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


The Gram-negative gammaproteobacterium Pseudomonas syringae is one of the most wide-spread plant pathogens and has been repeatedly reported to cause significant damage to crop plantations. Research on this pathogen is very intensive, but most of it is done on isolates that are pathogenic to Arabidopsis, tomato, and bean. Here, we announce a high-quality draft genome sequence of Pseudomonas syringae pv. syringae B64 which is the first published genome of a P. syringae strain isolated from wheat up to date. The genome sequence will assist in gaining insights into basic virulence mechanisms of this pathogen which has a relatively small complement of type III effectors.


Pseudomonas syringae strains have been isolated from more than 180 host species [1] across the entire plant kingdom, including many agriculturally important crops, such as bean, tomato, cucumber, as well as kiwi, stone fruit, and olive trees. Strains are divided into more than 50 pathovars primarily based on host-specificity, disease symptoms, and biochemical profiles [24]. The first strain of this species was isolated from a lilac tree (Syringa vulgaris), which gave origin to its name [5].The observed wide host range is reflected in a relatively large genetic heterogeneity among different pathovars. This is most pronounced in the complement of virulence factors, which is also assumed to be the key factor defining host specificity [6]. For successful survival and reproduction, both epiphytic and endophytic P. syringae strains deploy different sets of type III and type VI secretion system effectors, phytotoxins, EPS, and other types of secreted molecules [611]. Currently, there are three completely sequenced P. syringae genomes published: pathovar syringae strain B728a which causes brown spot disease of bean [12], pathovar tomato strain DC3000 which is pathogenic to tomato and Arabidopsis [13], and pathovar phaseolicola strain 1448A, causal agent of halo blight on bean [14]. There are also a number of incomplete genomes of various qualities available for other strains.

Pseudomonas syringae pv. syringae strain B64 was isolated from hexaploid wheat (Triticum aestivum) in Minnesota, USA [15]. The strain has been deployed in several studies mainly addressing phylogenetic diversity of P. syringae varieties [1518], but never as an infection model for wheat. The genome sequencing of the B64 strain and its comparison with the other published genomes should reveal wheat-specific adaptations and give insights in virulence strategies for colonizing monocot plants.

Classification and features

Pseudomonas syringae belongs to class Gammaproteobacteria. Detailed classification of this species is still under heavy debate. Young and colleagues have proposed to group all plant-pathogenic oxidase-negative and fluorescent Pseudomonas strains into a single species, P. syringae, which is to be further sub-divided into pathovars [4,19]. Several DNA hybridization studies have shown a large genetic heterogeneity among the groups, however biochemical characteristics, with a few exceptions, did not allow elevating those into distinct species [20,21]. Currently, the species is divided into five phylogenetic clades based on MLST analysis. P. syringae pv. syringae (Pss) strains belong to group II within this nomenclature [22]. The basic characteristics of Pss B64 are summarized in Table 1, while its phylogenetic position is depicted in Figure 1.

Figure 1.

Phylogenetic tree constructed using neighbor-joining method using MLST approach [40] and MEGA 5.10 software suit [41] with 1,000 bootstraps. The tree features the three completely sequenced P. syringae model strains Pto DC3000, Pss B728a, and Pph 1448A, the strain Pss B64 itself, as well as another wheat-isolated strain Pss SM. The model strains represent the major phylogenetic clades of P. syringae: I, II and III respectively. P. fluorescens Pf0-1 was used as an outgroup. The analysis confirms placement of Pss B64 into clade II.

Table 1. Classification and the general features of P. syringae pv. syringae B64 according to the MIGS recommendations [23]

Pss B64 has similar physiological properties as other representatives of its genus. It can grow in complex media such as LB [42] or King’s B [43], as well as in various defined minimal media: HSC [44], MG-agar [45], PMS [46], AB-agar [47], and SRMAF [48]. Even though the optimal growth temperature is 28°C, the bacterium can also replicate at 4°C. Growth is completely inhibited above 35°C. Pss B64 is capable of endophytic growth in the wheat leaf mesophyll, but does not seem to cause any symptoms unless a very high inoculation dose is applied.

