Skip to main content
SpringerLink
Log in

The Genomics of Xanthomonas oryzae

  • Chapter
  • First Online:
Genomics of Plant-Associated Bacteria

Abstract

Xanthomonas oryzae pathovars oryzae and oryzicola cause bacterial leaf blight and bacterial leaf streak of rice, respectively, two diseases that pose a significant threat to global rice yields. The first four complete genome sequences of X. oryzae strains yielded a wealth of information about virulence factor content, mobile genetic elements, and taxonomic differences among strains of X. oryzae pathovars oryzae and oryzicola. The genomes have been applied in systematic studies of gene function and expression and in comparative analyses of the differences between pathovars. X. oryzae genome sequences facilitated the current understanding of the evolutionary history and diversity of type III secreted effectors, including transcriptional activator-like (TAL) effectors, and contributed to the discovery of the code-mediating TAL effector recognition specificity. The genomes have also been instrumental in the development of improved tools for epidemiological typing and disease diagnostics. This chapter focuses on the contributions of genomic sequencing projects to the understanding of X. oryzae biology and diversity and the future questions that genomics will help address.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
eBook
USD 16.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Adachi N, Oku T (2000) PCR-mediated detection of Xanthomonas oryzae pv. oryzae by amplification of the 16S-23S rDNA spacer region sequence. J Gen Plant Pathol 66:303–309

    CAS  Google Scholar 

  • Akimoto-Tomiyama C, Furutani A, Tsuge S, Washington EJ, Nishizawa Y, Minami E, Ochiai H (2012) XopR, a type III effector secreted by Xanthomonas oryzae pv. oryzae, suppresses microbe-associated molecular pattern-triggered immunity in Arabidopsis thaliana. Mol Plant Microbe Interact 25:505–514

    CAS  PubMed  Google Scholar 

  • Aldrick SJ, Buddenhagen IW, Reddy APK (1973) The occurrence of bacterial leaf blight in wild and cultivated rice in Northern Australia. Crop Pasture Sci 24:219–227

    Google Scholar 

  • Awoderu VA, John VT (1984) Occurrence of bacterial leaf blight on rice in four Sahelian countries: Senegal, Mali, Niger and Upper Volta. WARDA Technol Newsl 5:36–39

    Google Scholar 

  • Bai J, Choi SH, Ponciano G, Leung H, Leach JE (2000) Xanthomonas oryzae pv. oryzae avirulence genes contribute differently and specifically to pathogen aggressiveness. Mol Plant Microbe Interact 13:1322–1329

    CAS  PubMed  Google Scholar 

  • Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant Microbe Interact 21:859–868

    CAS  PubMed  Google Scholar 

  • Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS, Cherkis K, Roach J, Grant SR, Jones CD, Dangl JL (2012) Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Path 7(7):e1002132

    Google Scholar 

  • Bart R, Cohn M, Kassen A, McCallum EJ, Shybut M, Petriello A, Krasileva K, Dahlbeck D, Medina C, Alicai T, Kumar L, Moreira LM, Neto JR, Verdier V, Santana MA, Kositcharoenkul N, Vanderschuren H, Gruissem W, Bernal A, Staskawicz BJ (2012) High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance. Proc Natl Acad Sci USA 109(28):E1972–E1979. doi:10.1073/pnas.1208003109

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bhasin H, Bhatia D, Raghuvanshi S, Lore JS, Sahi GK, Kaur B, Vikal Y, Singh K (2012) New PCR-based sequence-tagged site marker for bacterial blight resistance gene Xa38 of rice. Mol Breeding 30:607–611

    CAS  Google Scholar 

  • Bichsel M, Barbour AD, Wagner A (2013) Estimating the fitness effect of an insertion sequence. J Math Biol 66:95–114

    PubMed  Google Scholar 

  • Blair MW, Garris AJ, Iyer AS, Chapman B, Kresovich S, McCouch SR (2003) High resolution genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor Appl Genet 107(1):62–73

    CAS  PubMed  Google Scholar 

  • Blanvillain S, Meyer D, Boulanger A, Lautier M, Guynet C, Denance N, Vasse J, Lauber E, Arlat M (2007) Plant carbohydrate scavenging through TonB-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria. PLoS ONE 2:e224

    PubMed Central  PubMed  Google Scholar 

  • Block A, Alfano JR (2011) Plant targets for Pseudomonas syringae type III effectors: virulence targets or guarded decoys? Curr Opin Microbiol 14(1):39–46. doi:10.1016/j.mib.2010.12.011

    CAS  PubMed Central  PubMed  Google Scholar 

  • Boch J, Bonas U (2010) Xanthomonas AvrBs3 family-type III effectors: discovery and function. Annu Rev Phytopathol 48:419–436. doi:10.1146/annurev-phyto-080508-081936

    CAS  PubMed  Google Scholar 

  • Boch J, Scholze H, Schornack S, Landgraf A, Hahn S, Kay S, Lahaye T, Nickstadt A, Bonas U (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326:1509–1512. doi:10.1126/science.1178811

    CAS  PubMed  Google Scholar 

  • Bogdanove AJ, Koebnik R, Lu H, Furutani A, Angiuoli SV, Patil PB, Van Sluys MA, Ryan RP, Meyer DF, Han SW, Aparna G, Rajaram M, Delcher AL, Phillippy AM, Puiu D, Schatz MC, Shumway M, Sommer DD, Trapnell C, Benahmed F, Dimitrov G, Madupu R, Radune D, Sullivan S, Jha G, Ishihara H, Lee SW, Pandey A, Sharma V, Sriariyanun M, Szurek B, Vera-Cruz CM, Dorman KS, Ronald PC, Verdier V, Dow JM, Sonti RV, Tsuge S, Brendel VP, Rabinowicz PD, Leach JE, White FF, Salzberg SL (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. J Bacteriol 193(19):5450–5464. doi:10.1128/JB.05262-11

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bogdanove AJ, Schornack S, Lahaye T (2010) TAL effectors: finding plant genes for disease and defense. Curr Opin Plant Biol 13:394–401. doi:10.1016/j.pbi.2010.04.010

    CAS  PubMed  Google Scholar 

  • Bonas U, Stall RE, Staskawicz B (1989) Genetic and structural characterization of the avirulence gene avrBs3 from Xanthomonas campestris pv. vesicatoria. Mol Gen Genet 218:127–136

    CAS  PubMed  Google Scholar 

  • Briggs AW, Rios X, Chari R, Yang L, Zhang F, Mali P, Church GM (2012) Iterative capped assembly: rapid and scalable synthesis of repeat-module DNA such as TAL effectors from individual monomers. Nucleic Acids Res 40:e117

    CAS  PubMed Central  PubMed  Google Scholar 

  • Buddenhagen IW (1985) Rice disease evaluation in Madagascar. Int Rice Commiss Newsl 34:74–78

    Google Scholar 

  • Chamnongpol S, Vattanaviboon P, Loprasert S, Mongkolsuk S (1995) Atypical oxidative stress regulation of a Xanthomonas oryzae pv. oryzae monofunctional catalase. Can J Microbiol 41:541–547

