Integrated process of effector translocation.

<p>Effectors (blue) follow secretion routes (arrows) within a pathogen (orange), are secreted into host-parasite interfaces (grey), cross a membrane surrounding the host cell (green), and finally enter the host cell cytoplasm. Each translocation step is likely to be influenced by host- and parasite-derived mechanisms that need to be considered when studying effector trafficking.</p

List of conflicting studies on filamentous pathogen effector translocation inside plant cells.

a<p>Yes, results support finding; No, results do not support finding.</p>b<p>References not cited in the main text.</p>c<p>Article addendum.</p><p>AC, animal cells; AI, agroinfiltration; DB, dot blot; F., fungal; FP, fluorescent protein; HR, hypersensitive response; ITC, isothermal titration calorimetry; LB, liposome binding; NMR, nuclear magnetic resonance; Oo, oomycete; PB, particle bombardment; PEG, polyethylene glycol; PL, plant leaves; PR, plant roots; SPR, surface plasma resonance.</p

N-terminal effector domains proposed to mediate host-cell entry.

<p>Effectors from fungal (left) and oomycete (right) pathogens. Divergent oomycete and fungal effectors carry a general secretion signal peptide followed by non-conserved N-terminal regions called “uptake” or “targeting/translocation” domains that have been proposed to mediate host-cell entry. In oomycetes, small conserved amino acids motifs (e.g., RXLR, CHXC, or LFLAK) have been identified within these regions, which help to define effector families with many members.</p

Fungal and oomycete structures for effector secretion.

<p>Left panel. Oomycete and fungal plant parasites differentiate infection structures such as extracellular hyphae, as well as invasive hyphae and haustoria that penetrate the host cell cavity and invaginate the plasma membrane. Haustoria (a) and hyphae (b) secrete effectors that are translocated into host cell cytoplasm by unknown mechanisms. Right panel. Effectors secreted from haustoria (a) and hyphae (b) cross different biological interfaces (extra-haustorial matrix [EHMx]/extra-haustorial membrane [EHM] for effectors secreted from haustoria, and apoplast/plant cell wall/plant plasma membrane for effectors secreted from hyphae).</p

A genetically unlinked NLR network that modulates plant immunity against diverse pathogens originated from an ancestral gene cluster

NLR immune receptors in the NRC superclade form an intricate network that confers resistance to a multitude of plant pathogens. This network is comprised of sensor NLRs, specialized in detection of pathogen effectors, that require helper NLRs, known as NRCs, to initiate immune responses. The network originated from a linked NLR pair that evolved prior to the divergence of asterids and caryophyllales over 100 million years ago, and expanded to half of all NLRs in some asterid species. We used phylogenomics methods to reconstruct the evolutionary history of the NRC family. One of the NRCs, we termed NRC0, is the only family member shared among different asterid species, leading us to investigate its evolutionary history and genetic organization. In tomato, carrot, coffee and morning glory, NRC0 is closely linked to NLRs that are phylogenetically related to NRC-dependent sensors. This prompted us to hypothesize that the ancestral state of the NRC network is an NLR helper-sensor gene cluster that was present in early asterids. We validated this hypothesis by demonstrating that tomato NRC0 is essential for the hypersensitive cell death induced by its genetically linked NLR. We are testing the degree to which the functional dependency between NRC0 and the linked NLRs is conserved across asterids. These results revealed the evolutionary dynamics of NLR receptor networks and how coevolution with pathogens drivesthe expansion and diversification of NLRs.</p

Multiple virulence factors are deployed by <i>Saprolegnia parasitica</i> and an overview of oomycete phylogeny.

