Molecular techniques for classification and diagnosis of plant pathogenic oomycota

Abstract

With a delay of approximately 10 years, molecular techniques came in use for the investigation of phylogenetic, taxonomic, and diagnostic problems in oomycetes. The particular problem in plant pathogenic Oomycota lies in their biotrophic nature, which prohibits axenic cultivation of the majority of species, in particular downy mildews and white blister rusts, on artificial media. This impeded the broad employment of basic techniques such as RFLP (restriction fragment length polymorphism) in investigations of Oomycota and required the development of specific PCR-based tools for identification and detection of minute pathogen amounts. When the first sequence analysis of genomic loci of oomycetes was conducted in the late 1980s, specific primers became available which allowed selective analysis of oomycete DNA in the presence of much higher amounts of host DNA. Since about 8 years, these methods have become routine in this field of research and have started turning the systematics of Oomycota upside down. A wide array of tools for the amplification of coding and noncoding gene loci helped to differentiate pathogen accessions, to restructure the phylogeny, to form monophyletic entities on all taxonomic levels, and to resolve unrealistically broad species concepts. Recent progress in sequencing ancient DNA from Oomycota allows the extension of taxonomic studies to herbarium collections. This broadens the basis of samples considerably and gives the chance to link molecular phylogenetic taxonomy with the traditional phenotype-based system. Moreover, molecular techniques gain growing importance in the identification of downy mildews and white blister rusts in plant pathology and in ecological studies. Their employment allows detection of Oomycota in asymptomatic infections of host plants and enables the identification of infested seeds or soils in agriculture. With the first whole genome sequencing of a Phytophthora species in 2003, the basis for functional genomics studies has been established. This will not only stimulate phylogenetic, taxonomic, and diagnostic research in plant pathogenic Oomycota, but also provide the basis for gaining deeper insights in their biology and interaction with their hosts. © 2010 Springer-Verlag Berlin Heidelberg.