    CAS  Google Scholar 

  • Chan JZM, Pallen MJ, Oppenheim B, Constantinidou C (2012) Genome sequencing in clinical microbiology. Nat Biotechnol 30 (11):1068

    Google Scholar 

  • Chatterjee S, Sankaranarayanan R, Sonti RV (2003) PhyA, a secreted protein of Xanthomonas oryzae pv. oryzae, is required for optimum virulence and growth on phytic acid as a sole phosphate source. Mol Plant Microbe Interact 16(11):973–982

    CAS  PubMed  Google Scholar 

  • Chatterjee S, Sonti RV (2002) rpfF mutants of Xanthomonas oryzae pv. oryzae are deficient for virulence and growth under low iron conditions. Mol Plant Microbe Interact 15:463–471

    CAS  PubMed  Google Scholar 

  • Chatterjee S, Sonti RV (2005) Virulence deficiency caused by a transposon insertion in the purH gene of Xanthomonas oryzae pv. oryzae. Can J Microbiol 51(7):575–581

    CAS  PubMed  Google Scholar 

  • Chaudhary SU, Iqbal J, Hussain M (2012) Effectiveness of different fungicides and antibiotics against bacterial leaf blight in rice. J Agric Res 50:109–117

    Google Scholar 

  • Chen C, Zheng W, Huang X, Zhang D, Lin XQ (2006) Major QTL conferring resistance to bacterial leaf streak. Agric Sci China 5:216–220

    CAS  Google Scholar 

  • Chen LQ, Qu XQ, Hou BH, Sosso D, Osorio S, Fernie AR, Frommer WB (2012) Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science 335:207–211

    CAS  PubMed  Google Scholar 

  • Cheong H, Kim C-Y, Jeon J-S, Lee B-M, Moon JS, Hwang I (2013) Xanthomonas oryzae pv. oryzae type III effector XopN targets OsVOZ2 and a putative thiamine synthase as a virulence factor in rice. PLoS ONE 8(9):e73346

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chin C-S, Sorenson J, Harris JB, Robins WP, Charles RC, Jean-Charles RR, Bullard J, Webster DR, Kasarskis A, Peluso P, Paxinos EE, Yamaichi Y, Calderwood SB, Mekalanos JJ, Schadt EE, Waldor MK (2011) The origin of the Haitian cholera outbreak strain. New Eng J Med 364(1):33–42. doi:10.1056/NEJMoa1012928

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chittoor JM, Leach JE, White FF (1997) Differential induction of a peroxidase gene family during infection of rice by Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 10:861–871

    CAS  PubMed  Google Scholar 

  • Cho MS, Kang MJ, Kim CK, Seol Y-J, Hahn JH, Park SC, Hwang DJ, Ahn T-Y, Park DH, Lim CK (2011) Sensitive and specific detection of Xanthomonas oryzae pv. oryzae by real-time bio-PCR using pathovar-specific primers based on an rhs family gene. Plant Dis 95:589–594

    CAS  Google Scholar 

  • Choi SH, Leach JE (1994) Genetic manipulation of Xanthomonas oryzae pv. oryzae. Int Rice Res Notes 19:31–32

    Google Scholar 

  • Cunnac S, Chakravarthy S, Kvitko BH, Russell AB, Martin GB, Collmer A (2011) Genetic disassembly and combinatorial reassembly identify a minimal functional repertoire of type III effectors in Pseudomonas syringae. Proc Natl Acad Sci USA 108:2975–2980. doi:10.1073/pnas.1013031108 |PII:031108

    CAS  PubMed Central  PubMed  Google Scholar 

  • Daniels MD, Leach JE (1993) Genetics of Xanthomonas. In: Swings JG, Civerolo EL (eds) Xanthomonas. Chapman and Hall, London, pp 301–339

    Google Scholar 

  • Devadath S (1989) Chemical control of bacterial blight of rice. Bacterial blight of rice International Rice Research Institute. Manila, Philippines, pp 89–98

    Google Scholar 

  • Dharmapuri S, Sonti RV (1999) A transposon insertion in the gumG homologue of Xanthomonas oryzae pv. oryzae causes loss of extracellular polysaccharide production and virulence. FEMS Microbiol Lett 179:53–59

    CAS  PubMed  Google Scholar 

  • Doyle EL, Booher NJ, Standage DS, Voytas DF, Brendel VP, VanDyk JK, Bogdanove AJ (2012) TAL effector-nucleotide targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Res 40:W117–W122

    CAS  PubMed Central  PubMed  Google Scholar 

  • Doyle EL, Stoddard BL, Voytas DF, Bogdanove AJ (2013) TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins. Trends Cell Biol. doi:10.1016/j.tcb.2013.04.003

    PubMed  Google Scholar 

  • Driscoll JR (2009) Spoligotyping for molecular epidemiology of the Mycobacterium tuberculosis complex. Methods Mol Biol 551:117–128

    CAS  PubMed  Google Scholar 

  • Fang CT, Ren HC (1959) Further studies on the relationship of Leersia spp. with the bacterial leaf blight and the bacterial leaf streak disease of rice. Acta Phytopathol Sinica 2:004

    Google Scholar 

  • Ferreira-Tonin M, Rodrigues-Neto J, Harakava R, Destefano SAL (2011) Phylogenetic analysis of Xanthomonas based on partial rpoB gene sequences and species differentiation by PCR-RFLP. Int J Syst Evol Microbiol 62:1419–1424

    PubMed  Google Scholar 

  • Furutani A, Nakayama T, Ochiai H, Kaku H, Kubo Y, Tsuge S (2006) Identification of novel HrpXo regulons preceded by two cis-acting elements, a plant-inducible promoter box and a -10 box-like sequence, from the genome database of Xanthomonas oryzae pv. oryzae. FEMS Microbiol Lett 259:133–141

    CAS  PubMed  Google Scholar 

  • Furutani A, Takaoka M, Sanada H, Noguchi Y, Oku T, Tsuno K, Ochiai H, Tsuge S (2009) Identification of novel type III secretion effectors in Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 22:96–106

    CAS  PubMed  Google Scholar 

  • Ghasemie E, Kazempour MN, Padasht F (2008) Isolation and identification of Xathomonas oryzae pv. oryzae the causal agent of bacterial blight of rice in Iran. J Plant Protect Res 48:53–62

    CAS  Google Scholar 

  • Gnanamanickam SS, Priyadarisini VB, Narayanan NN, Vasudevan P, Kavitha S (1999) An overview of bacterial blight disease of rice and strategies for its management. Curr Sci 77(11):1435–1444

    Google Scholar 

  • Goel AK, Rajagopal L, Sonti RV (2001) Pigment and virulence deficiencies associated with mutations in the aroE gene of Xanthomonas oryzae pv. oryzae. Appl Environ Microbiol 67:245–250

    CAS  PubMed Central  PubMed  Google Scholar 

  • Goncalves ER, Rosato YB (2002) Phylogenetic analysis of Xanthomonas species based upon 16S-23S rDNA intergenic spacer sequences. Int J Syst Bacteriol 52:355–361

