Abramovitch, R. B., Anderson, J. C., and Martin, G. B. 2006. Bacterial
elicitation and evasion of plant innate immunity. Nat. Rev. Mol. Cell
Biol. 7:601-611.
Almeida, N. F., Yan, S., Lindeberg, M., Studholme, D. J., Schneider, D. J.,
Condon, B., Liu, H., Viana, C. J., Warren, A., Evans, C., Kemen, E.,
Maclean, D., Angot, A., Martin, G. B., Jones, J. D., Collmer, A.,
Setubal, J. C., and Vinatzer, B. A. 2009. A draft genome sequence of
Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire
significantly divergent from that of Pseudomonas syringae pv. tomato
DC3000. Mol. Plant-Microbe Interact. 22:52-62.
Arnold, D. L., Jackson, R. W., Fillingham, A. J., Goss, S. C., Taylor, J. D.,
Mansfield, J. W., and Vivian, A. 2001. Highly conserved sequences
flank avirulence genes: Isolation of novel avirulence genes from Pseudomonas
syringae pv. pisi. Microbiology 147:1171-1182.
Arnold, D. L., Lovell, H. C., Jackson, R. W., and Mansfield, J. W. 2011.
Pseudomonas syringae pv. phaseolicola: From ‘has bean’ to supermodel.
Mol. Plant Pathol. 12:617-627.
Baltrus, D. A., Nishimura, M. T., Romanchuk, A., Chang, J. H., Mukhtar,
M. S., Cherkis, K., Roach, J., Grant, S. R., Jones, C. D., and Dangl, J.
L. 2011. Dynamic evolution of pathogenicity revealed by sequencing
and comparative genomics of 19 Pseudomonas syringae isolates. PLoS
Pathog. 7:e1002132. Published online
Besemer, J., and Borodovsky, M. 2005. GeneMark: Web software for gene
finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res.
33:W451-W454.
Borhan, M. H., Gunn, N., Cooper, A., Gulden, S., Tör, M., Rimmer, S. R.,
and Holub, E. B. 2008. WRR4 encodes a TIR-NB-LRR protein that
confers broad-spectrum white rust resistance in Arabidopsis thaliana to
four physiological races of Albugo candida. Mol. Plant-Microbe Interact.
21:757-768.
Cai, R., Lewis, J., Yan, S., Liu, H., Clarke, C. R., Campanile, F., Almeida,
N. F., Studholme, D. J., Lindeberg, M., Schneider, D., Zaccardelli, M.,
Setubal, J. C., Morales-Lizcano, N. P., Bernal, A., Coaker, G., Baker,
C., Bender, C. L., Leman, S., and Vinatzer, B. A. 2011. The plant pathogen
Pseudomonas syringae pv. tomato is genetically monomorphic and
under strong selection to evade tomato immunity. PLoS Pathog.
7:e1002130. Published online.
Chang, J. H., Urbach, J. M., Law, T. F., Arnold, L. W., Hu, A., Gombar, S.,
Grant, S. R., Ausubel, F. M., and Dangl, J. L. 2005. A high-throughput,
near-saturating screen for type III effector genes from Pseudomonas syringae.
Proc. Natl. Acad. Sci. U.S.A. 102:2549-2554.
Cunnac, S., Chakravarthy, S., Kvitko, B. H., Russell, A. B., Martin, G. B.,
and Collmer, A. 2011. Genetic disassembly and combinatorial reassembly
identify a minimal functional repertoire of type III effectors in
Pseudomonas syringae. Proc. Natl. Acad. Sci. U.S.A. 108:2975-2980.
Delgado-Salinas, A., Bibler, R., and Lavin, M. 2006. Phylogeny of the genus
Phaseolus (Leguminosae): A recent diversification in an ancient
landscape. Syst. Bot. 31:779-791.
Do, C. B. 2005. ProbCons: Probabilistic consistency-based multiple sequence
alignment. Genome Res. 15:330-340.
Fan, J., Crooks, C., and Lamb, C. 2007. High-throughput quantitative luminescence assay of the growth in planta of Pseudomonas syringae
chromosomally tagged with Photorhabdus luminescens luxCDABE.
