Figure 1.
Phylogenetic tree of Stramenopiles species and distribution of CAZy genes in oomycete genomes.
A Bayesian analysis was performed for 300,000 generations using a GTR/gamma distributed with invariant sites model of evolution of 28S rRNA gene. Bayesian probabilities are shown next to each branch. The distribution of seven gene families predicted from the genome of oomycete species and associated to carbohydrate degradation was compared to the phylogenetic relatedness thereof. Gene families: GH54 (orange), α-L-arabinofuranosidase; GH85 (gray), endo-β-N-acetylglucosaminidase; GH11 (brown) and GH10 (green), endoxylanases; GH12 (red), xyloglucan-β-1,4-D-endoglucanase; CE8 (blue), pectin methylesterase; and cutinase within CE5 (purple). Gene copy numbers are indicated next to the bars. Diatoms: Phaeodactylum, Phaeodactylum tricornutum; and Thalassiosira, Thalassiosira pseudonana. Oomycetes: Ha, Hyaloperonospora arabidopsidis; Phin, Phytophthora infestans; Phso, Ph. sojae; Phra, Ph. ramorum; Pyve, Pythium vexans; Pyus, Py. ultimum var. sporangiiferum; Pyuu, Py. ultimum var. ultimum; Pyiw, Py. iwayamai; Pyir, Py. irregulare; Pyar, Py. arrhenomanes; and Pyap, Py. aphanidermatum.
Table 1.
Species of oomycetes and the corresponding carbohydrate-active enzymes (CAZymes) sorted according to the type of reaction catalyzed.
Figure 2.
Glycoside hydrolase (GH) families associated with cellulose metabolism.
Families GH1, GH3 and GH5 are cellulase candidates, i.e., 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 Figure 1.
Figure 3.
Average copy number of some CAZyme-gene families in Pythium and Phytophthora sorted by substrate.
Black line corresponds to the equal number of copies in Pythium and Phytophthora. Based on the GLM (loglinear/Poisson) test all gene families whose number of copies is significantly more abundant in Phytophthora than in Pythium are indicated: ***, ** and * represent p<0.001, p<0.01 and p<0.05, respectively.
Table 2.
Proportional growth of Pythium species on a minimal medium (MM) containing various carbon sources to its growth on V8 juice agar.
Figure 4.
Phylogenetic relationship among predicted xyloglucan-β-1,4-D-endoglucanases (GH12) of oomycetes.
Bayesian analysis was performed for 300,000 generations using Blosum model of evolution. Bayesian probabilities are shown next to each branch. An endoglucanase of Aspergillus clavatus (XP_001269687) was used as outgroup. Leaves indicate the locus number of predicted proteins in the genomes of each species (as defined in Figure 1).
Figure 5.
Phylogenetic relationship among predicted endoxylanases (GH10 and GH11) of straminipilous species.
Bayesian analysis was performed for 300,000 generations using Blosum model of evolution. An endoxylanase of Phaeodactylum tricornutum (XP_002178502) and Thalassiosira pseudonana (XP_002290930) were used as outgroups. Bayesian probabilities are shown next to each branch. Leaves indicate the predicted proteins: species abbreviations (as defined in Figure 1), and locus number within the corresponding genome. All entries correspond to GH10 endoxylanases, unless represented as GH11.
Figure 6.
Pectin degrading enzymes in oomycetes.
Bars correspond to one gene copy, unless indicated. Carbohydrate esterase (CE), pectin/pectate lyase (PL) and glycoside hydrolase (GH) gene families: CE1 = feruloyl esterase and others; PL3 = pectate lyase; PL1 = pectin/pectate lyase; GH28 = polygalacturonase; CE8 = pectin methyl esterase; CE12 = pectin acetylesterase; GH43 = endo-1,5-α-L-arabinosidase and β-xylosidase; CE13 = pectin acetylesterase; GH53 = endo-β-1,4-galactanase; GH78 = α-L-rhamnosidase; PL4 = rhamnogalacturonan lyase; GH35 = β-galactosidase; GH54 = arabinofurosidase and β-xylosidase; GH105 = unsaturated rhamnogalacturonyl hydrolase. Species abbreviations are as defined in Figure 1.
Figure 7.
Phylogenetic relationship among predicted cutinases of oomycete species.
The cutinase encoding genes identified from Hyaloperonospora arabidopsidis, Phytophthora spp. and Pythium spp. genomes were used for the phylogenetic analyses. A cutinase sequence from Frankia sp. EUN1f (ZP_06415970) was used as outgroup. The phylogeny was inferred using using Blosum model of evolution (300,000 generations) and displayed using the Interactive Tree of Life (iTOL) web server (http://itol.embl.de/). The same color indicates cutinase from the same genus, different shades indicate different species. Species abbreviations are as defined in Figure 1.