    CAS  Google Scholar 

  • Gonzalez C, Szurek B, Manceau C, Mathieu T, Sere Y, Verdier V (2007) Molecular and pathotypic characterization of new Xanthomonas oryzae strains from West Africa. Mol Plant Microbe Interact 20:534–546. doi:10.1094/MPMI-20-5-0534

    CAS  PubMed  Google Scholar 

  • Gonzalez JF, Degrassi G, Devescovi G, De Vleesschauwer D, Hafte M, Myers MP, Venturi V (2012) A proteomic study of Xanthomonas oryzae pv. oryzae in rice xylem sap. J Proteomics doi:10.1016/j.jprot.2012.07.019

  • González JF, Myers MP, Venturi V (2012) The inter-kingdom solo OryR regulator of Xanthomonas oryzae is important for motility. Mol Plant Pathol 14:211–221

    PubMed  Google Scholar 

  • Grau J, Wolf A, Reschke M, Bonas U, Posch S, Boch J (2013) Computational predictions provide insights into the biology of TAL effector target sites. PLoS Comput Biol 9:e1002962

    CAS  PubMed Central  PubMed  Google Scholar 

  • Gu K, Yang B, Tian D, Wu L, Wang D, Sreekala C, Yang F, Chu Z, Wang GL, White FF, Yin Z (2005) R gene expression induced by a type-III effector triggers disease resistance in rice. Nature 435(7045):1122–1125

    CAS  PubMed  Google Scholar 

  • Guo A, Leach JE (1989) Examination of rice hydathode water pores exposed to Xanthomonas campestris pv. oryzae. Phytopathology 79(4):433–436

    Google Scholar 

  • Guo W, Cui Y-P, Li Y-R, Che Y-Z, Yuan L, Zou L-F, Zou H-S, Chen G-Y (2012) Identification of seven Xanthomonas oryzae pv. oryzicola genes potentially involved in pathogenesis in rice. Microbiology 158:505–518. doi:10.1099/mic.0.050419-0

    CAS  PubMed  Google Scholar 

  • Hajri A, Brin C, Zhao S, David P, Feng JX, Koebnik R, Szurek B, Verdier V, Boureau T, Poussier S (2012) Multilocus sequence analysis and type III effector repertoire mining provide new insights into the evolutionary history and virulence of Xanthomonas oryzae. Mol Plant Pathol 13(3):288–302. doi:10.1111/j.1364-3703.2011.00745.x

    CAS  PubMed  Google Scholar 

  • Han QD, Chen ZW, Deng Y, Lan T, Guan HZ, Duan YL, Zhou YC, Lin MC, Wu WR (2008) Fine mapping of qBlsr5a, a QTL controlling resistance to bacterial leaf streak in rice. Acta Agron Sin 34:587–590

    CAS  Google Scholar 

  • He WA, Huang DH, Li RB, Qiu YF, Song JD, Yang HN, Zheng JX, Huang YY, Li XQ, Liu C, Zhang YX, Ma ZF, Yang Y (2012) Identification of a resistance gene bls1 to bacterial leaf streak in wild rice Oryza rufipogon Griff. J Integr Ag 11:962–969

    CAS  Google Scholar 

  • Hopkins CM, White FF, Choi SH, Guo A, Leach JE (1992) Identification of a family of avirulence genes from Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 5:451–459

    CAS  PubMed  Google Scholar 

  • Hummel AW, Doyle EL, Bogdanove AJ (2012) Addition of transcription activator-like effector binding sites to a pathogen strain-specific rice bacterial blight resistance gene makes it effective against additional strains and against bacterial leaf streak. New Phytol 195:883–893

    CAS  PubMed  Google Scholar 

  • Ichida H, Maeda K, Ichise H, Matsuyama T, Abe T, Yoneyama K, Koba T (2007) In silco restriction landmark genome scanning analysis of Xanthomonas oryzae pathovar oryzae MAFF 311018. Biochem Biophys Res Commun 363:852–856

    CAS  PubMed  Google Scholar 

  • Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17(12):1348–1354

    CAS  PubMed  Google Scholar 

  • Jacobs JM, Babujee L, Meng F, Milling A, Allen C (2012) The in planta transcriptome of Ralstonia solanacearum: conserved physiological and virulence strategies during bacterial wilt of tomato. mBio 3:e00114–00112. doi:10.1128/mBio.00114-12

  • Jeung JU, Heu SG, Shin MS, Vera Cruz CM, Jena KK (2006) Dynamics of Xanthomonas oryzae pv. oryzae populations in Korea and their relationship to known bacterial blight resistance genes. Phytopathology 96:867–875. doi:10.1094/PHYTO-96-0867

    CAS  PubMed  Google Scholar 

  • Jha G, Rajeshwari R, Sonti RV (2007) Functional interplay between two Xanthomonas oryzae pv. oryzae secretion systems in modulating virulence on rice. Mol Plant Microbe Interact 20(1):31–40

    CAS  PubMed  Google Scholar 

  • Jones RK, Barnes LW, Gonzalez CF, Leach JE, Alvarez AM, Benedict AA (1989) Identification of low virulence strains of Xanthomonas campestris pv. oryzae from rice in the United States. Phytopathology 79:984–990

    CAS  Google Scholar 

  • Kang MJ, Shim JK, Cho MS, Seol YJ, Hahn JH, Hwang DJ, Park DS (2008) Specific detection of Xanthomonas oryzae pv. oryzicola in infected rice plant by use of PCR assay targeting a membrane fusion protein gene. J Microbiol Biotechnol 18:1492

    CAS  PubMed  Google Scholar 

  • Katzen F, Ferreiro DU, Oddo CG, Lelmini MV, Becker A, Pauhler A, Lelpi L (1998) Xanthomonas campestris pv. campestris gum mutants: Effects on xanthan biosynthesis and plant virulence. J Bacteriol 180:1607–1617

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kauffman H, Reddy A, Hsiek S, Merca S (1973) An improved technique for evaluating resistance of rice varieties to Xanthomonas oryzae. Plant Dis Rep 57:537–541

    Google Scholar 

  • Khush GS, Angeles ER (1999) A new gene for resistance to race 6 of bacterial blight in rice, Oryza sativa L. Rice Genet Newsl 16:92–93

    Google Scholar 

  • Kim S, Kim J, Lee B, Cho J (2009) Mutational analysis of the gum gene cluster required for xanthan biosynthesis in Xanthomonas oryzae pv. oryzae. Biotech Lett 31:265–270

    CAS  Google Scholar 

  • Korlach J (2012) Single molecule, Real-Time DNA sequencing yields a clearer picture of biological complexity: Helps scientists close genomes, study linked variants, and detect base modifications. Indust Biotechnol 8(6):333–336

    CAS  Google Scholar 

  • Lang JM, Hamilton JP, Diaz MGQ, Van Sluys MA, Burgos MRG, Cruz CMV, Buell CR, Tisserat NA, Leach JE (2010) Genomics-based diagnostic marker development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. Plant Dis 94:311–319. doi:10.1094/Pdis-94-3-0311

