, <i>CSEP02</i>, <i>CSEP05</i>, <i>CSEP021</i> and a homologue to <i>Scp160</i>) was analysed by quantitative RT-PCR. Transcript abundance was normalised to the endogenous control β-tubulin gene <i>PxTUB</i>2 (KC333362). Relative expression of each gene was calibrated to the sample 8 h post inoculation. Points represent the mean ± standard deviation of three technical replicates from two cDNA samples obtained from two different zucchini cotyledons.</p

Pie chart representing the functional annotation of the <i>P</i>. <i>xanthii</i> secretome deduced from the predicted proteins from the epiphytic transcriptome.

<p>The diagram displays the relative abundance of GO categories among the total of 137 putatively secreted proteins identified; 84 secreted proteins were grouped by biological functions, and 53 had no GO terms and, consequently, were catalogued as candidate secreted effector proteins (CSEPs). The number of proteins within each functional category is presented in brackets. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163379#pone.0163379.t002" target="_blank">Table 2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0163379#pone.0163379.s006" target="_blank">S4 Table</a> for details.</p

Phylogenetic analysis of <i>P</i>. <i>xanthii</i> CSEPs.

<p>The unrooted phylogenetic tree is based on NJ analysis. The confidence of groupings was estimated by using 1,000 bootstrap replicates, and the percentage of replicate trees supporting each branch is shown next to the branching point. The analysis showed the existence of potential families within the <i>P</i>. <i>xanthii</i> CSEPs.</p

Conservation analysis of the <i>Pseudomonas syringae</i> pv. syringae UMAF0158 chromosome.

<p>From the outside in, the outermost circle (black) shows the scale line. Circles 2 to 4 display similarity (<i>E</i>-value ≤ 1×10⁻¹⁰) among UMAF0158 and the three <i>P</i>. <i>syringae</i> with complete genome sequences: DC3000 (grey), 1448A (orange) and B728a (red). Circles 5 to 7 display similarity (<i>E</i>-value ≤ 1×10⁻¹⁰) among UMAF0158 and the draft genomes of the three phylogenetically closest <i>P</i>. <i>syringae</i> strains among the 25 selected in this study: 642 (purple), BRIP39023 (green) and Cit 7 (blue). Circles 8 and 9 display putative horizontally transferred regions (red) and prophages (purple), respectively; circle 10 shows G+C in relation to the mean G+C in 2 kb windows (red); circle 11 shows trinucleotide composition (black).</p

Genomic organization of putative <i>Pseudomonas syringae</i> pv. syringae UMAF0158 secretion systems involved in effector translocation.

<p><b>A,</b> T6SS-1. <b>B,</b> T6SS-2. <b>C,</b> T3SS-1 (<i>hrc</i>-1). <b>D,</b> T3SS-2 (<i>rhc</i>). Genes presumably involved in secretion are shown in red. Components of the T6SS with no consensual name are labelled with their corresponding NCBI-annotated locus tags. Numbers below the arrows refer to bp positions in the chromosome.</p