Plant J. 53:393-399.
Ferrante, P., Clarke, C. R., Cavanaugh, K. A., Michelmore, R. W.,
Buonaurio, R., and Vinatzer, B. A. 2009. Contributions of the effector
gene hopQ1-1 to differences in host range between Pseudomonas syringae
pv. phaseolicola and P. syringae pv. tabaci. Mol. Plant Pathol.
10:837-842.
Gardan, L., Shafik, H., Belouin, S., Broch, R., Grimont, F., and Grimont,
P. A. 1999. DNA relatedness among the pathovars of Pseudomonas syringae
and description of Pseudomonas tremae sp. nov. and Pseudomonas
cannabina sp. nov. (ex Sutic and Dowson 1959). Int. J. Syst. Bacteriol.
492:469-478.
Gassmann, W., Hinsch, M. E., and Staskawicz, B. J. 1999. The Arabidopsis
RPS4 bacterial-resistance gene is a member of the TIR-NBS-LRR
family of disease-resistance genes. Plant J. 20:265-277.
Glickmann, E., Gardan, L., Jacquet, S., Hussain, S., Elasri, M., Petit, A.,
and Dessaux, Y. 1998. Auxin production is a common feature of most
pathovars of Pseudomonas syringae. Mol. Plant-Microbe Interact.
11:156-162.
Ham, J. H., Kim, M. G., Lee, S. Y., and Mackey, D. 2007. Layered basal
defenses underlie non-host resistance of Arabidopsis to Pseudomonas
syringae pv. phaseolicola. Plant J. 51:604-616.
Hirano, S. S., Charkowski, A. O., Collmer, A., Willis, D. K., and Upper, C.
D. 1999. Role of the Hrp type III protein secretion system in growth of
Pseudomonas syringae pv. syringae B728a on host plants in the field.
Proc. Natl. Acad. Sci. U.S.A. 96:9851-9856.
Holt, B. F., Belkhadir, Y., and Dangl, J. L. 2005. Antagonistic control of
disease resistance protein stability in the plant immune system. Science
309:929-932.
Hwang, M. S. H., Morgan, R. L., Sarkar, S. F., Wang, P. W., and Guttman,
D. S. 2005. Phylogenetic characterization of virulence and resistance
phenotypes of Pseudomonas syringae. Appl. Environ. Microbiol.
71:5182-5191.
Joardar, V., Lindeberg, M., Jackson, R. W., Selengut, J., Dodson, R.,
Brinkac, L. M., Daugherty, S. C., Deboy, R., Durkin, A. S., Giglio, M.
G., Madupu, R., Nelson, W. C., Rosovitz, M. J., Sullivan, S., Crabtree,
J., Creasy, T., Davidsen, T., Haft, D. H., Zafar, N., Zhou, L., Halpin, R.,
Holley, T., Khouri, H., Feldblyum, T., White, O., Fraser, C. M.,
Chatterjee, A. K., Cartinhour, S., Schneider, D. J., Mansfield, J.,
Collmer, A., and Buell, C. R. 2005. Whole-genome sequence analysis
of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence
among pathovars in genes involved in virulence and transposition. J.
Bacteriol. 187:6488-6498.
Jones, J. D. G., and Dangl, J. L. 2006. The plant immune system. Nature
444:323-329.
Kobayashi, D. Y., Tamaki, S. J., and Keen, N. T. 1989. Cloned avirulence
genes from the tomato pathogen Pseudomonas syringae pv. tomato
confer cultivar specificity on soybean. Proc. Natl. Acad. Sci. U.S.A.
86:157-161.
Lacombe, S. E. V., Rougon-Cardoso, A., Sherwood, E., Peeters, N.,
Dahlbeck, D., van Esse, H. P., Smoker, M., Rallapalli, G., Thomma, B.
P. H. J., Staskawicz, B., Jones, J. D. G., and Zipfel, C. 2010. Interfamily
transfer of a plant pattern-recognition receptor confers broad-spectrum
bacterial resistance. Nat. Biotechnol. 28:365-369.
