Non contiguous-finished genome sequence of Pseudomonas syringae pathovar syringae strain B64 isolated from wheat

Standards in Genomic Sciences

Volumn 8, Issue 3, 2013, Pages

  Dudnik, Alexey ^a   Dudler, Robert ^a  

^a UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Genome; Plant pathogen interactions; Pseudomonas syringae; Syringolin; Wheat

Indexed keywords

EXTRACHROMOSOMAL DNA; GENOMIC DNA; RNA 16S;

ARTICLE; BACTERIAL GROWTH; BACTERIAL ISOLATION; BACTERIAL STRAIN; BACTERIAL VIRULENCE; DNA HYBRIDIZATION; DNA ISOLATION; GENETIC ASSOCIATION; GENOME; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHOGENESIS; PHYLOGENETIC TREE; PSEUDOMONAS SYRINGAE;

EID: 84881064432     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3997732     Document Type: Article

References (61)

1. Bradbury JF. Guide to Plant Pathogenic Bacteria. Kew, England: CAB International Mycological Institute; 1985:175-177.
2. González AJ, Landeras E, Mendoza MC. Pathovars of Pseudomonas syringae causing bacterial brown spot and halo blight in Phaseolus vulgaris L. are distinguishable by ribotyping. Appl Environ Microbiol 2000; 66:850-854. [doi:10.1128/AEM.66.2.850-854.2000] [pmid:10653764]
3. Qi M, Wang D, Bradley CA, Zhao Y. Genome sequence analyses of Pseudomonas savastanoi pv. glycinea and subtractive hybridization-based comparative genomics with nine pseudomonads. PLoS ONE 2011; 6:e16451. [doi:10.1371/journal.pone.0016451] [pmid:21304594]
4. Young JM. Taxonomy of Pseudomonas syringae. Journal of Plant Pathology 2010;92:S1.5-S1.14. Available at: http://sipav.org/main/jpp/index.php/jpp/article/view/2501. Accessed March 20, 2013.
5. Palleroni N. Genus I. Pseudomonas. In: Garrity G, Brenner D, Krieg N, Staley J, eds. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B. Springer; 2005:374.
6. Lindeberg M, Cunnac S, Collmer A. The evolution of Pseudomonas syringae host specificity and type III effector repertoires. Mol Plant Pathol 2009; 10:767-775. [doi:10.1111/j.1364-3703.2009.00587.x] [pmid:19849783]
7. Haapalainen M, Mosorin H, Dorati F, Wu RF, Roine E, Taira S, Nissinen R, Mattinen L, Jackson R, Pirhonen M, Lin NC. Hcp2, a secreted protein of the phytopathogen Pseudomonas syringae pv. tomato DC3000, is required for fitness for competition against bacteria and yeasts. J Bacteriol 2012; 194:4810-4822. [doi:10.1128/JB.00611-12] [pmid:22753062]
8. Lindeberg M, Cunnac S, Collmer A. Pseudomonas syringae type III effector repertoires: last words in endless arguments. Trends Microbiol 2012; 20:199-208. [doi:10.1016/j.tim.2012.01.003] [pmid:22341410]
9. Schellenberg B, Ramel C, Dudler R. Pseudomonas syringae Virulence Factor Syringolin A Counteracts Stomatal Immunity by Proteasome Inhibition. Mol Plant Microbe Interact 2010; 23:1287-1293. [doi:10.1094/MPMI-04-10-0094] [pmid:20831408]
10. Bender CL, Alarcón-Chaidez F, Gross DC. Pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases. Microbiology and molecular biology reviews. Microbiol Mol Biol Rev 1999; 63:266-292. [pmid:10357851]
11. Denny TP. Involvement of bacterial polysaccharides in plant pathogenesis. Annu Rev Phytopathol 1995; 33:173-197. [doi:10.1146/annurev.py.33.090195.001133] [pmid:18999958]
12. Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E, et al. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci USA 2005; 102:11064-11069. [doi:10.1073/pnas.0504930102] [pmid:16043691]
13. Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, et al. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc Natl Acad Sci USA 2003; 100:10181-10186. [doi:10.1073/pnas.1731982100] [pmid:12928499]
14. Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, et al. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 2005; 187:6488-6498. [doi:10.1128/JB.187.18.6488-6498.2005] [pmid:16159782]
15. Denny TP. Phenotypic Diversity in Pseudomonas syringae pv. Tomato. Microbiology 1988; 134:1939-1948. [doi:10.1099/00221287-134-7-1939]
