Fifty years of oomycetes—from consolidation to evolutionary and genomic exploration

Lévesque, C. André

doi:10.1007/s13225-011-0128-7

Cited by 51 publications

(36 citation statements)

References 118 publications

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“…It is hypothesized that the oomycetes lost their algal plastid over the course of evolution, and as a consequence, are non-photosynthetic organisms with an osmotrophic lifestyle and filamentous growth habit (mycelium), similar to true Fungi [3], [4]. However, unlike Fungi, oomycetes are diploid with cell walls composed mainly of β-1,3-D-glucans, β-1,6-D-glucans, and cellulose [5] with a small amount of chitin or chitosaccharides [6], [7], [8], [9].…”

Section: Introductionmentioning

confidence: 99%

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

et al. 2013

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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 in silico analysis of CAZymes predicted from the genomes of seven Pythium species (Py. aphanidermatum, Py. arrhenomanes, Py. irregulare, Py. iwayamai, Py. ultimum var. ultimum, Py. ultimum var. sporangiiferum and Py. vexans) using the “CAZymes Analysis Toolkit” and “Database for Automated Carbohydrate-active Enzyme Annotation” and compared them to previously published oomycete genomes. Growth of Pythium spp. was assessed in a minimal medium containing selected carbon sources that are usually present in plants. The in silico analyses, coupled with our in vitro 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 Pythium 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 Pythium spp.. Comparative analyses of predicted CAZymes in oomycetes indicated distinct evolutionary histories. Furthermore, CAZyme gene families among Pythium spp. were not uniformly distributed in the genomes, suggesting independent gene loss events, reflective of the polyphyletic relationships among some of the species.

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Section: Introductionmentioning

confidence: 99%

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

et al. 2013

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“…)] are among the most diverse and widespread group of pathogens found in terrestrial and aquatic habitats, with hosts ranging from plants, invertebrates, and vertebrates to fungi, algae, and other microbes (Dick ). Despite broad pathogenic lifestyles, oomycetes are most notorious for their widespread pathogenicity to plants (Levesque ). Aside from a limited number of studies implicating oomycete pathogens as potentially important in negative PSFs and plant invasions (Klironomos ; Zhang et al.…”

Section: Introductionmentioning

confidence: 99%

Soil pathogen communities associated with native and non‐native Phragmites australis populations in freshwater wetlands

Nelson

Karp

2013

Ecology and Evolution

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Soil pathogens are believed to be major contributors to negative plant–soil feedbacks that regulate plant community dynamics and plant invasions. While the theoretical basis for pathogen regulation of plant communities is well established within the plant–soil feedback framework, direct experimental evidence for pathogen community responses to plants has been limited, often relying largely on indirect evidence based on above-ground plant responses. As a result, specific soil pathogen responses accompanying above-ground plant community dynamics are largely unknown. Here, we examine the oomycete pathogens in soils conditioned by established populations of native noninvasive and non-native invasive haplotypes of Phragmites australis (European common reed). Our aim was to assess whether populations of invasive plants harbor unique communities of pathogens that differ from those associated with noninvasive populations and whether the distribution of taxa within these communities may help to explain invasive success. We compared the composition and abundance of pathogenic and saprobic oomycete species over a 2-year period. Despite a diversity of oomycete taxa detected in soils from both native and non-native populations, pathogen communities from both invaded and noninvaded soils were dominated by species of Pythium. Pathogen species that contributed the most to the differences observed between invaded and noninvaded soils were distributed between invaded and noninvaded soils. However, the specific taxa in invaded soils responsible for community differences were distinct from those in noninvaded soils that contributed to community differences. Our results indicate that, despite the phylogenetic relatedness of native and non-native P. australis haplotypes, pathogen communities associated with the dominant non-native haplotype are distinct from those of the rare native haplotype. Pathogen taxa that dominate either noninvaded or invaded soils suggest different potential mechanisms of invasion facilitation. These findings are consistent with the hypothesis that non-native plant species that dominate landscapes may “cultivate” a different soil pathogen community to their rhizosphere than those of rarer native species.

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“…The internal transcribed spacer (ITS) region of ribosomal DNA is likely the most frequently sequenced region of DNA in fungi (Peay et al , ). Schoch et al () have recommended using ITS as the universal fungal barcode sequence, and as a consequence it has also been adopted for studies of oomycetes (Lévesque, ). Composed of sections with sequences of nucleotides that are highly conserved between species, interspersed with distinctly variable sections, the ITS region has lent itself to the development of sensitive generic primer sets capable of reliably selecting lengths of representative sequence with high variability between species, allowing PCR‐based detection and diagnosis of target oomycetes in complex environmental samples (Klemsdal et al , ; Lees et al , ).…”

Section: Molecular Approaches To Disease Diagnosismentioning

confidence: 99%

Diagnostic tests and their application in the management of soil- and water-borne oomycete pathogen species

Wakeham

Pettitt

2016

Ann Appl Biol

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Oomycete diseases cause significant losses across a broad range of crop and aquaculture commodities worldwide. These losses can be greatly reduced by disease management practices steered by accurate and early diagnoses of pathogen presence. Determinations of disease potential can help guide optimal crop rotation regimes, varietal selections, targeted control measures, harvest timings and crop post-harvest handling. Pathogen detection prior to infection can also reduce the incidence of disease epidemics. Classical methods for the isolation of oomycete pathogens are normally deployed only after disease symptom appearance. These processes are often time consuming, relying on culturing the putative pathogen(s) and the availability of expert taxonomic skills for accurate identification, a situation that frequently results in either delayed application, or routine 'blanket' over-application of control measures. Increasing concerns about pesticides in the environment and the food chain, removal or restriction of their usage combined with rising costs have focussed interest in the development and improvement of disease management systems. To be effective, these require timely, accurate and preferably quantitative diagnoses. A wide range of rapid diagnostic tools, from point of care immunodiagnostic kits to next generation nucleotide sequencing have potential application in oomycete disease management. Here we review currently available as well as promising new technologies in the context of commercial agricultural production systems, considering the impacts of specific biotic and abiotic and other important factors such as speed and ease of access to information and cost effectiveness.

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Fifty years of oomycetes—from consolidation to evolutionary and genomic exploration

Cited by 51 publications

References 118 publications

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

Soil pathogen communities associated with native and non‐native Phragmites australis populations in freshwater wetlands

Diagnostic tests and their application in the management of soil- and water-borne oomycete pathogen species

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