Comparative genomic analysis of rice-infecting <i>Pseudomonas</i> secretion apparatus.

<p>Genetic components of T1SS, T2SS, T3SS and T6SS apparatus of <i>P</i>. <i>fuscovaginae-like</i> (<i>Pfv</i>-like) IRRI 6609 was used to compare against 79 closely related <i>Pseudomonas</i> genomes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.s008" target="_blank">S1 Table</a>). The <i>apr</i>, <i>has</i>, <i>xcp</i>, <i>hxc</i>, <i>gsp</i>, SPI-1, and HSI-1 are previously characterized gene clusters found within each secretion system. Horizontal axis describes the number of species used for comparison. The rows were sorted by amino acid sequence identity with threshold set at 20%. The heat map was visualized in CodaChrome. Homology range values are shown in bottom right.</p

<i>P</i>. <i>fuscovaginae-like</i> (<i>Pfv</i>-like) strains are closely related to <i>P</i>. <i>fuscovaginae</i> (<i>Pfv</i>).

<p><b>A)</b> Average nucleotide identity (ANI) and average amino acid identity (AAI) clustering analysis of the eight rice-infecting <i>Pseudomonas</i> draft genomes. Clustering analysis identified two separated groups involving <i>Pfv</i>-like strains (orange) collected in the Philippines and <i>Pfv</i> strains (blue) collected elsewhere. Values scale is depicted in red, orange, yellow, and white colors in ANI (horizontal) and AAI (vertical) pairwise comparison. Value cut-offs with >95% reflect the possibility of same species grouping. The heatmap was generated in the R package gplots using the heatmap.2 function. <b>B)</b> Phylogenetic reconstruction of rice-infecting <i>Pseudomonas</i> and closely related <i>Pseudomonas</i> species using the concatenated housekeeping <i>rpoB</i> and <i>rpoD</i>. Maximum likelihood was used to infer the phylogenetic relationship with bootstrap of 1000 using the RAxML software [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref061" target="_blank">61</a>]. <i>Pfv</i> and <i>Pfv</i>-like are highlighted in blue and orange, respectively.</p

Infection caused by <i>P</i>. <i>fuscovaginae</i>-like strain IRRI 7007 in <i>O</i>. <i>sativa</i> cv. Azucena.

<p><b>A)</b> Plants were inoculated at 45 days after transplanting using toothpick method. <b>B)</b> Symptom development along the sheath showing brown necrotic lesions. <b>C)</b> Discolored inner sheath. <b>D)</b> Poorly emerged panicles with brown to dark brown grains. <b>E)</b> Emerged panicles with discolored grains and progressive necrotic stripes at maturity stage.</p

The pan-genome of rice-infecting <i>Pseudomonas</i> reveals high proportion of strain-specific genes.

<p><b>A)</b> Distribution of the 12,351 orthologous gene clusters according to strain-specific genes (only in one genome = 1), dispensable genes (in more than one genome = 2 ≥ x ≤ 7), and core genes (in all genomes = 8). <b>B</b>) Orthologous gene distribution in the <i>P</i>. <i>fuscovaginae</i> (blue) and <i>P</i>. <i>fuscovaginae</i>-like (orange) genomes depicting number of core, dispensable, and strain-specific gene clusters.</p

The genome of rice-infecting <i>Pseudomonas</i> harbor high level of structural polymorphism.

<p>Global comparison of eight rice-infecting <i>Pseudomonas</i> draft genomes using BLASTn. The inner most ring corresponds to the genomic position at IRRI 6609. The second and third rings indicate G+C content and G+C skew, respectively. The rest of the rings indicate presence and absence portions of the eight rice-infecting <i>Pseudomonas</i> draft genomes against IRRI 6609. Solid colors represent genomic regions with hits while white spaced represent gaps. <i>P</i>. <i>fuscovaginae</i> (<i>Pfv</i>) and <i>P</i>. <i>fuscovaginae</i>-like (<i>Pfv</i>-like) strains are depicted. Sequence identity is related to color intensity. Also included are locations of four intact prophage insertions found in <i>Pfv</i>-like IRRI 6609 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.s004" target="_blank">S4 Fig</a>). The global alignment was visualized using BRIG [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref043" target="_blank">43</a>].</p

Nucleotide identity and percentage of orthologous genes obtained in rice-infecting <i>Pseudomonas</i> draft genomes compared to IRRI 6609

<p>^a Identity based on BLASTn results</p><p>Nucleotide identity and percentage of orthologous genes obtained in rice-infecting <i>Pseudomonas</i> draft genomes compared to IRRI 6609</p

The core secretome of rice-infecting <i>Pseudomonas</i> has signatures of positive selection.

<p>Distribution of Ka/Ks ratio for 123 protein-coding genes, calculated with Yn00 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref059" target="_blank">59</a>] method on rice-infecting <i>Pseudomonas</i>-all (black, <i>P</i>-all, n = 8), <i>P</i>. <i>fuscovaginae</i> (blue, <i>Pfv</i>, n = 5), and <i>P</i>. <i>fuscovaginae</i>-like (orange, <i>Pfv</i>-like, n = 3) datasets. All secreted protein selected on this graph have <i>p</i>-values ≤ 0.01.</p

The core secretome of rice-infecting <i>Pseudomonas</i> harbor unique genes.

<p>Conservation of core secreted proteins from rice-infecting <i>Pseudomonas</i> was evaluated in 79 closely related <i>Pseudomonas</i> genomes (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.s008" target="_blank">S1 Table</a>). Columns were sorted by averaging the amino acid identity to identify conserved and species-specific proteins using threshold of 20%. Secreted proteins are also classified in: conserved in all <i>Pseudomonas</i>, non-conserved in all <i>Pseudomonas</i>, and <i>Pfv-</i> and <i>Pfv</i>-like-specific. Horizontal axis describes the number of species used for comparison. The heat map was visualized in CodaChrome [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0139256#pone.0139256.ref040" target="_blank">40</a>]. Homology range values are shown in bottom right.</p

General features of the eight rice-infecting <i>Pseudomonas</i> draft genomes.

<p>^a Country names: Philip = Philippines, Madag = Madagascar, and Aus = Australia.</p><p>General features of the eight rice-infecting <i>Pseudomonas</i> draft genomes.</p