The bacterium has a weak resistance to ampicillin (25 mg/L) and chloramphenicol (10 mg/L). It is also possible to develop spontaneous rifampicin-resistant mutants. In addition, the genomic sequence predicts this strain to be polymyxin B insensitive due to presence of the arn gene cluster.

Genome sequencing information

Genome project history

The organism was selected for sequencing because it has been identified to have a syringolin biosynthesis gene cluster [49]. Syringolin is a proteasome inhibitor produced by some strains of pathovar syringae. As a consequence of proteasome inactivation a number of plant intracellular pathways are being inhibited, including the entire salicylic acid-dependent defense pathway, thus promoting the entry of bacteria into leaf tissue and subsequent endophytic growth [9]. Since up to now it has not been possible to establish an infection model for syringolin in the model plant Arabidopsis, it was decided to explore another common research target and one of the most important crop plants, bread wheat (Triticum aestivum). The genome project has been deposited in the Genbank Database (ID 180994) and the genome sequence is available under accession number ANZF00000000. The version described in this paper is the first version, ANZF01000000. The details of the project are shown in Table 2.

Table 2. Genome sequencing project information

Growth conditions and DNA isolation

P. syringae pv. syringae strain B64 was grown in 40 mL of LB medium at 28°C, 220 rpm until OD600 of 1.0. Genomic DNA was isolated from the pelleted cell using a Qiagen Genomic-tip 100/G column (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

Genome sequencing and assembly

A 3kb paired-end library was generated and sequenced at the Functional Genomics Center Zurich on a Roche Genome Sequencer FLX+ platform. A total of 872,570 high-quality filtered reads with a total of 188,465,376 bases were obtained, resulting in 31.8-fold average sequencing coverage. The obtained reads were assembled de novo using Newbler 2.5.3. This resulted in 150 contigs combined into one 6 Mb-long super-scaffold and 3 smaller scaffolds of 5.29 kb, 2.84 kb and 2.74 kb in size. The largest of the minor scaffolds constituted a ribosomal RNA operon, the other two showed sequence similarity to non-ribosomal peptide synthase modules. A portion of intra-scaffold gaps have been closed by sequencing of PCR products using Sanger technology, decreasing the total number of contigs to 41 with a contig N50 value of 329.4 kb, the longest contig being 766.5 kb long. Note that the Genbank record contains 42 contigs due to fact that one of the contigs was split into two parts in order to start the assembly with the dnaA gene. While closing gaps it became possible to allocate the positions of all ribosomal operons by sequence overlap and thus to incorporate the largest of the minor scaffolds. However, it was not possible to precisely map the remaining two minor scaffolds. These must be located within two distinct remaining large gaps, but due to insignificance to the project they have been excluded from the assembly.

Genome annotation

Initial open-reading frame (ORF), tRNA, and rRNA prediction and functional annotation has been performed using the RAST (Rapid Annotation using Subsystem Technology) server [50]. For the purpose of comparison, the genome has also been annotated using Prokka [51], which utilizes Prodigal [52] for ORF prediction (the RAST server utilizes a modified version of Glimmer [53]). Start codons of all the predicted ORFs were further verified manually, using the position of potential ribosomal binding sites and BLASTP [54] alignments with homologous ORFs from other P. syringae strains as a reference. Functional annotations have also been refined for every ORF using BLASTP searches against the non-redundant protein sequence database (nr) and the NCBI Conserved-Domain search engine [55]. Functional category assignment and signal peptide prediction was done using the Integrated Microbial Genomes/Expert reviews (IMG/ER) system [56].

Genome properties

The genome of the strain B64 is estimated to be comprised of 5,930,035 base pairs with an average GC-content of 58.55 % (Table 3 and Figure 2), which is similar to what is observed in other P. syringae strains [12,13,53]. Of the 5,021 predicted genes, 4,947 were protein coding genes, 4 ribosomal RNA operons, and 61 tRNA genes; 78 were identified to be pseudo-genes. The majority of the protein-coding genes (83.65 %) were assigned a putative function, while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Figure 2.

