1. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici
- Author
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Darren Platt, Darrell L. Dinwiddie, Alon Savidor, Asaf Salamov, Stephen F. Kingsmore, Chris Detter, Jason P. Affourtit, Dylan Storey, Ryan S. Donahoo, Brian J. Haas, Sophien Kamoun, Joann Mudge, Sabra Finley, Olga Chertkov, Daniel Gobena, Jeremy Schmutz, Igor V. Grigoriev, Alan Kuo, Erika Lindquist, Sylvain Raffaele, Jerry Jenkins, James R. Knight, Edgar Huitema, Cliff Han, Brandon J. Rice, Rahul Sharma, Joe Win, Oscar P. Hurtado-Gonzales, Liliana M. Cano, Neil A. Miller, Kurt Lamour, Arvind K. Bharti, Marco Thines, Jon Hulvey, Remco Stam, University of Tennessee System, Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), Pioneer Hi-Bred International, United States Department of Energy, Joint Genome Institute (JGI), Hudson Alpha Institute for Biotechnology, Children’s Mercy Hospital, Mercy University Hospital, The Sainsbury Laboratory [Norwich] (TSL), IFASSWFREC, University of Florida [Gainesville] (UF), Division of Plant Science, University of Dundee, Plant Pathology Program, The James Hutton Institute, Department of Plant, Soil, and Insect Sciences, University of Massachusetts System (UMASS), Department of Molecular Biology and Ecology of Plants, Tel Aviv University [Tel Aviv], Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Goethe-Universität Frankfurt am Main-Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association, Institute of Ecology, Evolution and Diversity, Department of Biological Sciences, Goethe-Universität Frankfurt am Main, Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], School of Medicine, University of Patras [Greece], Roche Applied Science, Department of Energy, and Great Lakes Bioenergy Research Center (GLBRC)
- Subjects
0106 biological sciences ,Phytophthora ,Genotype ,Physiology ,Genetic Linkage ,Outcrossing ,champignon pathogène ,Biology ,01 natural sciences ,Genome ,Polymorphism, Single Nucleotide ,Article ,Loss of heterozygosity ,03 medical and health sciences ,Cucurbita ,Genetic variation ,protection des plantes ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,fungal pathogen ,030304 developmental biology ,Plant Diseases ,2. Zero hunger ,Oomycete ,Genetics ,0303 health sciences ,fungi ,Chromosome Mapping ,General Medicine ,biology.organism_classification ,Adaptation, Physiological ,Phytophthora capsici ,Gene Expression Regulation ,Capsicum ,Agronomy and Crop Science ,phytophthora capsici ,010606 plant biology & botany ,crop protection - Abstract
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/genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) and higher levels of SNVs than those reported for humans, plants, and P. infestans. 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 (SNV) 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.
- Published
- 2012