Figure 1.
Taxonomy and ancestral genomic features in S. parasitica.
(A) Animal pathogenic and plant pathogenic oomycetes reside in different taxonomic units. (B) Comparison of intron number in phytopathogenic oomycetes (the average count from the total genes of P. infestans, P. ramorum, P. sojae, Py. ultimum and H. arabidopsidis) and S. parasitica among all genes. (C) Significant difference in intron number in 4008 orthologous genes shared by S. parasitica and Phytophthora species (average intron count of P. infestans, P. sojae and P. ramorum). (Wilcoxon test, p<0.001). (D) Large number of chitinase genes belonging to CAZy family GH-18 in S. parasitica (red) compared to other oomycetes (black; Ps = P. sojae, Pr = P. ramorum, PITG = P. infestans, Hp = H. arabidopsidis, Pyu = Py. ultimum, ALNC = A. laibachii). The phylogenetic tree was constructed with chitinase genes from oomycetes using Maximum likelihood method.
Table 1.
Genome statistics and intron features of oomycetes.
Table 2.
Gene families potentially involved in pathogenesis in Saprolegnia parasitica.
Figure 2.
Metabolic adaptations to animal pathogenesis.
(A) 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. (B) Lineage specific expansion of amino acid transporters. Members from Pythium (black), Hyaloperonospora (green), Albugo (blue) and S. parasitica (red) are included. - The S. parasitica-specific clade is marked with red dots. (C) Secreted peptidase families in S. parasitica and phytopathogenic oomycetes (the average count from the total peptidase genes of P. infestans, P. ramorum, P. sojae, Py. ultimum and H. peronospora) . Peptidase_C1, Peptidase_S8 and Peptidase_S10 are the largest families in S. parasitica. (D) Lineage-specific expansion of peptidase_C1 family. Members from P. sojae, P. ramorum and P. infestans (black) and S. parasitica (red) are included. The S. parasitica-specific clade is marked with red dots.
Figure 3.
Specialized proteins in the secretome of S. parasitica.
(A) Distributions of major classes of specialized secreted proteins compared between animal and plant pathogenic oomycetes. P. infestans represents Phytophthora species. (B) S. parasitica secreted proteins that carry various lectin domain fusions are schematically drawn. Domains or domain architectures unique to S. parasitica are marked with an asterisk. Proteins containing single domains are also listed. (C) Phylogenetic relationship of lectins. The S. parasitica disintegrin gene (SPRG_01285 groups with bacterial homologs; gal_lectin gene (SPRG_05731)) groups with animal species. All other paralogous S. parasitica disintegrin and gal_lectin genes group closely with these two representatives, respectively, and are not shown.
Figure 4.
Rainbow trout IgM proteolysis by S. parasitica secreted proteases.
(A) 7-day old culture filtrates were capable of degrading rainbow trout IgM after an overnight incubation at 10°C. (B) Schematic drawing of the domains present in the protease SPRG_14567 (C) 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. (D) 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. (E) Fractions 2, 3 and soluble proteins from untransformed E. coli were tested for IgM-degrading activity with only the fraction containing the recombinant SPRG_14567 exhibiting proteolysis.
Table 3.
Predicted horizontally transferred genes that may be associated with pathogenesis in Saprolegnia parasitica.
Figure 5.
Differentially expressed genes detected by RNA-Seq.
(A) Percentage of differentially expressed genes in pair-wise comparisons of tissue types. Genes with 4 fold RPKM (reads per kilobase per million) differences were considered to be differentially expressed (negative binomial exact test p<0.001, p value adjusted with Benjamini & Hochberg correction, Table S12) (B) Gene families showing differential expression between vegetative tissue (mycelia and sporulating mycelia) and pre-infection tissues (cysts and germinating cysts). CBEL:fungal Cellulose Binding Domain Like protein, EGF:(Epidermal Growth Factor, gal_lectin: Galactose binding Lectin domain, HST: Heat shock factors, PLAC8: Placenta-specific gene 8 protein, SDF: Sodium Dicarboxylate symporter Family (Table S13). (C) Growth phase specific expression of peptidases and protease inhibitors (Table S14). (D) Relative abundance of S. parasitica and fish transcripts during interaction. (E). S. parasitica transcript distribution in pre-infection versus vegetative tissue. logFC = log2(pre-infection/vegetative/pre-infection); logConc = the log2 of average reads counts per million of each gene in the two tissue types,). Red dots indicate significant differences (p<0.001; negative binomial test).
Figure 6.
Molecular genetic events associated with the evolution of animal and plant pathogenesis in oomycetes.
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.