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Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Neha Potnis1, Ksenia Krasileva2, Virginia Chow3, Nalvo F Almeida4, Prabhu B Patil5, Robert P Ryan6, Molly Sharlach2, Franklin Behlau17, J Max Dow6, MT Momol1, Frank F White8, James F Preston3, Boris A Vinatzer9, Ralf Koebnik10, João C Setubal11, David J Norman12, Brian J Staskawicz2 and Jeffrey B Jones1*

  • * Corresponding author: Jeffrey B Jones

  • † Equal contributors

Author Affiliations

1 Department of Plant Pathology, University of Florida, Gainesville, FL, USA

2 Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA

3 Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA

4 Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil

5 Institute of Microbial Technology (CSIR), Sector 39A, Chandigarh 160036, India

6 BIOMERIT Research Centre, Biosciences Institute, University College Cork, Ireland

7 Fundecitrus - Fundo de Defesa da Citricultura, Av. Adhemar Pereira de Barros, 201, 14807-040 Araraquara, SP. Brazil

8 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA

9 Department of Plant Pathology, Physiology and Weed Sciences, Virginia Tech, Blacksburg, VA, USA

10 Laboratoire Génome et Développement des Plantes, IRD-CNRS-Université-de Perpignan, Centre IRD, 911 Av. Agropolis, BP64501, 34394 Montpellier, France

11 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA

12 Institute of Food and Agricultural Sciences, Mid-Florida Research & Education Center, University of Florida, Apopka, FL, USA

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BMC Genomics 2011, 12:146  doi:10.1186/1471-2164-12-146

Published: 11 March 2011



Bacterial spot of tomato and pepper is caused by four Xanthomonas 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, Xanthomonas euvesicatoria (Xcv) 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.


We sequenced the genomes of X. vesicatoria (Xv) strain 1111 (ATCC 35937), X. perforans (Xp) strain 91-118 and X. gardneri (Xg) strain 101 (ATCC 19865). The genomes were compared with each other and with the previously sequenced Xcv 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 Xg strain 101 and Xv 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 Xcv. 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.


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.