title: Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.
abstract: Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors.
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA.
authors.forename: Allison R
authors.initials: AR
authors.lastname: Schwartz
authors.affiliation: Department of Plant Pathology, University of Florida Gainesville, FL, USA.
authors.forename: Neha
authors.initials: N
authors.lastname: Potnis
authors.affiliation: Department of Plant Pathology, University of Florida Gainesville, FL, USA.
authors.forename: Sujan
authors.initials: S
authors.lastname: Timilsina
authors.affiliation: Donald Danforth Plant Science Center St. Louis, MO, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Wilson
authors.affiliation: Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil.
authors.forename: José
authors.initials: J
authors.lastname: Patané
authors.affiliation: Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil.
authors.forename: Joaquim
authors.initials: J
authors.lastname: Martins
authors.affiliation: Department of Plant Pathology, University of Florida Gainesville, FL, USA.
authors.forename: Gerald V
authors.initials: GV
authors.lastname: Minsavage
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: Dahlbeck
authors.affiliation: Department of Plant Pathology, Kansas State University Manhattan, KS, USA.
authors.forename: Alina
authors.initials: A
authors.lastname: Akhunova
authors.affiliation: School of Computing, Federal University of Mato Grosso do Sul Campo Grande, Brazil.
authors.forename: Nalvo
authors.initials: N
authors.lastname: Almeida
authors.affiliation: Gulf Coast Research and Education Center, University of Florida Wimauma, FL, USA.
authors.forename: Gary E
authors.initials: GE
authors.lastname: Vallad
authors.affiliation: Department of Plant Pathology, University of Wisconsin, Madison Madison, WI, USA.
authors.forename: Jeri D
authors.initials: JD
authors.lastname: Barak
authors.affiliation: Department of Plant Pathology, Kansas State University Manhattan, KS, USA.
authors.forename: Frank F
authors.initials: FF
authors.lastname: White
authors.affiliation: Department of Plant Pathology, Ohio Agricultural Research and Development Center Wooster, MA, USA.
authors.forename: Sally A
authors.initials: SA
authors.lastname: Miller
authors.affiliation: Department of Plant Pathology, NC State University Raleigh, NC, USA.
authors.forename: David
authors.initials: D
authors.lastname: Ritchie
authors.affiliation: Department of Plant Pathology, University of Florida Gainesville, FL, USA.
authors.forename: Erica
authors.initials: E
authors.lastname: Goss
authors.affiliation: Donald Danforth Plant Science Center St. Louis, MO, USA.
authors.forename: Rebecca S
authors.initials: RS
authors.lastname: Bart
authors.affiliation: Department of Biochemistry, Institute of Chemistry, University of São Paulo São Paulo, Brazil ; Virginia Bioinformatics Institute, Virginia Tech Blacksburg, VA, USA.
authors.forename: João C
authors.initials: JC
authors.lastname: Setubal
authors.affiliation: Department of Plant Pathology, University of Florida Gainesville, FL, USA.
authors.forename: Jeffrey B
authors.initials: JB
authors.lastname: Jones
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley Berkeley, CA, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Staskawicz
keywords: AvrBsT; Xanthomonas; XopQ; bacterial spot disease; host specificity; phylogenomics; type III effector repertoire