    CAS  Google Scholar 

  • Lang JM, Langlois P, Nguyen MHR, Triplett LR, Purdie L, Holton T, Djikeng A, Vera Cruz CM, Verdier V, Leach JE (2014) Sensitive detection of Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola by loop mediated isothermal amplification. Appl Environ Microbiol Accepted

    Google Scholar 

  • Leach JE, Leung H, Nelson RJ, Mew TW (1995) Population biology of Xanthomonas oryzae pv. oryzae and approaches to its control. Curr Opin Biotechnol 6:298–304

    CAS  Google Scholar 

  • Leach JE, Vera-Cruz CM, Bai J, Leung H (2001) Pathogen fitness penalty as a predictor of durability of disease resistance genes. Annu Rev Phytopathol 39:187–224

    CAS  PubMed  Google Scholar 

  • Leach JE, White FF (1996) Bacterial avirulence genes. Annu Rev Phytopathol 34:153–179

    CAS  PubMed  Google Scholar 

  • Lee BM, Park YJ, Park DS, Kang HW, Kim JG, Song ES, Park IC, Yoon UH, Hahn JH, Koo BS, Lee GB, Kim H, Park HS, Yoon KO, Kim JH, Jung CH, Koh NH, Seo JS, Go SJ (2005) The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res 33:577–586

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lee SW, Han SW, Bartley LE, Ronald PC (2006) Unique characteristics of Xanthomonas oryzae pv. oryzae AvrXa21 and implications for plant innate immunity. Proc Natl Acad Sci USA 103:18395–18400

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lee SW, Choi SH, Han SS, Lee DG, Lee BY (1999) Distribution of Xanthomonas oryzae pv. oryzae strains virulent to Xa21 in Korea. Phytopathology 89:928–933

    CAS  PubMed  Google Scholar 

  • Lei Y, Kang S, Gao J, Jia XS, Chen LL (2013) Improved annotation of a plant pathogen genome Xanthomonas oryzae pv. oryzae PXO99A. J Biomolec Struct Dyn 31:342–350. doi:10.1080/07391102.2012.698218

    CAS  Google Scholar 

  • Leung H, Zhu Y, Revilla-Molina I, Fan JX, Chen H, Pangga I, Vera Cruz C, Mew TW (2003) Using genetic diversity to achieve sustainable rice disease management. Plant Dis 87:11561169

    Google Scholar 

  • Li C, Tao J, Mao D, He C (2011) A novel manganese efflux system, YebN, is required for virulence by Xanthomonas oryzae pv. oryzae. PLoS ONE 6:e21983

    CAS  PubMed Central  PubMed  Google Scholar 

  • Li G, Song CF, Pang XM, Yang Y, Wang JS (2009a) Analysis of pathotypic and genotypic diversity of Xanthomonas oryzae pv. oryzae in China. J Phytopathol 157:208–218. doi:10.1111/j.1439-0434.2008.01471.x

    CAS  Google Scholar 

  • Li J, Wang N (2011) Genome-wide mutagenesis of Xanthomonas axonopodis pv. citri reveals novel genetic determinants and regulation mechanisms of biofilm formation. PLoS ONE 6(7):e21804

    CAS  PubMed Central  PubMed  Google Scholar 

  • Li P, Lu X, Shao M, Long J, Wang J (2004) Genetic diversity of Harpins from Xanthomonas oryzae and their activity to induce hypersensitive response and disease resistance in tobacco. Sci China Series C: Life Sci 47:461–469

    CAS  Google Scholar 

  • Li T, Huang S, Zhou J, Yang B (2013) Designer TAL effectors induce disease susceptibility and resistance to Xanthomonas oryzae pv. oryzae in rice. Mol Plant doi:10.1093/mp/sst034

  • Li T, Liu B, Spalding MH, Weeks DP, Yang B (2012) High-efficiency TALEN-based gene editing produces disease-resistant rice. Nat Biotechnol 30(5):390–392

    CAS  PubMed  Google Scholar 

  • Li W, Raoult D, Fournier PE (2009b) Bacterial strain typing in the genomic era. FEMS Micro Rev 33:892–916

    CAS  Google Scholar 

  • Liu H, Yang W, Hu B, Liu F (2007) Virulence analysis and race classification of Xanthomonas oryzae pv. oryzae in China. J Phytopathol 155:129–135. doi:10.1111/j.1439-0434.2007.01197.x

    CAS  Google Scholar 

  • Llano AI (1999) Factors affecting the development of bacterial leaf streak of rice (Oryza sativa L.) caused by Xanthomonas oryzae pv. oryzicola Swings et al.

    Google Scholar 

  • Loman NJ, Constantinidou C, Chan JZM, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ (2012) High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity. Nat Rev Microbiol 9:599–606

    Google Scholar 

  • Lozano JC (1977) Identification of bacterial blight in rice, caused by Xanthomonas oryzae, in America. Plant Dis Rep 61:644–648

    Google Scholar 

  • Lu H, Patil P, Van Sluys MA, White FF, Ryan RP, Dow JM, Rabinowicz P, Salzberg SL, Leach JE, Sonti R, Brendel V, Bogdanove A (2009) Acquisition and evolution of plant pathogenesis–associated gene clusters and candidate determinants of tissue-specificity in Xanthomonas. PLoS ONE 3(11):e3828

    Google Scholar 

  • Lv Q, Xu X, Shang J, Jiang G, Pang Z, Zhou Z, Wang J, Liu Y, Li T, Li X (2013) Functional analysis of Pid3-A4, an ortholog of rice blast resistance gene Pid3 revealed by allele mining in common wild rice. Phytopathology 103:594–599

    CAS  PubMed  Google Scholar 

  • Mahillon J, Chandler M (1998) Insertion sequences. Microbiol Mol Biol Rev 62(3):725–774

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mew TW (1993) Xanthomonas oryzae pathovars on rice: cause of bacterial blight and bacterial leaf streak. In: Swings JG, Civerolo EL (eds) Xanthomonas. Chapman and Hall, London, pp 30–40

    Google Scholar 

  • Mew TW, Alvarez AM, Leach JE, Swings J (1993) Focus on bacterial blight of rice. Plant Dis 77:5–12

    Google Scholar 

  • Mew TW, Mew IC, Huang J (1984) Scanning electron microscopy of virulent and avirulent strains of Xanthomonas campestris pv. oryzae on rice leaves. Phytopathology 74:635–641

    Google Scholar 

  • Mew TW, Vera C, C. M., Medalla ES (1992) Changes in race frequency of Xanthomonas oryzae pv. oryzae in response to rice cultivars planted in the Philippines. Plant Dis 76:1029

    Google Scholar 

  • Meyer DF, Bogdanove AJ (2009) Genomics-driven advances in Xanthomonas biology. In: Jackson RW (ed) Plant pathogenic bacteria: genomics and molecular biology. Horizon scientific press, UK, p 147–161