Li, R., Li, Y., Kristiansen, K., and Wang, J. 2008. SOAP: Short oligonucleotide
alignment program. Bioinformatics 24:713-714.
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan,
G., Kristiansen, K., Li, S., Yang, H., Wang, J., and Wang, J. 2010. De
novo assembly of human genomes with massively parallel short read
sequencing. Genome Res. 20:265-272.
Li, X., Lin, H., Zhang, W., Zou, Y., Zhang, J., Tang, X., and Zhou, J.-M.
2005. Flagellin induces innate immunity in nonhost interactions that is
suppressed by Pseudomonas syringae effectors. Proc. Natl. Acad. Sci.
U.S.A. 102:12990-12995.
Lin, N.-C., and Martin, G. B. 2007. Pto- and Prf-mediated recognition of
AvrPto and AvrPtoB restricts the ability of diverse Pseudomonas syringae
pathovars to infect tomato. Mol. Plant-Microbe Interact. 20:806-
815.
Lindeberg, M., Cunnac, S., and Collmer, A. 2009. The evolution of Pseudomonas
syringae host specificity and type III effector repertoires. Mol.
Plant Pathol. 10:767-775.
Lorang, J., Shen, H., and Kobayashi, D. 1994. avrA and avrE in Pseudomonas
syringae pv. tomato PT23 play a role in virulence on tomato
plants. Mol. Plant-Microbe Interact. 7:508-515.
Marco, M. L., Legac, J., and Lindow, S. E. 2005. Pseudomonas syringae
genes induced during colonization of leaf surfaces. Environ. Microbiol.
7:1379-1391.
Marques, A., Corbiere, R., Gardan, L., Tourte, C., Manceau, C., Taylor, J.,
and Samson, R. 2000. Multiphasic approach for the identification of the
different classification levels of Pseudomonas savastanoi pv. phaseolicola.
Eur. J. Plant Pathol. 106:715-734.
Mazzola, M., and White, F. F. 1994. A mutation in the indole-3-acetic acid
biosynthesis pathway of Pseudomonas syringae pv. syringae affects
growth in Phaseolus vulgaris and syringomycin production. J. Bacteriol.
176:1374-1382.
McClean, P., Lavin, M., Gepts, P., and Jackson, S. 2008. Phaseolus vulgaris:
A diploid model for soybean. Pages 55-78 in: Soybean Genomics.
Springer, Berlin.
McDermott, J., Corrigan, A., and Peterson, E. 2011. Computational prediction
of type III and IV secreted effectors in gram-negative bacteria.
Infect. Immun. 79:23-32.
Mellersh, D. G., and Heath, M. C. 2003. An investigation into the involvement
of defense signaling pathways in components of the nonhost
resistance of Arabidopsis thaliana to rust fungi also reveals a model
system for studying rust fungal compatibility. Mol. Plant-Microbe Interact.
16:398-404.
Morris, C. E., Sands, D. C., Vanneste, J. L., Montarry, J., Oakley, B.,
Guilbaud, C., and Glaux, C. 2010. Inferring the evolutionary history of
the plant pathogen Pseudomonas syringae from its biogeography in
headwaters of rivers in North America, Europe, and New Zealand.
mBio 1:e00107-00110-e00107-00120. Published online.
Mysore, K. S., and Ryu, C.-M. 2004. Nonhost resistance: How much do
we know? Trends Plant Sci. 9:97-104.
Ortiz-Martín, I., Macho, A. P., Lambersten, L., Ramos, C., and Beuzón,
C.R. 2006. Suicide vectors for antibiotic marker exchange and rapid
generation of multiple knockout mutants by allelic exchange in gramnegative
bacteria. J. Microbiol. Methods 67:395-407.
Ortiz-Martín, I., Thwaites, R., Macho, A. P., Mansfield, J. W., and Beuzón,
C. R. 2010. Positive regulation of the Hrp type III secretion system in
Pseudomonas syringae pv. phaseolicola. Mol. Plant-Microbe Interact.
23:665-681.
