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Large-Scale Gene Discovery in the Oomycete Phytophthora infestans Reveals Likely Components of Phytopathogenicity Shared with True Fungi

¹Syngenta Biotechnology Inc., 3054 Cornwallis Road, Research Triangle Park, NC 27709, U.S.A.; ²Department of Plant Pathology, The Ohio State University, Ohio Agricultural Research and Development Center, Wooster 44691, U.S.A.; ³Friedrich Miescher Institute, P. O. Box 2543, CH-4002 Basel, Switzerland; ⁴Department of Plant Pathology and Center for Plant Cell Biology, University of California, Riverside 92521, U.S.A.; ⁵Beijing Genomics Institute, Institute of Genetics, and Graduate School, Chinese Academy of Sciences, Beijing, China; ⁶Syngenta Limited, Jealott's Hill International Research Station, Bracknell, Berks RG42 6EY, U.K.; ⁷Syngenta Crop Protection AG, Werk Stein, Schaffhauserstrasse, CH-4332 Stein, Switzerland; ⁸Plant Pathogen Interactions Program, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, Scotland; ⁹Laboratory of Phytopathology, Wageningen University, 6709 PD Wageningen, The Netherlands; ¹⁰Department of Molecular and Cell Biology, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, Scotland, U.K.; ¹¹Department of Biology, University of Fribourg, CH-1700 Fribourg, Switzerland; ¹²National Center for Genome Resources, 1800 Old Pecos Trail, Santa Fe, NM 87505 U.S.A

To overview the gene content of the important pathogen Phytophthora infestans, large-scale cDNA and genomic sequencing was performed. A set of 75,757 high-quality expressed sequence tags (ESTs) from P. infestans was obtained from 20 cDNA libraries representing a broad range of growth conditions, stress responses, and developmental stages. These included libraries from P. infestans-potato and -tomato interactions, from which 963 pathogen ESTs were identified. To complement the ESTs, onefold coveragethe P. infestans genome was obtained and regions of coding potential identified. A unigene set of 18,256 sequences was derived from the EST and genomic data and characterized for potential functions, stage-specific patterns of expression, and codon bias. Cluster analysis of ESTs revealed major differences between the expressed gene content of mycelial and spore-related stages, and affinities between some growth conditions. Comparisons with databases of fungal pathogenicity genes revealed conserved elements of pathogenicity, such as class III pectate lyases, despite the considerable evolutionary distance between oomycetes and fungi. Thirty-seven genes encoding components of flagella also were identified. Several genes not anticipated to occur in oomycetes were detected, including chitin synthases, phosphagen kinases, and a bacterial-type FtsZ cell-division protein. The sequence data described are available in a searchable public database.