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Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

October 2012 , Volume 25 , Number  10
Pages  1,350 - 1,360

Kurt H. Lamour,1 Joann Mudge,2 Daniel Gobena,1 Oscar P. Hurtado-Gonzales,3 Jeremy Schmutz,4,5 Alan Kuo,4 Neil A. Miller,6 Brandon J. Rice,2 Sylvain Raffaele,7 Liliana M. Cano,7 Arvind K. Bharti,2 Ryan S. Donahoo,8 Sabra Finley,1 Edgar Huitema,9,10 Jon Hulvey,11 Darren Platt,4 Asaf Salamov,4 Alon Savidor,12 Rahul Sharma,13,14,15 Remco Stam,9,10 Dylan Storey,1 Marco Thines,13,14,15 Joe Win,7 Brian J. Haas,16 Darrell L. Dinwiddie,6,17 Jerry Jenkins,4,5 James R. Knight,18 Jason P. Affourtit,18 Cliff S. Han,19 Olga Chertkov,19 Erika A. Lindquist,4 Chris Detter,19 Igor V. Grigoriev,5 Sophien Kamoun,7 and Stephen F. Kingsmore6,17

1University of Tennessee, Knoxville 37996, U.S.A.; 2National Center for Genome Resources, Santa Fe, NM 87505, U.S.A.; 3Pioneer Hi-Bred International, Johnston, IA 50131, U.S.A.; 4United States Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, U.S.A.; 5Hudson Alpha Institute of Biotechnology, Huntsville, AL 35806, U.S.A.; 6Children's Mercy Hospital, Kansas City, MO 64108, U.S.A.; 7The Sainsbury Laboratory, Norwich NR4 7UH, U.K.; 8University of Florida, IFAS-SWFREC, Immokalee 34142, U.S.A.; 9Division of Plant Science, University of Dundee, Invergowrie, Dundee DD2 5DA, U.K.; 10Plant Pathology Program, James Hutton Institute, Invergowrie, Dundee DD2 5DA, U.K.; 11University of Massachusetts-Amherst, Department of Plant, Soil, and Insect Sciences, Amherst 01003, U.S.A.; 12Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv 69978, Israel; 13Biodiversity and Climate Research Centre, D-60325 Frankfurt am Main, Germany; 14Senckenberg Gesellschaft für Naturforschung, D-60325 Frankfurt am Main, Germany; 15Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, D-60323, Frankfurt am Main, Germany; 16Broad Institute, Cambridge, MA 02142, U.S.A.; 17School of Medicine, University of Missouri-Kansas City, Kansas City, MO 64108, U.S.A.; 18Roche Applied Science, Branford, Connecticut 06405, U.S.A.; 19Los Alamos National Laboratory, Department of Energy Joint Genome Institute, Los Alamos, NM 87545, U.S.A.

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Accepted 7 June 2012.

The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

© 2012 The American Phytopathological Society