Wicker, T., Institute of Plant Biology, University of Zurich, Zurich, Switzerland
Oberhaensli, S., Institute of Plant Biology, University of Zurich, Zurich, Switzerland
Parlange, F., Institute of Plant Biology, University of Zurich, Zurich, Switzerland
Buchmann, J.P., Institute of Plant Biology, University of Zurich, Zurich, Switzerland, MTT/BI Plant Genomics Laboratory, University of Helsinki, Helsinki, Finland
Shatalina, M., Institute of Plant Biology, University of Zurich, Zurich, Switzerland
Roffler, S., Institute of Plant Biology, University of Zurich, Zurich, Switzerland
Ben-David, R., Institute of Plant Biology, University of Zurich, Zurich, Switzerland, MTT/BI Plant Genomics Laboratory, University of Helsinki, Helsinki, Finland
Doležel, J., Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc-Holice, Czech Republic
Šimková, H., Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Olomouc-Holice, Czech Republic
Schulze-Lefert, P., Department of Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
Spanu, P.D., Department of Life Sciences, Imperial College London, London, United Kingdom
Bruggmann, R., Department of Biology, University of Bern, Bern, Switzerland, Department of Agronomy and Natural Resources, Volcani Center, Institute of Plant Sciences, Agronomy and Natural Resources (ARO), Bet Dagan, Israel
Amselem, J., Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France
Quesneville, H., Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Versailles, France
Ver Loren Van Themaat, E., Department of Plant Microbe Interactions, Max-Planck Institute for Plant Breeding Research, Cologne, Germany
Paape, T., Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
Shimizu, K.K., Institute of Plant Biology, University of Zurich, Zurich, Switzerland, Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
Keller, B., Institute of Plant Biology, University of Zurich, Zurich, Switzerland

Wheat powdery mildew, Blumeria graminis forma specialis tritici, is a devastating fungal pathogen with a poorly understood evolutionary history. Here we report the draft genome sequence of wheat powdery mildew, the resequencing of three additional isolates from different geographic regions and comparative analyses with the barley powdery mildew genome. Our comparative genomic analyses identified 602 candidate effector genes, with many showing evidence of positive selection. We characterize patterns of genetic diversity and suggest that mildew genomes are mosaics of ancient haplogroups that existed before wheat domestication. The patterns of diversity in modern isolates suggest that there was no pronounced loss of genetic diversity upon formation of the new host bread wheat 10,000 years ago. We conclude that the ready adaptation of B. graminis f.sp. tritici to the new host species was based on a diverse haplotype pool that provided great genetic potential for pathogen variation. © 2013 Nature America, Inc. All rights reserved.