Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
Kurt H Lamour
(1)
,
Joann Mudge
(2)
,
Daniel Gobena
(1)
,
Oscar P Hurtado-Gonzales
(3)
,
Jeremy Schmutz
(4, 5, 6)
,
Alan Kuo
(4, 5)
,
Neil A Miller
(7)
,
Brandon J Rice
(2)
,
Sylvain Raffaele
(8)
,
Liliana M Cano
(8)
,
Arvind K Bharti
(2)
,
Ryan S Donahoo
(9)
,
Sabra Finley
(1)
,
Edgar Huitema
(10, 11)
,
Jon Hulvey
(12)
,
Darren Platt
(4, 5)
,
Asaf Salamov
(4, 5)
,
Alon Savidor
(13)
,
Rahul Sharma
(14, 15, 16)
,
Remco Stam
(10, 11)
,
Dylan Storey
(1)
,
Marco Thines
(14, 15, 16)
,
Joe Win
(8)
,
Brian J Haas
(17)
,
Darrell L Dinwiddie
(7, 18)
,
Jerry Jenkins
(4, 5, 6)
,
James R Knight
(19)
,
Jason P Affourtit
(19)
,
Cliff S Han
(20, 5)
,
Olga Chertkov
(20, 5)
,
Erika A Lindquist
(4, 5)
,
Chris Detter
(20, 5)
,
Igor V Grigoriev
(6)
,
Sophien Kamoun
(8)
,
Stephen F Kingsmore
(7, 18)
1
University of Tennessee System
2 IRD [Nouvelle-Calédonie] - Institut de Recherche pour le Développement
3 Pioneer Hi-Bred International
4 United States Department of Energy
5 JGI - Joint Genome Institute
6 Hudson Alpha Institute for Biotechnology
7 Children’s Mercy Hospital
8 TSL - The Sainsbury Laboratory [Norwich]
9 IFASSWFREC
10 Division of Plant Science
11 Plant Pathology Program
12 Department of Plant, Soil, and Insect Sciences
13 Department of Molecular Biology and Ecology of Plants
14 SBiK-F - Senckenberg Biodiversity and Climate Research Centre
15 Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung
16 Institute of Ecology, Evolution and Diversity, Department of Biological Sciences,
17 BROAD INSTITUTE - Broad Institute of MIT and Harvard
18 School of Medicine
19 Roche Applied Science
20 Department of Energy
2 IRD [Nouvelle-Calédonie] - Institut de Recherche pour le Développement
3 Pioneer Hi-Bred International
4 United States Department of Energy
5 JGI - Joint Genome Institute
6 Hudson Alpha Institute for Biotechnology
7 Children’s Mercy Hospital
8 TSL - The Sainsbury Laboratory [Norwich]
9 IFASSWFREC
10 Division of Plant Science
11 Plant Pathology Program
12 Department of Plant, Soil, and Insect Sciences
13 Department of Molecular Biology and Ecology of Plants
14 SBiK-F - Senckenberg Biodiversity and Climate Research Centre
15 Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung
16 Institute of Ecology, Evolution and Diversity, Department of Biological Sciences,
17 BROAD INSTITUTE - Broad Institute of MIT and Harvard
18 School of Medicine
19 Roche Applied Science
20 Department of Energy
Alan Kuo
- Fonction : Auteur
- PersonId : 770173
- ORCID : 0000-0003-3514-3530
Sylvain Raffaele
- Fonction : Auteur
- PersonId : 1196494
- ORCID : 0000-0002-2442-9632
Joe Win
- Fonction : Auteur
- PersonId : 776794
- ORCID : 0000-0002-9851-2404
Sophien Kamoun
- Fonction : Auteur
- PersonId : 770142
- ORCID : 0000-0002-0290-0315
- IdRef : 152505393
Résumé
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.