Graphical map of the chromosome. From outside to the center: genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes: tRNAs - green, rRNAs - red, other RNAs - black, GC content, and GC skew

Table 3. Genome Statistics
Table 4. Number of genes associated with the 25 general COG functional categories

The genome contains a complete canonical type III secretion system and ten known effector proteins: AvrE1, HopAA1, HopI1, HopM1, HopAH1, HopAG1, HopAI1, HopAZ1, HopBA1, and HopZ3. Out of these ten, the first five are present in all other sequenced P. syringae strains, thereby constituting the effector core, whereas the latter five could be host-determinants for wheat. That there is such a small number of effectors is not something unusual, and is seen in other strains of clade II [22]. In addition, there are two complete type VI secretion system gene clusters and nine putative effector proteins belonging to the VgrG and Hcp1 families. Pss B64 genome also encodes gene clusters for biosynthesis of four phytotoxin: syringomycin, syringopeptin, syringolin, and mangotoxin. All of the above-mentioned genome components have been previously demonstrated to be involved in virulence, epiphytic fitness of P. syringae, as well as in competition with other microbial species [710,5759]. Additional identified virulence-associated traits are: exopolysaccharides alginate, Psl, and levan biosynthesis, surfactant syringofactin, type VI pili, large surface adhesins, siderophores pyoverdine and achromobactin, proteases and other secreted hydrolytic enzymes, RND-type transporters (including putative mexAB, mexCD, mexEF, and mexMN homologs [60,61]), all of which are found in other P. syringae strains. It is also notable that inaZ gene encoding ice-nucleation protein is truncated by a frameshift, thus making this strain ice-negative. The latter contradicts results of a previous study by Hwang and colleagues [16] in which Pss B64 has been identified to be ice-positive. This could be due to an assembly error, or the frameshift could have been introduced at a later point during propagation.


Pss :

Pseudomonas syringae pathovar syringae

Pto :

Pseudomonas syringae pathovar tomato

Pph :

Pseudomonas syringae pathovar phaseolicola


Exopolymeric sub-stances


non-ribosomal peptide synthetase


multilocus sequence typing


  1. 1.

    Bradbury JF. Guide to Plant Pathogenic. Kew, England: CAB International Mycological Institute; 1985:175–177.

    Google Scholar 

  2. 2.

    Gonzalez AJ, Landeras E, Mendoza MC. Pathovars of causing bacterial brown spot and halo blight in Phaseolus vulgaris L. are distinguishable by ribotyping. Appl Environ Microbiol 2000; 66:850–854

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  3. 3.

    Qi M, Wang D, Bradley CA, Zhao Y. Genome sequence analyses of pv. glycinea and subtractive hybridization-based comparative genomics with nine pseudomonads. PLoS ONE 2011; 6:e16451.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  4. 4.

    Young JM. Taxonomy of. Journal of Plant Pathology 2010; 92:S1.5–S1.14. Available at: w/2501. Accessed March 20, 2013.

    Google Scholar 

  5. 5.

    Palleroni N. Genus I.. 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. 6.

    Lindeberg M, Cunnac S, Collmer A. The evolution of host specificity and type III effector repertoires. Mol Plant Pathol 2009; 10:767–775.

    Article  CAS  PubMed  Google Scholar 

  7. 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 pv. tomato DC3000, is required for fitness for competition against bacteria and yeasts. J Bacteriol 2012; 194:4810–4822.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  8. 8.

    Lindeberg M, Cunnac S, Collmer A. type III effector repertoires: last words in endless arguments. Trends Microbiol 2012; 20:199–208;. PubMed

    Article  CAS  PubMed  Google Scholar 

  9. 9.

    Schellenberg B, Ramel C, Dudler R. Virulence Factor Syringolin A Counteracts Stomatal Immunity by Proteasome Inhibition. Mol Plant Microbe Interact 2010; 23:1287–1293;. PubMed

    Article  CAS  PubMed  Google Scholar 

  10. 10.

    Bender CL, Alarcón-Chaidez F, Gross DC. 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;. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  11. 11.

