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.

TALE-induced bHLH transcription factors that activate a pectate lyase contribute to water soaking in bacterial spot of tomato

“…We observed a dark, apoplastic water soaking when X. gardneri, but not XgΔavrHah1, was infiltrated into tomato, pepper, and Nicotiana benthamiana, the known hosts of X. gardneri (24). This symptom was enhanced when infected plants were placed in a mist chamber.…”

“…Xg153 (SM194-10) is from a collection of X. gardneri strains isolated between 2010 and 2012 in diseased tomato fields in Ohio and Michigan. Activation of Bs3 in pepper 30R, Southern blot analysis, and Sanger sequencing confirmed the identity of the single TALE in Xg153 as avrHah1 (24). All X. gardneri mutants were constructed in the Xg153 background.…”

Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas

“…Interestingly, in several Xanthomonas species, a correlation was observed between pathovars and the composition of T3E repertoires (57)(58)(59), further suggesting that T3E repertoires play a major role in determining the host specificity of strains. A role of two T3Es (AvrBsT and XopQ) in shaping the host range of Xanthomonas perforans among solanaceous species has recently been revealed (117). However, within pathovars, the picture is much more complicated: Whereas in some cases T3E variations observed within a pathovar were linked to the host of isolation of the strains (57,58), in other cases no correlation could be observed between T3E variations and pathotypes or races (12,51,55,112).…”

Induction of defence-related enzymes in tomato (Solanum lycopersicum) plants treated with Bacillus subtilis CBR05 against Xanthomonas campestris pv. vesicatoria

“…The genus Xanthomonas comprises numerous pathogenic species infecting approximately 400 different host plants, resulting in significant losses in economically important crops worldwide (Hayward, 1993;Schwartz et al, 2015;Timilsina et al, 2015, Wu et al 2015Areas et al 2015). Studies have shown a wide range of incongruity among Xanthomonas strains that cause bacterial spot disease on tomato (Solanum lycopersicum) and pepper (Capsicum annuum).…”