Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

<p>Abstract</p> <p>Background</p> <p>Bacterial spot of tomato and pepper is caused by four <it>Xanthomonas </it>species and is a major plant disease in warm humid climates. The four species are distinct from each other based on physiological and molecular characteristics. The genome sequence of strain 85-10, a member of one of the species, <it>Xanthomonas euvesicatoria </it>(<it>Xcv</it>) has been previously reported. To determine the relationship of the four species at the genome level and to investigate the molecular basis of their virulence and differing host ranges, draft genomic sequences of members of the other three species were determined and compared to strain 85-10.</p> <p>Results</p> <p>We sequenced the genomes of <it>X. vesicatoria </it>(<it>Xv</it>) strain 1111 (ATCC 35937), <it>X. perforans </it>(<it>Xp</it>) strain 91-118 and <it>X. gardneri </it>(<it>Xg</it>) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced <it>Xcv </it>strain 85-10. In addition, the molecular features were predicted that may be required for pathogenicity including the type III secretion apparatus, type III effectors, other secretion systems, quorum sensing systems, adhesins, extracellular polysaccharide, and lipopolysaccharide determinants. Several novel type III effectors from <it>Xg </it>strain 101 and <it>Xv </it>strain 1111 genomes were computationally identified and their translocation was validated using a reporter gene assay. A homolog to Ax21, the elicitor of XA21-mediated resistance in rice, and a functional Ax21 sulfation system were identified in <it>Xcv</it>. Genes encoding proteins with functions mediated by type II and type IV secretion systems have also been compared, including enzymes involved in cell wall deconstruction, as contributors to pathogenicity.</p> <p>Conclusions</p> <p>Comparative genomic analyses revealed considerable diversity among bacterial spot pathogens, providing new insights into differences and similarities that may explain the diverse nature of these strains. Genes specific to pepper pathogens, such as the O-antigen of the lipopolysaccharide cluster, and genes unique to individual strains, such as novel type III effectors and bacteriocin genes, have been identified providing new clues for our understanding of pathogen virulence, aggressiveness, and host preference. These analyses will aid in efforts towards breeding for broad and durable resistance in economically important tomato and pepper cultivars.</p

Mapping and Identification of the RXopJ4 Resistance Gene and the Search for New Sources of Durable Resistance to Bacterial Spot Disease of Tomato

Bacterial spot of tomato (Solanum lycopersicum) is a devastating disease that severely limits yields in important tomato-­growing regions, including the southeastern United States, where the predominant bacterial spot pathogen species is Xanthomonas perforans. Attempts to control the disease with antibiotics and copper-­based pesticides have led to the selection of bacterial strains that are resistant to these treatments. Therefore, we turn to genetic sources of resistance as a sustainable path to reduce crop losses to bacterial spot disease.This work describes the fine mapping and identification of the RXopJ4 disease resistance locus from the wild tomato relative Solanum pennellii LA716. RXopJ4 resistance depends on recognition of the X. perforans type III effector protein XopJ4. We developed a collection of fourteen molecular markers to map on a segregating F2 population from a cross between the susceptible parent S. lycopersicum FL8000 and the resistant parent RXopJ4 8000 OC7. In the F2 population, a 190-­kb segment on chromosome 6 cosegregated with resistance. This fine mapping enabled the identification of three RXopJ4 candidate genes, all of which encode putative intracellular serine-­threonine protein kinases. Transient coexpression of the XopJ4 effector with each kinase revealed a promising RXopJ4 candidate gene that triggered a hypersensitive response (HR) in Nicotiana benthamiana. Mutations in both XopJ4 and RXopJ4 identified conserved residues required for recognition and the induction of a hypersensitive cell death phenotype. Homozygous transgenic tomato plants containing the RXopJ4 candidate gene have been constructed and will soon be evaluated for disease resistance.In addition, we undertook a genomic survey of fourteen X. perforans field isolates from all five fresh market tomato production zones of Florida, revealing a preliminary set of core type III effectors common to all isolates. We used this set of core effectors to inform a search for new sources of resistance to bacterial spot disease and identified accessions of Nicotiana and Solanum americanum that recognize core X. perforans effectors. Finally, we performed disease assays on 224 wild tomato accessions and found nine potential sources of bacterial spot disease resistance