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Background  The oomycete  Plasmopara viticola  (Berk. and Curt.) Berl. and de Toni causes downy mildew in grapevine ( Vitis vinifera  L.). This pathogen is strictly biotrophic, thus completely dependent on living host cells for its survival. The molecular basis of compatibility and disease development in this system is poorly understood. We have carried out a large-scale cDNA-AFLP analysis to identify grapevine and  P. viticola  genes associated with the infection process.    Results  We carried out cDNA-AFLP analysis on artificially infected leaves of the susceptible cultivar Riesling at the oil spot stage, on water-treated leaves and on a sample of pure sporangia as controls. Selective amplifications with 128 primer combinations allowed the visualization of about 7000 transcript-derived fragments (TDFs) in infected leaves, 1196 of which (17%) were differentially expressed. We sequenced 984 fragments, 804 of which were identified as grapevine transcripts after homology searching, while 96 were homologous to sequences in  Phytophthora  spp. databases and were attributed to  P. viticola . There were 82 orphan TDFs. Many grapevine genes spanning almost all functional categories were downregulated during infection, especially genes involved in photosynthesis. Grapevine genes homologous to known resistance genes also tended to be repressed, as were several resistance gene analogs and carbonic anhydrase (recently implicated in pathogen resistance). In contrast, genes encoding cytoskeletal components, enzymes of the phenylpropanoid and beta-oxidation pathways, and pathogenesis related proteins were primarily upregulated during infection. The majority of  P. viticola  transcripts expressed  in planta  showed homology to genes of unknown function or to genomic  Phytophthora  sequences, but genes related to metabolism, energy production, transport and signal transduction were also identified.    Conclusion  This study provides the first global catalogue of grapevine and  P. viticola  genes expressed during infection, together with their functional annotations. This will help to elucidate the molecular basis of the infection process and identify genes and chemicals that could help to inhibit the pathogen.

cDNA-AFLP analysis of plant and pathogen genes expressed in grapevine infected with Plasmopara viticola