    Denny TP. Involvement of bacterial polysaccharides in plant pathogenesis. Annu Rev Phytopathol 1995; 33:173–197. PubMed 001133

    Article  CAS  PubMed  Google Scholar 

  12. 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 pv. syringae B728a and pv. tomato DC3000. Proc Natl Acad Sci USA 2005; 102:11064–11069.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  13. 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 pv. tomato DC3000. Proc Natl Acad Sci USA 2003; 100:10181–10186.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  14. 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 pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J Bacteriol 2005; 187:6488–6498.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  15. 15.

    Denny TP. Phenotypic Diversity in pv. tomato. Microbiology 1988; 134:1939–1948.

    Article  Google Scholar 

  16. 16.

    Hwang MSH, Morgan RL, Sarkar SF, Wang PW, Guttman DS. Phylogenetic characterization of virulence and resistance phenotypes of. Appl Environ Microbiol 2005; 71:5182–5191.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  17. 17.

    Sundin GW, Demezas DH, Bender CL. Genetic and plasmid diversity within natural populations of with various exposures to copper and streptomycin bactericides. Appl Environ Microbiol 1994; 60:4421–4431.

    PubMed Central  CAS  PubMed  Google Scholar 

  18. 18.

    Denny TP, Gilmour MN, Selander RK. Genetic Diversity and Relationships of Two Pathovars of. J Gen Microbiol 1988; 134:1949–1960.

    CAS  PubMed  Google Scholar 

  19. 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. 397

    Article  Google Scholar 

  20. 20.

    Gardan L, Shafik H, Belouin S, Broch R, Grimont F, Grimont PAD. DNA relatedness among the pathovars of and description of sp. nov. and sp. nov. (ex Sutic and Dowson 1959). Int J Syst Bacteriol 1999; 49:469–478.

    Article  CAS  PubMed  Google Scholar 

  21. 21.

    Gardan L, Bollet C, Abu Ghorrah M, Grimont F, Grimont PAD. DNA Relatedness among the Pathovar Strains ofastanoi Janse (1982) and Proposal of sp. nov. Int J Syst Bacteriol 1992; 42:606–612.

    Article  CAS  Google Scholar 

  22. 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 isolates. PLoS Pathog 2011; 7:e1002132.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  23. 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. PubMed

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  24. 24.

    Woese CR. Towards a Natural System of Organisms: Proposal for the Domains,, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576–4579.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  25. 25.

    Garrity GM, Bell JA, Lilburn T. Phylum XIV. 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

    Google Scholar 

  26. 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.

  27. 27.

    Garrity GM, Bell JA, Lilburn T. Class III. 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.

    Chapter  Google Scholar 

  28. 28.

    Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225–420.

    Article  Google Scholar 

  29. 29.

    Orla-Jensen S. The main lines of the natural bacterial system. J Bacteriol 1921; 6:263–273. PubMed

    PubMed Central  CAS  PubMed  Google Scholar 

  30. 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.

    Chapter  Google Scholar 

  31. 31.

    Winslow CEA, Broadhurst J, Buchanan RE, Krumwiede C, Rogers LA, Smith GH. The Families and Genera of the: Preliminary Report of the Committee of the Society of American Bacteriologists on Characterization and Classification of Bacterial Types. J Bacteriol 1917; 2:505–566.

    PubMed Central  CAS  PubMed  Google Scholar 

  32. 32.

    Migula W. Über ein neues System der Bakterien. Arb. Bakteriol. Inst. Karlsruhe 1894; 1:235–238.

    Google Scholar 

  33. 33.

    Doudoroff M, Palleroni NJ. Genus 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.

    Google Scholar 

  34. 34.

    Judicial Commission. Opinion 5: Conservation of the Generic Name Migula 1894 and Designation of Aeruginosa (Schroeter) Migula 1900 as Type Species. Int Bull Bacteriol Nomencl Taxon 1952; 2:121–122.

    Google Scholar 

  35. 35.

    van Hall CJJPD. Dissertation, University of Amsterdam, 1902, p. 198.

  36. 36.

