Characterization of strain fields in Si1-xGex island structures by means of quantitative high-resolution electron microscopy

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Rainbow trout IgM proteolysis by <i>S. parasitica</i> secreted proteases.

<p>(<b>A</b>) 7-day old culture filtrates were capable of degrading rainbow trout IgM after an overnight incubation at 10°C. (<b>B</b>) Schematic drawing of the domains present in the protease SPRG_14567 (<b>C</b>) Expression pattern of SPRG_14567 in different life stages. The RKPM of RNA-seq data is plotted, and the previously identified effector SpHTP-1 is plotted to show contrasting expression patterns. (<b>D</b>) The recombinant subtilisin-like protease SPRG_14567 was partially purified through tandem ion exchange (SO₃⁻) and nickel affinity columns (Fractions 1 to 4) following detection in a Western blot using anti-(His)₅ HRP antibody. (<b>E</b>) Fractions 2, 3 and soluble proteins from untransformed <i>E. coli</i> were tested for IgM-degrading activity with only the fraction containing the recombinant SPRG_14567 exhibiting proteolysis.</p

Predicted horizontally transferred genes that may be associated with pathogenesis in <i>Saprolegnia parasitica</i>.

a<p>Subcellular localization is predicted by the N-terminal signal peptide, mitochondrial targeting motif and transmembrane domains.</p>b<p>The time of horizontal gene transfer is estimated by the presence in other oomycetes and coding potential of a given gene. ‘a recently acquired gene’ refers to a gene occurring only in <i>Saprolegnia</i> and having an uncharacteristic coding potential.</p

Specialized proteins in the secretome of <i>S. parasitica</i>.

<p><i>(A)</i> Distributions of major classes of specialized secreted proteins compared between animal and plant pathogenic oomycetes. <i>P. infestans</i> represents <i>Phytophthora</i> species. <i>(B) S. parasitica</i> secreted proteins that carry various lectin domain fusions are schematically drawn. Domains or domain architectures unique to <i>S. parasitica</i> are marked with an asterisk. Proteins containing single domains are also listed. <i>(C)</i> Phylogenetic relationship of lectins. The <i>S. parasitica</i> disintegrin gene (SPRG_01285 groups with bacterial homologs; gal_lectin gene (SPRG_05731)) groups with animal species. All other paralogous <i>S. parasitica</i> disintegrin and gal_lectin genes group closely with these two representatives, respectively, and are not shown.</p

Metabolic adaptations to animal pathogenesis.

<p><i>(A)</i> Independent degeneration of nitrite and sulfite metabolic pathways in animal pathogens and obligate biotrophic plant pathogens. Red cross indicates the gene encoding the enzyme is absent in the genome. <i>(B)</i> Lineage specific expansion of amino acid transporters. Members from <i>Pythium</i> (black), <i>Hyaloperonospora</i> (green), <i>Albugo</i> (blue) and <i>S. parasitica</i> (red) are included. - The <i>S. parasitica</i>-specific clade is marked with red dots. <i>(C)</i> Secreted peptidase families in <i>S. parasitica</i> and phytopathogenic oomycetes (the average count from the total peptidase genes of <i>P. infestans</i>, <i>P. ramorum</i>, <i>P. sojae</i>, <i>Py. ultimum</i> and <i>H. peronospora</i>) . Peptidase_C1, Peptidase_S8 and Peptidase_S10 are the largest families in <i>S. parasitica</i>. <i>(D)</i> Lineage-specific expansion of peptidase_C1 family. Members from <i>P. sojae</i>, <i>P. ramorum</i> and <i>P. infestans</i> (black) and <i>S. parasitica</i> (red) are included. The <i>S. parasitica</i>-specific clade is marked with red dots.</p

Taxonomy and ancestral genomic features in <i>S. parasitica</i>.

<p><i>(A)</i> Animal pathogenic and plant pathogenic oomycetes reside in different taxonomic units. <i>(B)</i> Comparison of intron number in phytopathogenic oomycetes (the average count from the total genes of <i>P. infestans</i>, <i>P. ramorum</i>, <i>P. sojae</i>, <i>Py. ultimum</i> and <i>H. arabidopsidis</i>) and <i>S. parasitica</i> among all genes. <i>(C)</i> Significant difference in intron number in 4008 orthologous genes shared by <i>S. parasitica</i> and <i>Phytophthora</i> species (average intron count of <i>P. infestans</i>, <i>P. sojae</i> and <i>P. ramorum</i>). (Wilcoxon test, p<0.001). <i>(D)</i> Large number of chitinase genes belonging to CAZy family GH-18 in <i>S. parasitica</i> (red) compared to other oomycetes (black; Ps = <i>P. sojae</i>, Pr = <i>P. ramorum</i>, PITG = <i>P. infestans</i>, Hp = <i>H. arabidopsidis</i>, Pyu = <i>Py. ultimum</i>, ALNC = <i>A. laibachii</i>). The phylogenetic tree was constructed with chitinase genes from oomycetes using Maximum likelihood method.</p

Molecular genetic events associated with the evolution of animal and plant pathogenesis in oomycetes.

<p>The lineages of animal pathogens are colored red and the lineages of plant pathogens are colored green. The basal lineage is colored brown. S and N pathways refer to sulfite and nitrite assimilation, respectively.</p

Genome statistics and intron features of oomycetes.

a<p>Total contig length adjusted for the regions of haplotype assemblies.</p>b<p>Genome statistics derived from publication of these genomes.</p>c<p>Measured by repeatMasker with de novo RepeatScout.</p>d<p>The repeat content in the assembled sequence is listed in the brackets.</p