    Google Scholar 

  • Min J, Lin D, Zhang Q, Zhang J, Yu Z (2012) Structure-based virtual screening of novel inhibitors of the uridyltransferase activity of Xanthomonas oryzae pv. oryzae GlmU. Eur J Med Chem 53:150–158

    CAS  PubMed  Google Scholar 

  • Mira A, Pushker R, Rodriguez-Valera F (2006) The Neolithic revolution of bacterial genomes. Trends Micro 14(5):200–206

    CAS  Google Scholar 

  • Morales CQ, Posada J, Macneale E, Franklin D, Rivas I, Bravo M, Minsavage J, Stall RE, Whalen MC (2005) Functional analysis of the early chlorosis factor gene. Mol Plant Microbe Interact 18(5):477–486. doi:10.1094/MPMI-18-0477

    CAS  PubMed  Google Scholar 

  • Moscou MJ, Bogdanove AJ (2009) A simple cipher governs DNA recognition by TAL effectors. Science 326(5959):1501. doi:10.1126/science.1178817

    CAS  PubMed  Google Scholar 

  • Noda T, Yamamoto T, Kaku H, Horino O (1996) Geographical distribution of pathogenic races of Xanthomonas oryzae pv. oryzae in Japan in 1991 and 1993. Ann Phytopathol Soc Jpn 62:549–553

    Google Scholar 

  • Ochiai H, Horino O, Miyajima K, Kaku H (2000) Genetic diversity of Xanthomonas oryzae pv. oryzae strains from Sri Lanka. Phytopathology 90(4):415–421. doi:10.1094/Phyto.2000.90.4.415

    CAS  PubMed  Google Scholar 

  • Ochiai H, Inoue V, Takeya M, Sasaki A, Kaku H (2005) Genome sequence of Xanthomonas oryzae pv. oryzae suggests contribution of large numbers of effector genes and insertion sequences to its race diversity. JARQ 39 (4):275–287

    Google Scholar 

  • Ogawa T, Lin L, Tabien RE, Khush GS (1987) A new recessive gene for resistance to bacterial blight of rice. Rice Genet Newsl 4:98–100

    Google Scholar 

  • Ogawa T, Tabien RE, Yamamoto T, Busto GA, Ikeda R (1990) Breeding for near-isogenic lines for resistance to bacterial blight in rice. Rice Genet Newsl 7(10)

    Google Scholar 

  • Ogawa T, Yamamoto K, Khush G, Mew T (1991) Breeding of near-isogenic lines of rice with single genes for resistance to bacterial blight pathogen (Xanthomonas campestris pv. oryzae). Jpn J Breed 41:523–529

    Google Scholar 

  • Ogawa T, Yamamoto T (1987) Selection of recurrent parents to develop near-isogenic lines resistant to bacterial leaf blight of rice. Jpn Agri Res 21:65–69

    Google Scholar 

  • Ou SH (1985) Rice Diseases, 2nd edn. Association Applied Biology, Surrey

    Google Scholar 

  • Pandey A, Sonti RV (2010) Role of the FeoB protein and siderophore in promoting virulence of Xanthomonas oryzae pv. oryzae on rice. J Bacteriol 192(12):3187–3203. doi:10.1128/JB.01558-09

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pandey MP, Singh H, Mani SC (1986) Breakdown of Xa4 gene for resistance to bacterial blight (BB) at Pantnagar, India. Int Rice Res News 11:19–20

    Google Scholar 

  • Parkinson N, Cowie C, Heeney J, Stead D (2009) Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences. Int J Syst Evol Microbiol 59(2):264–274

    CAS  PubMed  Google Scholar 

  • Patil PB, Sonti RV (2004) Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice. BMC Microbiol 4:40

    PubMed Central  PubMed  Google Scholar 

  • Pradhan BB, Ranjan M, Chatterjee S (2012) XadM, a novel adhesin of Xanthomonas oryzae pv. oryzae, exhibits similarity to Rhs family proteins and is required for optimum attachment, biofilm formation, and virulence. Mol Plant Microbe Interact 25(9):1157–1170

    CAS  PubMed  Google Scholar 

  • Qian G, Liu C, Wu G, Yin F, Zhao Y, Zhou Y, Zhang Y, Song Z, Fan J, Hu B (2012a) AsnB, regulated by diffusible signal factor and global regulator Clp, is involved in aspartate metabolism, resistance to oxidative stress and virulence in Xanthomonas oryzae pv. oryzicola. Mol Plant Pathol 14:145–157

    PubMed  Google Scholar 

  • Qian G, Zhang Y, Zhou Y, Liu C, Zhao Y, Song Z, Fan J, Hu B, Liu F (2012b) epv, encoding a hypothetical protein, is regulated by DSF-mediating quorum sensing as well as global regulator Clp and is required for optimal virulence in Xanthomonas oryzae pv. oryzicola. Phytopathology 102:841–847

    CAS  PubMed  Google Scholar 

  • Qian G, Zhou Y, Zhao Y, Song Z, Wang S, Fan J, Hu B, Venturi V, Liu F (2013) Proteomic analysis reveals novel extracellular virulence-associated proteins and functions regulated by the diffusible signal factor (DSF) in Xanthomonas oryzae pv. oryzicola. J Proteome Res doi:10.1021/pr4001543

  • Rai R, Ranjan M, Pradhan BB, Chatterjee S (2012) Atypical regulation of virulence-associated functions by a diffusible signal factor in Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 25:789–801

    CAS  PubMed  Google Scholar 

  • Rajeshwari R, Jha G, Sonti RV (2005) Role of an in planta-expressed xylanase of Xanthomonas oryzae pv. oryzae in promoting virulence on rice. Mol Plant Microbe Interact 18(8):830–837

    CAS  PubMed  Google Scholar 

  • Ray SK, Rajeshwari R, Sharma Y, Sonti RV (2002) A high molecular weight outer membrane protein of Xanthomonas oryzae pv. oryzae exhibits similarity to non-fimbrial adhesins of animal pathogenic bacteria and is required for optimum virulence. Mol Microbiol 46(3):637–647

    CAS  PubMed  Google Scholar 

  • Ray SK, Rajeshwari R, Sonti RV (2000) Mutants of Xanthomonas oryzae pv. oryzae deficient in general secretory pathway are virulence deficient and unable to secrete xylanase. Mol Plant Microbe Interact 13:394–401

    CAS  PubMed  Google Scholar 

  • Raymundo AK, Briones AM, Ardales EY, Perez MT, Fernandez LC, Leach JE, Mew TW, Ynalvez MA, McLaren CG, Nelson RJ (1999) Analysis of DNA polymorphism and virulence in Philippine strains of Xanthomonas oryzae pv. oryzicola. Plant Dis 83(5):434–440

    Google Scholar 

  • Reddy APK, Mackenzie DR, Rouse DI, Rao AV (1979) Relationship of bacterial leaf-blight severity to grain-yield of rice. Phytopathology 69:967–969

    Google Scholar 

  • Reddy V, Kumar Y, Raghavendra A, Sowjenya G, Kumar S, Ramyasree G, Reddy G (2012) In silico model of DSF synthase RpfF protein from Xanthomonas oryzae pv. oryzae: a novel target for bacterial blight of rice disease. Bioinformation 8:504

