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

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

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

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

MOESM1 of Editing of the urease gene by CRISPR-Cas in the diatom Thalassiosira pseudonana

Additional file 1: Figure S1. Final spreadsheet for choosing sgRNAs

Figure 3-source data 1

Figure 3-source data

Additional file 1 of nQuire: a statistical framework for ploidy estimation using next generation sequencing

Supplementary figures addressing the effect of denoising, as well as the effect of high coverage outliers on the likelihood of Gaussian and binomial mixtures. (PDF 144 kb

Genetic distance between individual isolates of clonal lineages HERB-1, US-1, and EC-1 of <i>P. infestans</i>.

a<p>Sequences from Martin et al. (2013) <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Martin1" target="_blank">[11]</a>.</p>b<p>Sequences from Yoshida et al. (2013) <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Yoshida1" target="_blank">[10]</a>.</p>c<p>Bold letters indicates comparisons within a clonal lineage; genetic distance was estimated based on 2,359,452 SNPs as described in Yoshida et al. (2013) <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Yoshida1" target="_blank">[10]</a>.</p

The rise and fall of <i>P. infestans</i> lineages in the British Isles.

<p>Frequency of genotypes over the years from the potato blight outbreaks in the British Isles (adapted from Cooke et al. (2012) <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Cooke1" target="_blank">[28]</a>). Isolates of genotypes that occurred at a low frequency in a single year were grouped under the category termed <i>‘misc’</i>. Two mating types of <i>P. infestans</i>, A1 and A2, are necessary for sexual reproduction. The shading between the bars indicates the proportion of A1- and A2-mating-type isolates, with pink referring to the A1 mating type and blue to A2. The data of 1845–1875 and 1978 were from Yoshida et al. (2013) <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Yoshida1" target="_blank">[10]</a> and Fry et al. (1992) <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Fry3" target="_blank">[39]</a>, respectively. A template for the figure was kindly provided by Dr. David Cooke, James Hutton Institute, Dundee <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004028#ppat.1004028-Cooke1" target="_blank">[28]</a>.</p