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

    Affiliations
    Authors and Affiliations
    • Kurt H. Lamour1
    • Joann Mudge2
    • Daniel Gobena1
    • Oscar P. Hurtado-Gonzales3
    • Jeremy Schmutz4 5
    • Alan Kuo4
    • Neil A. Miller6
    • Brandon J. Rice2
    • Sylvain Raffaele7
    • Liliana M. Cano7
    • Arvind K. Bharti2
    • Ryan S. Donahoo8
    • Sabra Finley1
    • Edgar Huitema9 10
    • Jon Hulvey11
    • Darren Platt4
    • Asaf Salamov4
    • Alon Savidor12
    • Rahul Sharma13 14 15
    • Remco Stam9 10
    • Dylan Storey1
    • Marco Thines13 14 15
    • Joe Win7
    • Brian J. Haas16
    • Darrell L. Dinwiddie6 17
    • Jerry Jenkins4 5
    • James R. Knight18
    • Jason P. Affourtit18
    • Cliff S. Han19
    • Olga Chertkov19
    • Erika A. Lindquist4
    • Chris Detter19
    • Igor V. Grigoriev5
    • Sophien Kamoun7
    • Stephen F. Kingsmore6 17

      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.