    Palleroni N. Genus I.. 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.

    Google Scholar 

  37. 37.

    Palleroni N. Genus I.. 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.

    Google Scholar 

  38. 38.

    Young JM, Luketina RC, Marshall AM. The Effects on Temperature on Growth in vitro of and pruni. J Appl Bacteriol 1977; 42:345–354.

    Article  CAS  PubMed  Google Scholar 

  39. 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. PubMed

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  40. 40.

    Sarkar SF, Guttman DS. Evolution of the Core Genome of, a Highly Clonal, Endemic Plant Pathogen. Appl Environ Microbiol 2004; 70:1999–2012.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  41. 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. PubMed

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  42. 42.

    Bertani G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic. J Bacteriol 1951; 62:293–300.

    PubMed Central  CAS  PubMed  Google Scholar 

  43. 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. PubMed

    CAS  PubMed  Google Scholar 

  44. 44.

    Palmer DA, Bender CL. Effects of Environmental and Nutritional Factors on Production of the Polyketide Phytotoxin Coronatine by pv. Glycinea. Appl Environ Microbiol 1993; 59:1619–1626.

    PubMed Central  CAS  PubMed  Google Scholar 

  45. 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 Isolates. Aust J Biol Sci 1970; 23:585–596.

    Google Scholar 

  46. 46.

    Gasson MJ. Indicator Technique for Antimetabolic Toxin Production by Phytopathogenic Species of. Appl Environ Microbiol 1980; 39:25–29.

    PubMed Central  CAS  PubMed  Google Scholar 

  47. 47.

    Clark DJ, Maaløe O. DNA replication and the division cycle in. J Mol Biol 1967; 23:99–112.

    Article  CAS  Google Scholar 

  48. 48.

    Mo YY, Gross DC. Plant signal molecules activate the syrB gene, which is required for syringomycin production by pv. syringae. J Bacteriol 1991; 173:5784–5792.

    PubMed Central  CAS  PubMed  Google Scholar 

  49. 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 pv. syringae B301 D-R. Molecular plant-microbe interactions. Mol Plant Microbe Interact 2004; 17:90–97.

    Article  CAS  PubMed  Google Scholar 

  50. 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. PubMed

    PubMed Central  Article  PubMed  Google Scholar 

  51. 51.

    Seemann T. Prokka: Prokaryotic Genome Annotation System. 2012. Available at:

  52. 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. PubMed

    PubMed Central  Article  PubMed  Google Scholar 

  53. 53.

    Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007; 23:673–679. PubMed

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  54. 54.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410. PubMed

    Article  CAS  PubMed  Google Scholar 

  55. 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. PubMed

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  56. 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. PubMed

    Article  CAS  PubMed  Google Scholar 

  57. 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. PubMed

    Article  CAS  PubMed  Google Scholar 

  58. 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. Proc Natl Acad Sci USA 2011; 108:2975–2980.

    PubMed Central  Article  CAS  PubMed  Google Scholar 

  59. 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 pv. syringae. International microbiology: the official journal of the Spanish Society for Microbiology 2009; 12:87–95.

    CAS  Google Scholar 

  60. 60.

    Poole K. Multidrug efflux pumps and antimicrobial resistance in and related organisms. J Mol Microbiol Biotechnol 2001; 3:255–264.

    CAS  PubMed  Google Scholar 

  61. 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. Microbiol Immunol 2005; 49:999–1002.

    Article  CAS  PubMed  Google Scholar 

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The authors would like to thank Dr. Daria Zhurina for her useful suggestions on the gap closure and the annotation procedures. This project was supported by the Swiss National Science Foundation (31003A-134936) and the Foundation for Research in Science and the Humanities at the University of Zurich.

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Correspondence to Robert Dudler.

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Dudnik, A., Dudler, R. Non contiguous-finished genome sequence of Pseudomonas syringae pathovar syringae strain B64 isolated from wheat. Stand in Genomic Sci 8, 420–429 (2013).

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  • Pseudomonas syringae
  • genome
  • syringolin
  • wheat
  • plant-pathogen interactions