    PubMed Central  PubMed  Google Scholar 

  • Reyon D, Tsai SQ, Khayter C, Foden JA, Sander JD, Joung JK (2012) FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30:460–465

    CAS  PubMed Central  PubMed  Google Scholar 

  • Robin GP, Ortiz E, Szurek B, Brizard JP, Koebnik R (2013) Comparative proteomics reveal new HrpX-regulated proteins of Xanthomonas oryzae pv. oryzae. J Proteomics doi:10.1016/j.jprot.2013.04.010

  • Ryan RP, Vorholter F-J, Potnis N, Jones JB, Van Sluys M-A, Bogdanove AJ, Dow JM (2011) Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat Rev Microbiol 9:344–355

    CAS  PubMed  Google Scholar 

  • Ryba-White M, Notteghem JL, Leach JE (1995) Comparison of Xanthomonas oryzae pv. oryzae strains from Africa, North America, and Asia by restriction fragment length polymorphism analysis. Int Rice Res News 20:25–26

    Google Scholar 

  • Salzberg SL, Sommer DD, Schatz MC, Phillippy AM, Rabinowicz PD, Tsuge S, Furutani A, Ochiai H, Delcher AL, Kelley D, Madupu R, Puiu D, Radune D, Shumway M, Trapnell C, Aparna G, Jha G, Pandey A, Patil PB, Ishihara H, Meyer DF, Szurek B, Verdier V, Koebnik R, Dow JM, Ryan RP, Hirata H, Tsuyumu S, Won Lee S, Ronald PC, Sonti RV, Van Sluys MA, Leach JE, White FF, Bogdanove AJ (2008) Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A. BMC Genomics 9:204

    Google Scholar 

  • Savary S, Willocquet L, Elazegui FA, Castilla NP, Teng PS (2000a) Rice pest constraints in tropical Asia: quantification of yield losses due to rice pests in a range of production situations. Plant Dis 84:357–369

    Google Scholar 

  • Savary S, Willocquet L, Elazegui FA, Teng PS, Du PV, Zhu D, Tang Q, Huang S, Lin Z, Singh HM, Srivastava RK (2000b) Rice pest constraints in tropical Asia: characterization of injury profiles in relation to production situations. Plant Dis 84:156–341

    Google Scholar 

  • Semenova E, Nagornykh M, Pyatnitskiy M, Artamonova II, Severinov K (2009) Analysis of CRISPR system function in plant pathogen Xanthomonas oryzae. FEMS Microbiol Lett 296:110–116

    CAS  PubMed  Google Scholar 

  • Seo YS, Sriariyanun M, Wang L, Pfeiff J, Phetsom J, Lin Y, Jung KH, Chou HH, Bogdanove A, Ronald P (2008) A two-genome microarray for the rice pathogens Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola and its use in the discovery of a difference in their regulation of hrp genes. BMC Microbiol 8:99

    PubMed Central  PubMed  Google Scholar 

  • Y-p Shen, L-f Zou, Y-r Li, H-s Zou, X-l Liu, G-y Chen (2012) Xoryp_08180 of Xanthomonas oryzae pv. oryzicola, encoding a hypothetical protein, is regulated by HrpG and HrpX and required for full virulence in rice. J Integr Ag 11:600–610

    Google Scholar 

  • Siguier P, Filee J, Chandler M (2006) Insertion sequences in prokaryotic genomes. Curr Opin Microbiol 9:526–531

    CAS  PubMed  Google Scholar 

  • Sinha D, Gupta MK, Patel HK, Ranjan A, Sonti RV (2013) Cell Wall Degrading Enzyme Induced Rice Innate Immune Responses Are Suppressed by the Type 3 Secretion System Effectors XopN, XopQ, XopX and XopZ of Xanthomonas oryzae pv. oryzae. PLoS ONE 8(9):e75867

    CAS  PubMed Central  PubMed  Google Scholar 

  • Song C, Yang B (2010) Mutagenesis of 18 Type III effectors reveals virulence function of XopZPXO99 in Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 23:893–902

    CAS  PubMed  Google Scholar 

  • Song W-Y, Wang G-L, Chen L-L, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai W-X, Zhu L-H, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806

    CAS  PubMed  Google Scholar 

  • Soto-Suarez M, Bernal D, Gonzalez C, Szurek B, Guyot R, Tohme J, Verdier V (2010a) In planta gene expression analysis of Xanthomonas oryzae pathovar oryzae, African strain MAI1. BMC Microbiol 10:170. doi:10.1186/1471-2180-10-170

    PubMed Central  PubMed  Google Scholar 

  • Soto-Suarez M, Gonzalez C, Piegu B, Tohme J, Verdier V (2010b) Genomic comparison between Xanthomonas oryzae pv. oryzae and Xanthomonas oryzae pv. oryzicola, using suppression-subtractive hybridization. FEMS Microbiol Lett 308(1):16–23. doi:10.1111/j.1574-6968.2010.01985.x

    CAS  PubMed  Google Scholar 

  • Sriariyanun M, Seo YS, Phetsom J (2012) Identification of PhoP regulon members in Xanthomonas oryzae pv. oryzae PXO99A. In: 4th international conference on chemical, biological and environmental engineering, IACSIT Press, Singapore. doi:10.7763/IPCBEE

  • Subramoni S, Pandey A, Vishnupriya MR, Patel HK, Sonti RV (2012) The ColRS system of Xanthomonas oryzae pv. oryzae is required for virulence and growth in iron-limiting conditions. Mol Plant Pathol 13:690–703. doi:10.1111/j.1364-3703.2011.00777.x

    CAS  PubMed  Google Scholar 

  • Subramoni S, Sonti RV (2005) Growth deficiency of a Xanthomonas oryzae pv. oryzae fur mutant in rice leaves is rescued by ascorbic acid supplementation. Mol Plant Microbe Interact 18(7):644–651. doi:10.1094/MPMI-18-0644

    CAS  PubMed  Google Scholar 

  • Sugio A, Yang B, Zhu T, White FF (2007) Two type III effector genes of Xanthomonas oryzae pv. oryzae control the induction of the host genes OsTFIIAγ1 and OsTFX1 during bacterial blight of rice. Proc Natl Acad Sci 104:10720

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sukchawalit R, Vattanaviboon P, Utamapongchai S, Vaughn G, Mongkolsuk S (2006) Characterization of Xanthomonas oryzae pv. oryzae recX, a gene that is required for high level expression of recA. FEMS Microbiol Lett 205(1):83–89

    Google Scholar 

  • Sun Q, Wu W, Qian W, Hu J, Fang R, He C (2006) High quality mutant libraries of Xanthomonas oryzae pv. oryzae and X. campestris pv. campestris generated by an efficient transposon mutagenesis system. FEMS Microbiol Lett 226:145–150

