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

March 2005 , Volume 18 , Number  3
Pages  229 - 243

Thomas A. Randall , 1 Rex A. Dwyer , 1 Edgar Huitema , 2 Katinka Beyer , 3 Cristina Cvitanich , 4 Hemant Kelkar , 1 Audrey M. V. Ah Fong , 4 Krista Gates , 1 Samuel Roberts , 4 Einat Yatzkan , 1 Thomas Gaffney , 1 Marcus Law , 1 Antonino Testa , 2 Trudy Torto-Alalibo , 2 Meng Zhang , 5 Li Zheng , 1 Elisabeth Mueller , 6 John Windass , 6 Andres Binder , 7 Paul R. J. Birch , 8 Ulrich Gisi , 7 Francine Govers , 9 Neil A. Gow , 10 Felix Mauch , 11 Pieter van West , 10 Mark E. Waugh , 12 Jun Yu , 5 Thomas Boller , 3 Sophien Kamoun , 2 Stephen T. Lam , 1 and Howard S. Judelson 4

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


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Accepted 7 November 2004.

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.



© 2005 The American Phytopathological Society