Syntenic analyses of stramenopile genomes.

<p>The circle is a graphical representation of the selected regions from <i>Pythium arrhenomanes</i> (contigs 8, 17, 26, 41, 68, 131, 170, 285, 707) <i>Pythium irregulare</i> (contigs 28, 92, 103, 106, 119, 123, 129, 132, 140, 163, 195, 226, 372, 396), <i>Pythium aphanidermatum</i> (scaffolds 4, 6, 23, 80, 88, 96, 115, 150, 327), <i>Pythium iwayamai</i> (contigs 18, 28, 29, 61, 235), <i>Pythium ultimum</i> var. <i>sporangiiferum</i> (contigs 4, 6, 34, 106, 121, 134, 150, 173, 181, 222, 231, 257, 319, 404, 437, 458, 533, 726), <i>Pythium vexans</i> (contigs 9, 31,42, 94, 151, 160, 209, 220, 347), <i>Phytophthora infestans</i> (supercontig 1.2), <i>Hyaloperonospora arabidopsidis</i> (scaffolds 5, 6, 7, 8, 9) and <i>Thalassiosira pseudonana</i> (chromosome 3). Numbers along each ideogram are sequence lengths in kbp. Syntenic regions were identified through reciprocal best matches between gene models and block identification using MCscan <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075072#pone.0075072-Tang1" target="_blank">[88]</a>. Each line radiating from <i>Py. ultimum</i> var. <i>ultimum</i> (scf1117875581354) links a syntenic gene pair. Each species is represented by a genus-species abbreviation and colored as <i>Pythium ultimum</i> var. <i>ultimum</i> (Pult) in blue, <i>Pythium arrhenomanes</i> (Par) in orange, <i>Pythium irregulare</i> (Pir) in yellow, <i>Pythium aphanidermatum</i> (Pap) in dark brown, <i>Pythium iwayamai</i> (Piw) in green, <i>Pythium ultimum</i> var. <i>sporangiiferum</i> (Puls) in dark red, <i>Pythium vexans</i> (Pve) in purple, <i>Phytophthora infestans</i> (Phin) in brick red, <i>Hyaloperonospora arabidopsidis</i> (Hpa) in olive green, and <i>Thalassiosira pseudonana</i> (Thaps) in light purple.</p

Species of oomycetes and the corresponding carbohydrate-active enzymes (CAZymes) sorted according to the type of reaction catalyzed.

<p><b>Oomycete species</b>: <i>Pyap</i> = <i>Pythium aphanidermatum</i>; <i>Pyar</i> = <i>Py. arrhenomanes</i>; <i>Pyir</i> = <i>Py. irregulare</i>; <i>Pyiw</i> = <i>Py. iwayamai</i>; <i>Pyuu</i> = <i>Py. ultimum</i> var. <i>ultimum</i>; <i>Pyus</i> = <i>Py. ultimum</i> var. <i>sporangiiferum</i>; <i>Pyve</i> = <i>Py. vexans</i>; <i>Phra</i> = <i>Phytophthora ramorum</i>; <i>Phso</i> = <i>Ph. sojae</i>; <i>Phin</i> = <i>Ph. infestans</i>; and <i>Ha</i> = <i>Hyaloperonospora arabidopsidis</i>.</p><p><b>CAZymes categories</b>: CBM = carbohydrate-binding modules; GH = glycoside hydrolases; GT = glycosyl transferases; PL = polysaccharide lyases; PME = pectin methyl esterase; other CE = carbohydrate esterases excluding cutinases and PME; total = total number of CAZymes.</p>*<p>Assembly genome sizes were according to data published by: Lévesque <i>et al.</i> for <i>Pyuu</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072572#pone.0072572-Lvesque1" target="_blank">[12]</a>, Adhikar <i>et al.</i> for the other species of <i>Pythium</i> (Adhikari, <i>et al.</i> companion paper, PLoS One, this issue), Haas <i>et al.</i> for <i>Phin</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072572#pone.0072572-Haas1" target="_blank">[10]</a>, Tyler <i>et al.</i> for <i>Phra</i> and <i>Phso</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072572#pone.0072572-Tyler1" target="_blank">[2]</a>, and Baxter <i>et al.</i> for <i>Ha</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0072572#pone.0072572-Baxter1" target="_blank">[13]</a>.</p

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

Pythium ultimum var. sporangiiferum BR650 Genome Assembly and Annotation

Pythium ultimum var. sporangiiferum BR650 Genome Assembly and Annotation Contents: pug3_functional_annotation.txt; pug3.maker.proteins.fasta; pug3.maker.transcripts.fasta; pug3_contigs_asm.fasta; pug3_contigs_asm.maker.gff

Pythium arrhenomanes ATCC 12531 Genome Assembly and Annotation

Pythium arrhenomanes ATCC 12531 Genome Assembly and Annotation Contents: par_functional_annotation.txt; par.maker.proteins.fasta; par.maker.transcripts.fasta; par_contigs_asm.fasta; par_contigs_asm.maker.gff

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

Distribution of various carbohydrate-active enzymes (CAZymes) in stramenopile genomes.

<p>The CAZymes coding genes were annotated using the CAZymes Analysis Toolkit- CAT <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075072#pone.0075072-Park1" target="_blank">[62]</a> according to the CAZy database <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075072#pone.0075072-Cantarel1" target="_blank">[61]</a> in combination with protein family domain analyses. Gene families absent in at least 2 species are underlined. Comparison of total CAZymes from different classes is listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075072#pone.0075072.s007" target="_blank">Table S6</a>. CE, carbohydrate esterase; GH, glycoside hydrolase; GT, glycosyl transferase; PL, polysaccharide lyase; Pap, <i>Pythium aphanidermatum</i>; Par, <i>Pythium arrhenomanes</i>; Pir, <i>Pythium irregulare</i>; Piw, <i>Pythium iwayamai</i>; Pult, <i>Pythium ultimum</i> var. <i>ultimum</i>; Puls, <i>Pythium ultimum</i> var. <i>sporangiiferum</i>; Pve, <i>Pythium vexans</i>; Phin, <i>Phytophthora infestans</i>; Phrm, <i>Phytophthora ramorum</i>; Phsj, <i>Phytophthora sojae</i>; Hpa, <i>Hyaloperonospora arabidopsidis</i>; Thps, <i>Thalassiosira pseudonana</i>; Phtr, <i>Phaeodactylum tricornutum</i>.</p

Gene families shared by <i>Pythium</i> species.

<p>The predicted proteomes of the seven <i>Pythium</i> species were clustered using OrthoMCL <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0075072#pone.0075072-Li1" target="_blank">[59]</a> to identify orthologs and close paralogs. The number of gene families shared between the species and total number of clustered genes (numbers in parentheses) are indicated. The numbers outside the Venn diagram show the total number of orthologous clusters and number of genes (in parentheses) within those clusters for each species. Pap, <i>Pythium aphanidermatum;</i> Par, <i>Pythium arrhenomanes</i>; Pir, <i>Pythium irregulare</i>; Piw, <i>Pythium iwayamai</i>; Puls, <i>Pythium ultimum</i> var. <i>sporangiiferum</i>; Pult, <i>Pythium ultimum</i> var. <i>ultimum</i>; Pve, <i>Pythium vexans.</i></p

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