Patil, S. S., Hayward, A., and Emmons, R. 1974. An ultraviolet-induced
nontoxigenic mutant of Pseudomonas phaseolicola of altered pathogenicity.
Phytopathology 64:590-595.
Perchepied, L., Kroj, T., Tronchet, M., Loudet, O., and Roby, D. 2006.
Natural variation in partial resistance to Pseudomonas syringae is controlled
by two major QTLs in Arabidopsis thaliana. PLoS ONE 1:e123.
Published online.
Qi, M., Wang, D., Bradley, C. A., and Zhao, Y. 2011. Genome sequence
analyses of Pseudomonas savastanoi pv. glycinea and subtractive hybridization-
based comparative genomics with nine pseudomonads.
PLoS ONE 6:e16451. Published online.
Rico, A., and Preston, G. M. 2008. Pseudomonas syringae pv. tomato
DC3000 uses constitutive and apoplast-induced nutrient assimilation
pathways to catabolize nutrients that are abundant in the tomato apoplast.
Mol. Plant-Microbe Interact. 21:269-282.
Roine, E., Wei, W., Yuan, J., Nurmiaho-Lassila, E. L., Kalkkinen, N.,
Romantschuk, M., and He, S. Y. 1997. Hrp pilus: An hrp-dependent
bacterial surface appendage produced by Pseudomonas syringae pv. tomato
DC3000. Proc. Natl. Acad. Sci. U.S.A. 94:3459-3464.
Schulze-Lefert, P., and Panstruga, R. 2011. A molecular evolutionary concept
connecting nonhost resistance, pathogen host range, and pathogen
speciation. Trends Plant Sci. 16:117-125.
Shan, L., He, P., Li, J., Heese, A., Peck, S. C., Nürnberger, T., Martin, G.
B., and Sheen, J. 2008. Bacterial effectors target the common signaling
partner BAK1 to disrupt multiple MAMP receptor-signaling complexes
and impede plant immunity. Cell Host Microbe 4:17-27.
Sohn, K. H., Saucet, S. B., Clarke, C. R., Vinatzer, B. A., O’Brien, H. E.,
Guttman, D. S., and Jones, J. D. G. 2011. HopAS1 recognition significantly
contributes to Arabidopsis nonhost resistance to Pseudomonas
syringae pathogens. New Phytol. 193:58-66.
Song, J., Bradeen, J. M., Naess, S. K., Raasch, J. A., Wielgus, S. M.,
Haberlach, G. T., Liu, J., Kuang, H., Austin-Phillips, S., Buell, C. R.,
Helgeson, J. P., and Jiang, J. 2003. Gene RB cloned from Solanum
bulbocastanum confers broad spectrum resistance to potato late blight.
Proc. Natl. Acad. Sci. U.S.A. 100:9128-9133.
Stamatakis, A. 2004. RAxML-III: A fast program for maximum likelihood-
based inference of large phylogenetic trees. Bioinformatics
21:456-463.
Stamatakis, A. 2006. RAxML-VI-HPC: Maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics
22:2688-2690.
Staskawicz, B. J., Dahlbeck, D., and Keen, N. T. 1984. Cloned avirulence
gene of Pseudomonas syringae pv. glycinea determines race-specific
incompatibility on Glycine max (L.) Merr. Proc. Natl. Acad. Sci. U.S.A.
81:6024-6028.
Stevens, C., Bennett, M. A., Athanassopoulos, E., Tsiamis, G., Taylor, J.
D., and Mansfield, J. W. 1998. Sequence variations in alleles of the
avirulence gene avrPphE.R2 from Pseudomonas syringae pv. phaseolicola lead to loss of recognition of the AvrPphE protein within bean
cells and a gain in cultivar-specific virulence. Mol. Microbiol. 29:165-
177.
Studholme, D. J. 2011. Application of high-throughput genome sequencing
to intrapathovar variation in Pseudomonas syringae. Mol. Plant
Pathol. 12:829-838.
Tai, T. H., Dahlbeck, D., Clark, E. T., Gajiwala, P., Pasion, R., Whalen, M.