16. Hwang MSH, Morgan RL, Sarkar SF, Wang PW, Guttman DS. Phylogenetic characterization of virulence and resistance phenotypes of Pseudomonas syringae. Appl Environ Microbiol 2005; 71:5182-5191. [doi:10.1128/AEM.71.9.5182-5191.2005] [pmid:16151103]
17. Sundin GW, Demezas DH, Bender CL. Genetic and plasmid diversity within natural populations of Pseudomonas syringae with various exposures to copper and streptomycin bactericides. Appl Environ Microbiol 1994; 60:4421-4431. [pmid:7811082]
18. Denny TP, Gilmour MN, Selander RK. Genetic Diversity and Relationships of Two Pathovars of Pseudomonas syringae. J Gen Microbiol 1988; 134:1949-1960. [pmid:2907755]
19. Young JM, Dye DW, Bradbury JF, Panagopoulos CG, Robbs CF. A proposed nomenclature and classification for plant pathogenic bacteria. N Z J Agric Res 1978; 21:153-177. [doi:10.1080/00288233.1978.10427397]
20. Gardan L, Shafik H, Belouin S, Broch R, Grimont F, Grimont PAD. 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 1999; 49:469-478. [doi:10.1099/00207713-49-2-469] [pmid:10319466]
21. Gardan L, Bollet C, Abu Ghorrah M, Grimont F, Grimont PAD. DNA Relatedness among the Pathovar Strains of Pseudomonas syringae subsp. savastanoi Janse (1982) and Proposal of Pseudomonas savastanoi sp. nov. Int J Syst Bacteriol 1992; 42:606-612. [doi:10.1099/00207713-42-4-606]
22. Baltrus DA, Nishimura MT, Romanchuk A, Chang JH, Mukhtar MS, Cherkis K, Roach J, Grant SR, Jones CD, Dangl JL. Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PLoS Pathog 2011; 7:e1002132. [doi:10.1371/journal.ppat.1002132] [pmid:21799664]
23. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. [doi:10.1038/nbt1360] [pmid:18464787]
24. Woese CR. Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. [doi:10.1073/pnas.87.12.4576] [pmid:2112744]
25. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
26. Validation of publication of new names and new combinations previously effectively published outside the IJSEM. List no. 106. Int J Syst Evol Microbiol 2005; 55:2235-2238. [doi:10.1099/ijs.0.64108-0]
27. Garrity GM, Bell JA, Lilburn T. Class III. Gammaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B, Springer, New York, 2005, p. 1.
28. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420. [doi:10.1099/00207713-30-1-225]
29. Orla-Jensen S. The main lines of the natural bacterial system. J Bacteriol 1921; 6:263-273. [pmid:16558921]
30. Garrity G, Bell J, Lilburn T. Order IX. Pseudomonales. In: Garrity G, Brenner D, Krieg N, Staley J, eds. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B. Springer, New York; 2005:323.
31. Winslow CEA, Broadhurst J, Buchanan RE, Krumwiede C, Rogers LA, Smith GH. The Families and Genera of the Bacteria: Preliminary Report of the Committee of the Society of American Bacteriologists on Characterization and Classification of Bacterial Types. J Bacteriol 1917; 2:505-566. [pmid:16558764]
32. Migula W. Über ein neues System der Bakterien. Arb. Bakteriol. Inst. Karlsruhe 1894; 1:235-238.
33. Doudoroff M, Palleroni NJ. Genus Pseudomonas Migula 1894, 237; Nom. cons. Opin. 5, Jud. Comm. 1952, 121. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 217-243.
34. Judicial Commission. Opinion 5: Conservation of the Generic Name Pseudomonas Migula 1894 and Designation of Pseudomonas Aeruginosa (Schroeter) Migula 1900 as Type Species. Int Bull Bacteriol Nomencl Taxon 1952; 2:121-122.
35. Van Hall CJJPD. Dissertation, University of Amsterdam, 1902, p. 198.
36. Palleroni N. Genus I. Pseudomonas. In: Garrity G, Brenner D, Krieg N, Staley J, eds. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B. Springer, New York; 2005:373-377.
37. Palleroni N. Genus I. Pseudomonas. In: Garrity G, Brenner D, Krieg N, Staley J, eds. Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 2, Part B. Springer, New York; 2005:323-357.
38. Young JM, Luketina RC, Marshall AM. The Effects on Temperature on Growth in vitro of Pseudomonas syringae and Xanthomonas pruni. J Appl Bacteriol 1977; 42:345-354. [doi:10.1111/j.1365-2672.1977.tb00702.x] [pmid:885818]
39. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. [doi:10.1038/75556] [pmid:10802651]
40. Sarkar SF, Guttman DS. Evolution of the Core Genome of Pseudomonas syringae, a Highly Clonal, Endemic Plant Pathogen. Appl Environ Microbiol 2004; 70:1999-2012. [doi:10.1128/AEM.70.4.1999-2012.2004] [pmid:15066790]
41. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731-2739. [doi:10.1093/molbev/msr121] [pmid:21546353]
42. Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 1951; 62:293-300. [pmid:14888646]
43. King EO, Ward M, Raney D. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301-307. [pmid:13184240]
44. Palmer DA, Bender CL. Effects of Environmental and Nutritional Factors on Production of the Polyketide Phytotoxin Coronatine by Pseudomonas syringae pv. Glycinea. Appl Environ Microbiol 1993; 59:1619-1626. [pmid:16348941]
45. Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, Lykidis A, Trong S, Nolan M, Goltsman E. Crown Gall of Stone Fruit II. Identification and Nomenclature of Agrobacterium Isolates. Aust J Biol Sci 1970; 23:585-596.
46. Gasson MJ. Indicator Technique for Antimetabolic Toxin Production by Phytopathogenic Species of Pseudomonas. Appl Environ Microbiol 1980; 39:25-29. [pmid:16345492]
47. Clark DJ, Maaløe O. DNA replication and the division cycle in Escherichia coli. J Mol Biol 1967; 23:99-112. [doi:10.1016/S0022-2836(67)80070-6]
48. Mo YY, Gross DC. Plant signal molecules activate the syrB gene, which is required for syringomycin production by Pseudomonas syringae pv. syringae. J Bacteriol 1991; 173:5784-5792. [pmid:1885550]
49. Amrein H, Makart S, Granado J, Shakya R, Schneider-Pokorny J, Dudler R. Functional analysis of genes involved in the synthesis of syringolin A by Pseudomonas syringae pv. syringae B301 D-R. Molecular plant-microbe interactions. Mol Plant Microbe Interact 2004; 17:90-97. [doi:10.1094/MPMI.2004.17.1.90] [pmid:14714872]
50. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75. [doi:10.1186/1471-2164-9-75] [pmid:18261238]
51. Seemann T. Prokka: Prokaryotic Genome Annotation System. 2012. Available at: http://vicbioinformatics.com/.
52. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119. [doi:10.1186/1471-2105-11-119] [pmid:20211023]
53. Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673-679. [doi:10.1093/bioinformatics/btm009] [pmid:17237039]
54. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. [pmid:2231712]
55. Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 2011; 39:D225-D229. [doi:10.1093/nar/gkq1189] [pmid:21109532]
56. Markowitz VM, Mavromatis K, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. [doi:10.1093/bioinformatics/btp393] [pmid:19561336]
57. Groll M, Schellenberg B, Bachmann AS, Archer CR, Huber R, Powell TK, Lindow S, Kaiser M, Dudler R. A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism. Nature 2008; 452:755-758. [doi:10.1038/nature06782] [pmid:18401409]
58. Cunnac S, Chakravarthy S, Kvitko BH, Russell AB, Martin GB, Collmer A. Genetic disassembly and combinatorial reassembly identify a minimal functional repertoire of type III effectors in Pseudomonas syringae. Proc Natl Acad Sci USA 2011; 108:2975-2980. [doi:10.1073/pnas.1013031108] [pmid:21282655]
59. Arrebola E, Cazorla FM, Codina JC, Gutiérrez-Barranquero JA, Pérez-García A, De Vicente A. Contribution of mangotoxin to the virulence and epiphytic fitness of Pseudomonas syringae pv. syringae. International microbiology: the official journal of the Spanish Society for Microbiology 2009;12:87-95.
60. Poole K. Multidrug efflux pumps and antimicrobial resistance in Pseudomonas aeruginosa and related organisms. J Mol Microbiol Biotechnol 2001; 3:255-264. [pmid:11321581]
61. Mima T, Sekiya H, Mizushima T, Kuroda T, Tsuchiya T. Gene cloning and properties of the RND-type multidrug efflux pumps MexPQ-OpmE and MexMN-OprM from Pseudomonas aeruginosa. Microbiol Immunol 2005; 49:999-1002. [pmid:16301811]