<p>(A) Schematic representation of a <i>Saprolegnia parasitica</i> hypha (light blue) deploying virulence factors against a fish cell (salmon color). SpHtp1 is translocated inside the host cell, and other factors are secreted to the cell surface (lectins [green circles]) or the extracellular space (proteases [red circles], CHAPs [pink triangles], toxins [HlyE, which presumably targets the host membrane, green bolts] and nucleases [purple squares]). B. An overview of oomycete phylogeny. The main genera are displayed with the plant pathogenic lineages in green, animal parasites in red, and saprophytes in blue. Some genera, such as <i>Pythium</i> and <i>Aphanomyces</i>, include both plant and animal parasitic species. The early branching <i>Eurychasma</i> is an obligate pathogen of marine brown algae.</p

Petre_Slide_CategoricalScatterplotFigShare.pptx

Categorical scatterplots with R for biologists: a step-by-step guide   Benjamin Petre1, Aurore Coince2, Sophien Kamoun1 1 The Sainsbury Laboratory, Norwich, UK; 2 Earlham Institute, Norwich, UK   Weissgerber and colleagues (2015) recently stated that ‘as scientists, we urgently need to change our practices for presenting continuous data in small sample size studies’. They called for more scatterplot and boxplot representations in scientific papers, which ‘allow readers to critically evaluate continuous data’ (Weissgerber et al., 2015). In the Kamoun Lab at The Sainsbury Laboratory, we recently implemented a protocol to generate categorical scatterplots (Petre et al., 2016; Dagdas et al., 2016). Here we describe the three steps of this protocol: 1) formatting of the data set in a .csv file, 2) execution of the R script to generate the graph, and 3) export of the graph as a .pdf file.   Protocol • Step 1: format the data set as a .csv file. Store the data in a three-column excel file as shown in Powerpoint slide. The first column ‘Replicate’ indicates the biological replicates. In the example, the month and year during which the replicate was performed is indicated. The second column ‘Condition’ indicates the conditions of the experiment (in the example, a wild type and two mutants called A and B). The third column ‘Value’ contains continuous values. Save the Excel file as a .csv file (File -> Save as -> in ‘File Format’, select .csv). This .csv file is the input file to import in R. • Step 2: execute the R script (see Notes 1 and 2). Copy the script shown in Powerpoint slide and paste it in the R console. Execute the script. In the dialog box, select the input .csv file from step 1. The categorical scatterplot will appear in a separate window. Dots represent the values for each sample; colors indicate replicates. Boxplots are superimposed; black dots indicate outliers. • Step 3: save the graph as a .pdf file. Shape the window at your convenience and save the graph as a .pdf file (File -> Save as). See Powerpoint slide for an example.   Notes • Note 1: install the ggplot2 package. The R script requires the package ‘ggplot2’ to be installed. To install it, Packages & Data -> Package Installer -> enter ‘ggplot2’ in the Package Search space and click on ‘Get List’. Select ‘ggplot2’ in the Package column and click on ‘Install Selected’. Install all dependencies as well. • Note 2: use a log scale for the y-axis. To use a log scale for the y-axis of the graph, use the command line below in place of command line #7 in the script. #7 Display the graph in a separate window. Dot colors indicate replicates graph + geom_boxplot(outlier.colour='black', colour='black') + geom_jitter(aes(col=Replicate)) + scale_y_log10() + theme_bw()   References Dagdas YF, Belhaj K, Maqbool A, Chaparro-Garcia A, Pandey P, Petre B, et al. (2016) An effector of the Irish potato famine pathogen antagonizes a host autophagy cargo receptor. eLife 5:e10856. Petre B, Saunders DGO, Sklenar J, Lorrain C, Krasileva KV, Win J, et al. (2016) Heterologous Expression Screens in Nicotiana benthamiana Identify a Candidate Effector of the Wheat Yellow Rust Pathogen that Associates with Processing Bodies. PLoS ONE 11(2):e0149035 Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015) Beyond Bar and Line Graphs: Time for a New Data Presentation Paradigm. PLoS Biol 13(4):e1002128 https://cran.r-project.org/ http://ggplot2.org/    </p

Nep-Like Protein in H.pseudoalbidus

<p>Protein structure modelling of sequence with identity to amino acid sequence of NLPpya_3GNU. The known NLP is on the left, the model of the putative NLP is on the right.</p

Wheat infected with the blast fungus (February 24, 2019, Meherpur, Bangladesh).

Wheat infected with the blast fungus (February 24, 2019, Meherpur, Bangladesh).</p

Recommendations for responding to plant health emergencies¹.

Recommendations for responding to plant health emergencies1.</p