    Google Scholar 

  • Tabei H (1977) Anatomical studies of rice plant affected with bacterial leaf blight, Xanthomonas oryzae (Uyeda et Ishiyama Dowson). Bull Kyushu Agri Expt Sta 19:193–257

    Google Scholar 

  • Tang D, Wu W, Li W, Lu H, Worland AJ (2000) Mapping of QTLs conferring resistance to bacterial leaf streak in rice. Theor Appl Genet 101:286–291

    CAS  Google Scholar 

  • Tang JL, Feng JX, Li QQ, Wen HX, Zhou DL, Wilson TJ, Dow JM, Ma QS, Daniels MJ (1996) Cloning and characterization of the rpfC gene of Xanthomonas oryzae pv. oryzae: involvement in exopolysaccharide production and virulence to rice. Mol Plant Microbe Interact 9:664–666

    CAS  PubMed  Google Scholar 

  • Triplett LR, Hamilton JP, Buell CR, Tisserat NA, Verdier V, Zink F, Leach JE (2011) Genomic analysis of Xanthomonas oryzae isolates from rice grown in the United States reveals substantial divergence from known X. oryzae pathovars. Appl Environ Microbiol 77(12):3930–3937. doi:10.1128/AEM.00028-11

    CAS  PubMed Central  PubMed  Google Scholar 

  • Vera Cruz C, Bai J, Oña I, Leung H, Nelson R, Mew T, Leach JE (2000) Predicting durability of a disease resistance gene based on an assessment of the fitness loss and epidemiological consequences of avirulence gene mutation. Proc Natl Acad Sci USA 97:13500–13505

    CAS  PubMed Central  PubMed  Google Scholar 

  • Verdier V, Triplett LR, Hummel AW, Corral R, Cernadas RA, Schmidt CL, Bogdanove AJ, Leach JE (2012a) Transcription activator-like (TAL) effectors targeting OsSWEET genes enhance virulence on diverse rice (Oryza sativa) varieties when expressed individually in a TAL effector-deficient strain of Xanthomonas oryzae. New Phytol 196(4):1197–1207. doi:10.1111/j.1469-8137.2012.04367.x

    CAS  PubMed  Google Scholar 

  • Verdier V, Vera Cruz C, Leach JE (2012b) Controlling rice bacterial blight in Africa: needs and prospects. J Biotechnol 159:320–328. doi:10.1016/j.jbiotec.2011.09.020

    CAS  PubMed  Google Scholar 

  • Verdier V, Vera Cruz C, Leach JE (2012c) Controlling rice bacterial blight in Africa: needs and prospects. J Biotechnol 159(4):320–328. doi:10.1016/j.jbiotec.2011.09.020

    CAS  PubMed  Google Scholar 

  • Wang GL, Ruan DL, Song WY, Sideris S, Chen L, Pi LY, Zhang S, Zhang Z, Fauquet C, Gaut BS, Whalen MC, Ronald PC (1998) Xa21D encodes a receptor-like molecular with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution. Plant Cell 10:765–780

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wang L, Makino S, Subedee A, Bogdanove AJ (2007) Novel candidate virulence factors in rice pathogen Xanthomonas oryzae pv. oryzicola as revealed by mutational analysis. Appl Environ Microbiol 73(24):8023–8027

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wang L, Vinogradov EV, Bogdanove AJ (2013a) Requirement of the lipopolysaccharide O-chain biosynthesis gene wxocB for type III secretion and virulence of Xanthomonas oryzae pv. oryzicola J Bacteriol doi:10.1128/JB.02299-12

  • Wang Y, Kim SG, Wu J, Huh HH, Lee SJ, Rakwal R, Agrawal GK, Park ZY, Kang KY, Kim ST (2013b) Secretome analysis of the rice bacterium Xanthomonas oryzae (Xoo) using in vitro and in planta systems. Proteomics:n/a-n/a

    Google Scholar 

  • Weber E, Gruetzner R, Werner S, Engler C, Marillonnet S (2011) Assembly of designer TAL effectors by Golden Gate cloning. PLoS ONE 6:e19722

    CAS  PubMed Central  PubMed  Google Scholar 

  • White FF, Potnis N, Jones JB, Koebnik R (2009) The type III effectors of Xanthomonas. Mol Plant Pathol 10(6):749–766

    CAS  PubMed  Google Scholar 

  • White TJ, Gonzalez CR (1995) Electroporation of Xanthomonas. Electroporation Protoc Microorganisms 47:135

    CAS  Google Scholar 

  • Wonni I, Ouedraogo L, Verdier V (2011) First report of bacterial leaf streak caused by Xanthomonas oryzae pv. oryzicola on rice in Burkina faso. Plant Dis 95(1):72–73. doi:10.1094/Pdis-08-10-0566

    Google Scholar 

  • Xiang Y, Cao Y, Xu C, Li X, Wang S (2006) Xa3, conferring resistance for rice bacterial blight and encoding a receptor kinase-like protein, is the same as Xa26. Theor Appl Genet 113(7):1347–1355

    CAS  PubMed  Google Scholar 

  • Xie G, Sun S, Chen J, Zhu X, Chen J, Ye Y, Feng Z, Liang M (1990) Studies on rice seed inspection of Xanthomonas campestris pv. oryzicola: Immunoradiometric assay. Chinese J Rice Sci 4:127–132

    Google Scholar 

  • Xu J, Wu M, He C (2012) Identification and functional analysis of Tdrxoo, the member of TonB-dependent-receptor family proteins in Xanthomonas oryzae pv. oryzae. Acta Microbiol Sinica 50:155

    Google Scholar 

  • Yamaguchi K, Nakamura Y, Ishikawa K, Yoshimura Y, Tsuge S, Kawasaki T (2013a) Suppression of rice immunity by Xanthomonas oryzae type III effector Xoo2875. Biosci Biotechnol Biochem 77(4):796–801

    CAS  PubMed  Google Scholar 

  • Yamaguchi K, Yamada K, Ishikawa K, Yoshimura S, Hayashi N, Uchihashi K, Ishihama N, Kishi-Kaboshi M, Takahashi A, Tsuge S, Ochiai H, Tada Y, Shimamoto K, Yoshioka H, Kawasaki T (2013b) A receptor-like cytoplasmic kinase targeted by a plant pathogen effector is directly phosphorylated by the chitin receptor and mediates rice immunity. Cell Host Microbe 13(3):347–357. doi:10.1016/j.chom.2013.02.007

    CAS  PubMed  Google Scholar 

  • Yang B, Sugio A, White FF (2006) Os8N3 is a host disease-susceptibility gene for bacterial blight of rice. Proc Natl Acad Sci USA 103:10503–10508. doi:10.1073/pnas.0604088103

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yang B, White FF (2004) Diverse members of the AvrBs3/PthA family of type III effectors are major virulence determinants in bacterial blight disease of rice. Mol Plant Microbe Interact 17:1192–1200. doi:10.1094/MPMI.2004.17.11.1192

    CAS  PubMed  Google Scholar 

  • Yang F, Tian F, Sun L, Chen H, Wu M, Yang C-H, He C (2012) A novel two-component system PdeK/PdeR regulates c-di-GMP turnover and virulence of Xanthomonas oryzae pv. oryzae. Mol Plant Microbe Interact 25:1361–1369