C., Stall, R. E., and Staskawicz, B. J. 1999. Expression of the Bs2 pepper
gene confers resistance to bacterial spot disease in tomato. Proc.
Natl. Acad. Sci. U.S.A. 96:14153-14158.
Takeuchi, K., Taguchi, F., Inagaki, Y., Toyoda, K., Shiraishi, T., and
Ichinose, Y. 2003. Flagellin glycosylation island in Pseudomonas syringae
pv. glycinea and its role in host specificity. J. Bacteriol. 185:6658-
6665.
Taylor, J., Teverson, D., and Allen, D. 1996. Identification and origin of
races of Pseudomonas syringae pv. phaseolicola from Africa and other
bean growing areas. Plant Pathol. 45:469-478.
Tsiamis, G., Mansfield, J. W., Hockenhull, R., Jackson, R. W., Sesma, A.,
Athanassopoulos, E., Bennett, M. A., Stevens, C., Vivian, A., Taylor, J.
D., and Murillo, J. 2000. Cultivar-specific avirulence and virulence
functions assigned to avrPphF in Pseudomonas syringae pv. phaseolicola,
the cause of bean halo-blight disease. EMBO (Eur. Mol. Biol.
Organ.) J. 19:3204-3214.
Vera Cruz, C. M., Bai, J., Ona, I., Leung, H., Nelson, R. J., Mew, T. W.,
and Leach, J. E. 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. U.S.A.
97:13500-13505.
Vinatzer, B. A., Teitzel, G. M., Lee, M.-W., Jelenska, J., Hotton, S., Fairfax,
K., Jenrette, J., and Greenberg, J. T. 2006. The type III effector repertoire
of Pseudomonas syringae pv. syringae B728a and its role in survival
and disease on host and non-host plants. Mol. Microbiol. 62:26-
44.
Warren, R. F., Merritt, P. M., Holub, E., and Innes, R. W. 1999. Identification
of three putative signal transduction genes involved in R genespecified
disease resistance in Arabidopsis. Genetics 152:401-412.
Wei, C.-F., Kvitko, B. H., Shimizu, R., Crabill, E., Alfano, J. R., Lin, N.-
C., Martin, G. B., Huang, H.-C., and Collmer, A. 2007. A Pseudomonas
syringae pv. tomato DC3000 mutant lacking the type III effector
HopQ1-1 is able to cause disease in the model plant Nicotiana benthamiana.
Plant J. 51:32-46.
Weingart, H., Ullrich, H., Geider, K., and Völksch, B. 2001. The role of
ethylene production in virulence of Pseudomonas syringae pvs. glycinea
and phaseolicola. Phytopathology 91:511-518.
Wen, C., Tang, X., Su, Z., and Zhou, J. 2010. Effector-triggered and pathogen-
associated molecular pattern-triggered immunity differentially contribute
to basal resistance to Pseudomonas syringae. Mol. Plant-Microbe
Interact. 23:940-948.
Wroblewski, T., Caldwell, K. S., Piskurewicz, U., Cavanaugh, K. A., Xu,
H., Kozik, A., Ochoa, O., McHale, L. K., Lahre, K., Jelenska, J., Castillo,
J. A., Blumenthal, D., Vinatzer, B. A., Greenberg, J. T., and Michelmore,
R. W. 2009. Comparative large-scale analysis of interactions between
several crop species and the effector repertoires from multiple pathovars
of Pseudomonas and Ralstonia. Plant Physiol. 150:1733-1749.
Xiang, T., Zong, N., Zou, Y., Wu, Y., Zhang, J., Xing, W., Li, Y., Tang, X.,
Zhu, L., Chai, J., and Zhou, J.-M. 2008. Pseudomonas syringae effector
AvrPto blocks innate immunity by targeting receptor kinases. Curr.
Biol. 18:74-80.
Zumaquero, A., Macho, A. P., Rufián, J. S., and Beuzón, C. R. 2010.
Analysis of the role of the type III effector inventory of Pseudomonas
syringae pv. phaseolicola 1448a in interaction with the plant. J. Bacteriol.
192:4474-4488.