Ln-transformed expression levels of poplar transcripts.

<p>(A) Venn-diagram of expressed poplar transcripts measured by whole-genome oligoarray and RNA-Seq. Numbers in brackets correspond to the percentage of the coding genome; numbers in parentheses correspond to the highly expressed (HE) transcripts and numbers in parentheses and in bold correspond to HE transcripts validated by oligoarrays (i.e. VHE transcripts). (B) RNA-Seq and oligoarrays average expression levels correlation. The black rectangle indicates the area containing the 1,794 VHE transcripts discussed in the text.</p

Summary of 454-pyrosequencing transcriptome data from poplar leaves infected by <i>M. larici-populina.</i>

a<p>Number of poplar transcripts expressed in all conditions.</p>b<p>Number of poplar transcripts with an average number of 10 reads (i.e. a total of 60 reads in the 6 conditions).</p>c<p>Normalised number of reads per conditions used for quantitative analysis is 102,813 (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044408#pone.0044408.s011" target="_blank">Table S1</a>).</p

Expression profile of <i>PtSultr3;5</i>.

<p>(A) Expression pattern of <i>PtSultr3;5</i> (Poptr_0006s16150) assessed by oligoarray, RT-qPCR and RNA-Seq. RNA-Seq and RT-qPCR values are Ln-transformed. For RNA-Seq, both results from the contig-blast (cb) and the read-mapping (rm) methods are presented. Values are in arbitrary units. (B) Detailed RT-qPCR profile of <i>PtSultr3;5</i> between 0 and 48 hours post-inoculation (hpi). Expression values are normalized to the ubiquitin reference gene expression (see methods).</p

RNA-Seq and oligoarray two-by-two expression levels correlations along time-course infection of poplar leaves by <i>M. larici-populina</i>.

<p>Ln-transformed expression levels of the 1,794 validated highly expressed (VHE) transcripts are plotted for RNA-Seq on the up-right, and expression levels of the 34,964 transcripts detected on oligoarrays are plotted on the bottom-left. Arrows indicate values corresponding to the sulfate transporter PtSultr3;5 (Poptr_0006s16150) transcript discussed in the text.</p

List of selected <i>M. larici-populina</i> (Mlp) genes expressed at early stages of poplar leaf infection and cumulating three reads for all time-points assessed in the study with any of the read assignment method.

a<p>Protein ID number of corresponding best gene model in the <i>M. larici-populina</i> genome sequence (JGI; <a href="http://genome.jgi-psf.org/programs/fungi/index.jsf" target="_blank">http://genome.jgi-psf.org/programs/fungi/index.jsf</a>);</p>b<p>Based on annotation details available on the JGI website and homology searches against the non-redundant database and the conserved domain database at the NCBI;</p>c<p>predicted small secreted protein (SSP; ≤300 amino acids);</p>d<p>Based on expression data reported in Duplessis et al. 2011b <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0044408#pone.0044408-Duplessis4" target="_blank">[<b>21</b>]</a>;</p><p>NA, not available on oligoarray;</p><p>ND, not detected on oligoarray.</p

ChECs antagonizing plant cell death and supporting multiplication of plant pathogenic bacteria.

<p>(A) Infiltration scheme for the transient co-expression assay. Agrobacteria containing constructs for ChEC or YFP expression were mixed with those for cell death-inducer (CDI) expression. Mixtures were infiltrated into opposite sides of <i>N. benthamiana</i> leaves to allow pair-wise comparisons and to take account of leaf-to-leaf variation in necrosis manifestation. Thus, an infiltrated site expressing YFP/ChNLP1 was included as an internal control in every infiltrated leaf, to which the site expressing ChEC/ChNLP1 was compared. (B, C) Examples of infiltration site pairs 8 dpi. ChEC3 abolishes ChNLP1-induced necrosis (B, dotted circle), but a fungal secreted chitinase does not (C). (D) Quantification of cell death-suppressing activity of four wave 2 effectors (ChEC3, 3a, 6, 36), three wave 3 effectors (ChEC89, 34, 13) and an <i>in vitro</i>-expressed effector (ChEC5). Histograms show the proportion of sites expressing ChEC/CDI that displayed reduced necrosis compared to control sites expressing YFP/CDI. *, ** and *** indicate significant difference from the respective chitinase control with and without signal peptide at P<0,02, <0.005 and <0.0002, respectively (Student's t-test). <i>P. infestans</i> effector Avr3a^KI was used as positive control for suppression of INF1-induced cell death. Data represent means of at least three independent experiments, with at least 15 leaves/experiment/co-expression combination (± standard error). (E) Bacterial titers in <i>Arabidopsis</i> Col-0 leaves infected with <i>Pseudomonas syringae</i> pv <i>tomato</i> expressing ChECs as fusions with a bacterial effector mediating delivery into plant cells <i>via</i> type III secretion. <i>Hyaloperonospora arabidopsidis</i> ATR13^Emco5<a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002643#ppat.1002643-Sohn1" target="_blank">[27]</a> and YFP were included as positive and negative controls, respectively. Colony forming units were determined 0 and 3 days after spray inoculation. * and ** indicate significant difference from the YFP control at P<0.03 and P<0.0005, respectively. Data represent means of 4 replicates (± standard error).</p

Appressorial pores as an interface for focal ChEC delivery.