    CAS  PubMed  Google Scholar 

  • Yang SQ, Liu SY, Zhao S, Yu Y-H, Li RB, Duan CJ, Tang JL, Feng JX (2013) Molecular and pathogenic characterization of new Xanthomonas oryzae pv. oryzae strains from the coastline region of Fangchenggang city in China. World J Microbiol Biotechnol 29:713–720. doi:10.1007/s11274-012-1227-7

    PubMed  Google Scholar 

  • Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, Kono I, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci USA 95(4):1663–1668

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yu Y, Streubel J, Balzergue S, Champion A, Boch J, Koebnik R, Feng J, Verdier V, Szurek B (2011) Colonization of rice leaf blades by an African strain of Xanthomonas oryzae pv. oryzae depends on a new TAL effector that induces the rice nodulin-3 Os11N3 gene. Mol Plant Microbe Interact 24(9):1102–1113. doi:10.1094/MPMI-11-10-0254

    CAS  PubMed  Google Scholar 

  • Zang N, Tang DJ, Wei ML, He YQ, Chen B, Feng JX, Xu J, Gan YQ, Jiang BL, Tang JL (2007) Requirement of a mip-like gene for virulence in the phytopathogenic bacterium Xanthomonas campestris pv. campestris. Mol Plant Microbe Interact 20(1):21–30. doi:10.1094/MPMI-20-0021

    CAS  PubMed  Google Scholar 

  • Zhang H, Wang S (2013) Rice versus Xanthomonas oryzae pv. oryzae: a unique pathosystem. Curr Opin Plant Biol doi:10.1016/j.pbi.2013.02.008

  • Zhang X, Gao S, Wu M, He C (2009) DNA microarray expression analysis of Xanthomonas oryzae pv. oryzae in rice leaves at early infection stages using selective bacterial transcript labeling with genome-directed primers. Scientia Agricultura Sinica 10:3501–3508

    Google Scholar 

  • Zhao B, Ardales E, Raymundo A, Bai J, Trick HN, Leach JE, Hulbert S (2004a) The avrRxo1 gene from the rice pathogen Xanthomonas oryzae pv. oryzicola confers a nonhost defense reaction on maize with resistance gene Rxo1. Mol Plant Microbe Interact 17:771–779

    CAS  PubMed  Google Scholar 

  • Zhao B, Lin X, Poland J, Trick H, Leach J, Hulbert S (2005) A maize resistance gene functions against bacterial streak disease in rice. Proc Natl Acad Sci USA 102(43):15383–15388

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zhao BY, Ardales E, Brasset E, Claflin LE, Leach JE, Hulbert SH (2004b) The Rxo1/ Rba1 locus of maize controls resistance reactions to pathogenic and non-host bacteria. Theor Appl Genet 109(1):71–79

    CAS  PubMed  Google Scholar 

  • Zhao S, Mo WL, Wu F, Tang W, Tang JL, Szurek B, Verdier V, Koebnik R, Feng JX (2013) Identification of non-TAL effectors in Xanthomonas oryzae pv. oryzae Chinese strain 13,751 and analysis of their role in the bacterial virulence. World J Microbiol Biotechnol 29:733–744. doi:10.1007/s11274-012-1229-5

    PubMed  Google Scholar 

  • Zhao S, Poulin L, Rodriguez RL, Serna NF, Liu SY, Wonni I, Szurek B, Verdier V, Leach JE, He YQ, Feng JX, Koebnik R (2012a) Development of a variable number of tandem repeats typing scheme for the bacterial rice pathogen Xanthomonas oryzae pv. oryzicola. Phytopathology 102:948–956. doi:10.1094/PHYTO-04-12-0078-R

    CAS  PubMed  Google Scholar 

  • Zhao Y, Qian G, Fan J, Yin F, Zhou Y, Liu C, Shen Q, Hu B, Liu F (2012b) Identification and characterization of a novel gene, hshB, in Xanthomonas oryzae pv. oryzicola co-regulated by quorum sensing and clp. Phytopathology 102:252–259

    CAS  PubMed  Google Scholar 

  • Zhao Y, Qian G, Yin F, Fan J, Zhai Z, Liu C, Hu B, Liu F (2011) Proteomic analysis of the regulatory function of DSF-dependent quorum sensing in Xanthomonas oryzae pv. oryzicola. Microb Pathogenesis 50:48–55

    CAS  Google Scholar 

  • Zheng JS, Li YZ, Fang XJ (2005) Detection of QTL conferring resistance to bacterial leaf streak in rice chromosome 2 (O. sativa L. ssp. indica). Agri Sci China 38:1923–1925

    Google Scholar 

  • Zhu PL, Zhao S, Tang JL, Feng JX (2011) The rsmA-like gene rsmAXoo of Xanthomonas oryzae pv. oryzae regulates bacterial virulence and production of diffusible signal factor. Mol Plant Pathol 12(3):227–237

    CAS  PubMed  Google Scholar 

  • Zhu W, MaGbanua MM, White FF (2000) Identification of two novel hrp-associated genes in the hrp gene cluster of Xanthomonas oryzae pv. oryzae. J Bacteriol 182:1844–1853

    CAS  PubMed Central  PubMed  Google Scholar 

  • Zou HS, Song X, Zou LF, Yuan L, Li YR, Guo W, Che YZ, Zhao WX, Duan YP, Chen GY (2012) EcpA, an extracellular protease, is a specific virulence factor required by Xanthomonas oryzae pv. oryzicola but not by X. oryzae pv. oryzae in rice. Microbiology 158:2372–2383

    CAS  PubMed  Google Scholar 

  • Zou L, Li YR, Chen GY (2011) A non-marker mutagenesis strategy to generate poly-hrp gene mutants in the rice pathogen Xanthomonas oryzae pv. oryzicola. J Integr Ag 10:1139–1150

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1177, USA

    Lindsay Triplett, Valerie Verdier & Jan E. Leach

  2. Institut de Recherche pour le Développement, UMR Résistance des Plantes aux Bioagresseurs, IRD-CIRAD-UM2, 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France

    Ralf Koebnik & Valerie Verdier

Authors
  1. Lindsay Triplett
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ralf Koebnik
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Valerie Verdier
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jan E. Leach
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jan E. Leach .

Editor information

Editors and Affiliations

  1. Dep Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, USA

    Dennis C. Gross

  2. United States Department of Agriculture Nat Inst Food and Agriculture, Washington, District of Columbia, USA

    Ann Lichens-Park

  3. Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, India

    Chittaranjan Kole

Rights and permissions

Reprints and permissions

Copyright information

© 2014 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Triplett, L., Koebnik, R., Verdier, V., Leach, J.E. (2014). The Genomics of Xanthomonas oryzae . In: Gross, D., Lichens-Park, A., Kole, C. (eds) Genomics of Plant-Associated Bacteria. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55378-3_6

Download citation

Publish with us

Policies and ethics

Search

Navigation