Glycoside hydrolase (GH) families associated with cellulose metabolism.

<p>Families GH1, GH3 and GH5 are cellulase candidates, <i>i.e.</i>, they may or may not be related to cellulose metabolism. Genes belonging to GH6 and GH7 encode enzymes that are strictly related to cellulose metabolism, either to the oomycete cell wall (membrane attached) or to the plant cellulose catabolism (extracellular directed). Species abbreviations are as defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072572#pone-0072572-g001" target="_blank">Figure 1</a>.</p

Pythium irregulare DAOM BR486 Genome Assembly and Annotation

Pythium irregulare DAOM BR486 Genome Assembly and Annotation Contents: pir_functional_annotation.txt; pir.maker.proteins.fasta; pir.maker.transcripts.fasta; pir_contigs_asm.fasta; pir_contigs_asm.maker.gff

Carbohydrate-Active Enzymes in <i>Pythium</i> and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

<div><p>Carbohydrate-active enzymes (CAZymes) are involved in the metabolism of glycoconjugates, oligosaccharides, and polysaccharides and, in the case of plant pathogens, in the degradation of the host cell wall and storage compounds. We performed an <i>in silico</i> analysis of CAZymes predicted from the genomes of seven <i>Pythium</i> species (<i>Py. aphanidermatum</i>, <i>Py. arrhenomanes</i>, <i>Py. irregulare</i>, <i>Py. iwayamai</i>, <i>Py. ultimum</i> var. <i>ultimum</i>, <i>Py. ultimum</i> var. <i>sporangiiferum</i> and <i>Py. vexans</i>) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of <i>Pythium</i> spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. The <i>in silico</i> analyses, coupled with our <i>in vitro</i> growth assays, suggest that most of the predicted CAZymes are involved in the metabolism of the oomycete cell wall with starch and sucrose serving as the main carbohydrate sources for growth of these plant pathogens. The genomes of <i>Pythium</i> spp. also encode pectinases and cellulases that facilitate degradation of the plant cell wall and are important in hyphal penetration; however, the species examined in this study lack the requisite genes for the complete saccharification of these carbohydrates for use as a carbon source. Genes encoding for xylan, xyloglucan, (galacto)(gluco)mannan and cutin degradation were absent or infrequent in <i>Pythium</i> spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among <i>Pythium</i> spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.</p></div

Experimental design and sample collection.

<p>A 1×10⁵ sporangia/ml solution of <i>Pseudoperonospora cubensis</i> was used to inoculate the abaxial leaf surface of cucumber cultivar ‘Vlaspik’. Samples were collected using a #3 cork borer to minimize uninfected tissue (black circles) at 1, 2, 3, 4, 6, and 8 days post-inoculation (dpi). Leaf disks were used for microscopic analysis of infection stages or pooled for RNA extraction. mRNA-Seq libraries were made for each time point from 2 biological replicates. Within a biological replicate, libraries were barcoded and sequenced in multiple lanes. The sporangia-only library (SP) was not barcoded and was sequenced on its own.</p

Phylogenetic relationship among predicted xyloglucan-β-1,4-D-endoglucanases (GH12) of oomycetes.

<p>Bayesian analysis was performed for 300,000 generations using Blosum model of evolution. Bayesian probabilities are shown next to each branch. An endoglucanase of <i>Aspergillus clavatus</i> (XP_001269687) was used as outgroup. Leaves indicate the locus number of predicted proteins in the genomes of each species (as defined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072572#pone-0072572-g001" target="_blank">Figure 1</a>).</p

Heat map of the eigengenes representing each gene module.

<p>The columns in the heat map represent time points, and the rows represent eigengenes for each of the six identified co-expression modules <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035796#pone.0035796-Langfelder2" target="_blank">[50]</a>. The numbers of genes in each module are given in parentheses. The cells in the heat map show eigengene values between 0 and 1, indicators of relative expression levels of all genes in the module (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0035796#s3" target="_blank">Materials and Methods</a>). dpi = days post-inoculation.</p

Symptoms and microscopy images of <i>Pseudoperonospora cubensis</i> infected <i>Cucumis sativus</i> cultivar ‘Vlaspik’ of time points used for transcriptome analysis.

<p>Symptom images were collected of the adaxial (top row) and abaxial (middle row) at 1, 2, 3, 4, 6, and 8 days post-inoculation (dpi). Microscopy (bottom row) to assess stages of <i>Ps. cubensis</i> invasion were collected from the same time points using ethanol-cleared, trypan blue stained samples. Scale bars at 1–4 dpi are 25 µm. Scale bars at 6 and 8 dpi are 50 µm. Dotted lines represent position of stomata relative to the pathogen structure. e = encysted zoospore. s = stomate. h = haustorium.</p

CAL_genome_asm_v2.2_1000_rmscaff.fasta

Final genome assembly for C. gigante

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

<div><p>The kingdom Stramenopile includes diatoms, brown algae, and oomycetes. Plant pathogenic oomycetes, including <i>Phytophthora</i>, <i>Pythium</i> and downy mildew species, cause devastating diseases on a wide range of host species and have a significant impact on agriculture. Here, we report comparative analyses on the genomes of thirteen straminipilous species, including eleven plant pathogenic oomycetes, to explore common features linked to their pathogenic lifestyle. We report the sequencing, assembly, and annotation of six <i>Pythium</i> genomes and comparison with other stramenopiles including photosynthetic diatoms, and other plant pathogenic oomycetes such as <i>Phytophthora</i> species, <i>Hyaloperonospora arabidopsidis,</i> and <i>Pythium ultimum</i> var. <i>ultimum</i>. Novel features of the oomycete genomes include an expansion of genes encoding secreted effectors and plant cell wall degrading enzymes in <i>Phytophthora</i> species and an over-representation of genes involved in proteolytic degradation and signal transduction in <i>Pythium</i> species. A complete lack of classical RxLR effectors was observed in the seven surveyed <i>Pythium</i> genomes along with an overall reduction of pathogenesis-related gene families in <i>H. arabidopsidis</i>. Comparative analyses revealed fewer genes encoding enzymes involved in carbohydrate metabolism in <i>Pythium</i> species and <i>H. arabidopsidis</i> as compared to <i>Phytophthora</i> species, suggesting variation in virulence mechanisms within plant pathogenic oomycete species. Shared features between the oomycetes and diatoms revealed common mechanisms of intracellular signaling and transportation. Our analyses demonstrate the value of comparative genome analyses for exploring the evolution of pathogenesis and survival mechanisms in the oomycetes. The comparative analyses of seven <i>Pythium</i> species with the closely related oomycetes, <i>Phytophthora</i> species and <i>H. arabidopsidis</i>, and distantly related diatoms provide insight into genes that underlie virulence.</p></div

Pythium aphanidermatum DAOM BR444 Genome Assembly and Annotation

Pythium aphanidermatum DAOM BR444 Genome Assembly and Annotation Contents: pag1_functional_annotation.txt; pag1.maker.proteins.fasta; pag1.maker.transcripts.fasta; pag1_scaffolds_asm.fasta; pag1_scaffolds_asm.maker.gff