<p>Transformant appressoria expressing the wave 2 effectors ChEC36:mRFP (A–O) and ChEC6:mRFP (P, Q). Appressoria or penetration sites after removal of appressoria were examined by confocal laser scanning microscopy viewed from above (A, B, E–I, O–Q) or from the side (C, D), and with transmission electron microscopy (J, K) and scanning electron microscopy (L–N). (A–D) Bright field and maximum fluorescence intensity overlay images of appressoria. Black arrows indicate the anticlinal plant cell wall and white arrows the penetration pore. (E) Fluorescence overlay image of an appressorium showing weak peripheral labelling of intracellular structures. (F, G) Fluorescence recorded with identical settings at the base (F) and the center (G) of the appressorium shown in (E). Arrow indicates a fluorescent ring surrounding the brightly fluorescing pore. (H, I) Fluorescence overlays recorded with identical settings focused on appressorial pores (H) or biotrophic hyphae (BH) formed beneath a penetrated appressorium (arrow). (J) Median section through an appressorium viewed with transmission electron microscopy (fixed with glutaraldehyde-osmium tetroxide and embedded in epoxy resin). A penetration hypha evaginates from the pore (P). An additional layer of the appressorial wall (asterisk) forms a thickened ring (arrowheads) around the pore, continuous with the penetration hypha wall. PW, plant cell wall. (K) Immunogold labelling of an appressorial pore (arrow) using antibodies recognizing mRFP (cells fixed in formaldehyde-glutaraldehyde and embedded in acrylic resin). PW, plant cell wall. WD, host cell wall deposits. (L) Scanning electron microscope image showing attached turgid appressorium (A) and collapsed conidium (C) on a leaf surface. (M) Plant-exposed underside of detached appressoria with penetration pores (black arrows) and remnants of extracellular matrix and/or plant cuticle (white arrow). (N, O) Penetration sites from which appressoria were detached completely. (N) The lobed outline of a former appressorium is still visible (arrowheads) with a mark representing the penetration point (arrow). (O) Micrograph series representing different focal planes as fluorescence overlay (top panels) and corresponding black on white conversion of the fluorescence channel (bottom panels), focusing from the penetration point (left) downwards into the plant cell wall (right). Arrow: inserted penetration hypha. (P, Q) Fluorescence overlays focused on the appressorial pore (P) and the underlying plant cell wall (Q). Arrow, anticlinal plant cell wall. Images were recorded at 24 hours post inoculation (hpi) (A–G, K, P, Q), 32 hpi (J, L–O), 40 hpi (H, I). Scale bars: 5 µm (A, H, L, N, O, P) and 2 µm (C, E, M), 1 µm (J), 500 nm (K). See also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002643#ppat.1002643.s004" target="_blank">Figure S4</a>.</p

Expression profiling of selected biotrophy-associated ChEC and putative toxin genes by qRT-PCR.

<p>Expression levels are shown relative to the mean expression of actin and α-tubulin. Genes with highest expression <i>in planta</i> are highlighted with colours, indicating distinct waves of effector gene expression. <i>In vitro</i> cell types are: dormant spores (SP), saprotrophic mycelium (MY) and mature appressoria (VA). <i>In planta</i> stages are: unpenetrated appressoria (UA), penetrated appressoria with nascent biotrophic hyphae beneath (PA), biotrophy to necrotrophy switch (SW) and late necrotrophy (LN).</p

ChEC delivery to the biotrophic interface and host apoplast.

<p>Transformant biotrophic hyphae expressing CHEC89:mRFP (wave 3 effector) viewed with confocal laser scanning microscopy. (A) Maximum fluorescence intensity overlay projection of appressoria (arrows) and underlying biotrophic hyphae showing fluorescent foci (arrowheads) on the hyphal surface. (B) Single optical section from (A) showing labelling of the plant cell wall (arrows). (C, D) Mature biotrophic hypha, viewed as in (A and B), showing fluorescence accumulation in hyphal concavities (arrowheads). Arrow: appressorium. (E) Epidermal cell infected by a biotrophic hypha (arrows) showing fluorescence in the apoplastic space (*) enlarged by plasmolysis. Arrowheads demarcate the host plasma membrane. V, vacuole of the host protoplast. See <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002643#ppat.1002643.s007" target="_blank">Figure S7</a> for the corresponding bright field image. (F) Unlabelled necrotrophic hypha (arrow) emerging from a biotrophic hypha. Images were recorded at 43 hpi (A–E) and 55 hpi (F). Scale bars: 10 µm (E) and 5 µm (A, C, F). BH, biotrophic hypha. See also <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1002643#ppat.1002643.s006" target="_blank">Figure S6</a>.</p

ChECs accumulate in interfacial bodies and diffuse into the host cell wall.

<p>Transformant biotrophic hyphae expressing ChEC34:mRFP (wave 3 effector). (A, B) Bright field micrograph and corresponding maximum fluorescence intensity projection. Arrows: fluorescent foci. (C, D) Biotrophic hypha expressing CHEC34:mRFP viewed with confocal laser scanning microscopy settings optimized to show fluorescence in the penetrated epidermal cell wall (arrows). Arrowheads: unpenetrated wall of the same cell. (E, F) Transmission electron microscopy of a wild-type appressorium that produced a biotrophic hypha underneath with interfacial bodies (arrowheads). Arrows indicate the penetration site of the host cell wall. Cells were fixed with glutaraldehyde-osmium tetroxide and embedded in epoxy resin. (F) Close-up of an interfacial body (white asterisk) located between the plant plasma membrane (black arrowheads) and the fungal cell wall (black asterisk). (G, H) Immunogold cytochemistry using an antibody recognizing mRFP labels (G) interfacial bodies (arrows) or (H) the plant-fungal interface. Cells were fixed in formaldehyde-glutaraldehyde and embedded in acrylic resin. A, appressorium. FC, fungal cytoplasm. PC, plant cytoplasm. V, plant vacuole. BH, biotrophic hypha. (*) Fungal cell wall. Images were recorded at 40 hpi (A, B) and 43 hpi (C–H). Scale bars: 5 µm (A, C), 2.5 µm (E), 500 nm (F, G) and 250 nm (H).</p