title: Analysis of Sequenced Genomes of Xanthomonas perforans Identifies Candidate Targets for Resistance Breeding in Tomato.
abstract: Bacterial disease management is a challenge for modern agriculture due to rapid changes in pathogen populations. Genome sequences for hosts and pathogens provide detailed information that facilitates effector-based breeding strategies. Tomato genotypes have gene-for-gene resistance to the bacterial spot pathogen Xanthomonas perforans. The bacterial spot populations in Florida shifted from tomato race 3 to 4, such that the corresponding tomato resistance gene no longer recognizes the effector protein AvrXv3. Genome sequencing showed variation in effector profiles among race 4 strains collected in 2006 and 2012 and compared with a race 3 strain collected in 1991. We examined variation in putative targets of resistance among Florida strains of X. perforans collected from 1991 to 2006. Consistent with race change, avrXv3 was present in race 3 strains but nonfunctional in race 4 strains due to multiple independent mutations. Effectors xopJ4 and avrBs2 were unchanged in all strains. The effector avrBsT was absent in race 3 strains collected in the 1990s but present in race 3 strains collected in 2006 and nearly all race 4 strains. These changes in effector profiles suggest that xopJ4 and avrBsT are currently the best targets for resistance breeding against bacterial spot in tomato.
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Sujan
authors.initials: S
authors.lastname: Timilsina
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Peter
authors.initials: P
authors.lastname: Abrahamian
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Neha
authors.initials: N
authors.lastname: Potnis
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Gerald V
authors.initials: GV
authors.lastname: Minsavage
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Frank F
authors.initials: FF
authors.lastname: White
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Staskawicz
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Jones
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Gary E
authors.initials: GE
authors.lastname: Vallad
authors.affiliation: First, fourth, fifth, seventh, and ninth authors: Department of Plant Pathology, University of Florida, Gainesville; first, second and eighth authors: Gulf Coast Research and Education Center, University of Florida, Wimauma; third author: U.S. Vegetable Laboratory, 2700 Savannah Highway, USDA, Charleston, SC; sixth author: Department of Plant and Microbial Biology, University of California, Berkeley; and ninth author: Emerging Pathogens Institute, University of Florida, Gainesville.
authors.forename: Erica M
authors.initials: EM
authors.lastname: Goss
mesh_terms: D001483:Base Sequence; D001947:Breeding; D016680:Genome, Bacterial / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D018551:Solanum lycopersicum / Q000235:genetics* / Q000276:immunology* / Q000382:microbiology; D010935:Plant Diseases / Q000276:immunology* / Q000382:microbiology; D017422:Sequence Analysis, DNA; D014974:Xanthomonas / Q000235:genetics*
keywords: avirulence; recombination; type III effectors