Short description
(English)
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The aim of this project is to provide ultra-detailed characterization of complex oomycete populations represented by the two main genera Phytophthora and Pythium rapidly and inexpensively in natural and forest ecosystems. The data obtained will enable us to i) determine the true diversity in the Oomycetes; ii) accelerate research on diagnostic methods and protocols and iii) allow cost effective exploration of changes in oomycete community structure, including less common species in the biosphere, in both space and time. These results will also translate into improved data mining techniques that allow greatly enhanced understanding of phylogenetic relationships within the class, a prerequisite for the development of a toolbox effective for molecular diagnostic of pathogenic members. Project deliverables are oriented towards greatly accelerating research on this important group of organisms. The data will be available online through a publicly accessible information resource for oomycetes.
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Partners and International Organizations
(English)
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AT, BE, BG, CH, DE, DK, ES, FI, FR, GR, IE, IT, LT, LV, NL, NO, PL, PT, RO, RS, SE, SK, TR, UK
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Abstract
(English)
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Oomycetes within stramenopiles form a diverse group of the Eukarya. They represent an essential component of terrestrial and aquatic ecosystems mainly as decomposers and pathogens. Plant-pathogenic oomycetes cause devastating diseases in numerous crop, ornamental, and native plants. They include more than 100 species of the genus Phytophthora that are arguably the most devastating pathogens of dicotyledonous plants. Despite the agricultural and ecological importance of oomycetes, their ecology, genetics, evolution and even their basic biology and classification are as yet poorly understood. The recent application of molecular biology for characterization of oomycetes mainly the genus Phytophthora has led to important advances in our understanding of their phylogeny genetics and evolution. Unfortunately progress remains slow as suggested by the few studies in the literature compared to the remaining groups such as fungi. This is mainly due to the limited knowledge of oomycete diversity in natural ecosystems and the lack of clear phylogenetic relationships of the different genera as well as useful markers such as generic or taxon specific primers. Therefore, extensive knowledge of the extent of environmental diversity of this group is warranted, with the prerequisite that a sensitive high-throughput technology is used to overcome this bottleneck. The recent emergence of powerful methods for environmental survey and novel molecular taxa identification such as partial ribosome amplification and pyrosequencing (PRAPS) open the way towards shading the light on the environmental diversity and effective exploration of changes in oomycete community structure over space and time in this important eukaryotic group. Using PRAPS this project aims at providing deep analysis of the environmental diversity of the major representatives of this group, Phytophthora and pythium and comparing this technology to classical methods yet to be validated for oomycetes: Full ribosomal amplification, cloning and sanger sequencing (FRACS) and profiling techniques. This knowledge will be then translated mining solving basic and practical problems encountered frequently in this stramenopilus group. Our strategy involves i) exploration of oomycete diversity in diverse forest and environmental samples ii) identification and validation of true phylogenetic relationships iii) the use of these data mainly those generated by FRACS to generate curated sequence databases strangely missing as yet iv) Definition of highly discriminative generic primers class and genus specific and v) Development of unambiguous profiling techniques: rapid, accurate and cost effective tools yet missing for monitoring oomycete community changes over time and space. The outcome of this project will be a molecular toolbox for oomycete-specific environmental monitoring and diagnostics highly useful for ecosystems health authorities and end users to help preventing highly damaging diseases caused by oomycetes.
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