Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica.

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica

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

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

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

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