Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity

Smits THM, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B (2010)
BMC Genomics 11(1).

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Abstract
Background: Erwinia pyrifoliae is a newly described necrotrophic pathogen, which causes fire blight on Asian (Nashi) pear and is geographically restricted to Eastern Asia. Relatively little is known about its genetics compared to the closely related main fire blight pathogen E. amylovora. Results: The genome of the type strain of E. pyrifoliae strain DSM 12163(T), was sequenced using both 454 and Solexa pyrosequencing and annotated. The genome contains a circular chromosome of 4.026 Mb and four small plasmids. Based on their respective role in virulence in E. amylovora or related organisms, we identified several putative virulence factors, including type III and type VI secretion systems and their effectors, flagellar genes, sorbitol metabolism, iron uptake determinants, and quorum-sensing components. A deletion in the rpoS gene covering the most conserved region of the protein was identified which may contribute to the difference in virulence/host-range compared to E. amylovora. Comparative genomics with the pome fruit epiphyte Erwinia tasmaniensis Et1/99 showed that both species are overall highly similar, although specific differences were identified, for example the presence of some phage gene-containing regions and a high number of putative genomic islands containing transposases in the E. pyrifoliae DSM 12163T genome. Conclusions: The E. pyrifoliae genome is an important addition to the published genome of E. tasmaniensis and the unfinished genome of E. amylovora providing a foundation for re-sequencing additional strains that may shed light on the evolution of the host-range and virulence/pathogenicity of this important group of plant-associated bacteria.
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Smits THM, Jaenicke S, Rezzonico F, et al. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics. 2010;11(1).
Smits, T. H. M., Jaenicke, S., Rezzonico, F., Kamber, T., Goesmann, A., Frey, J. E., & Duffy, B. (2010). Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics, 11(1).
Smits, T. H. M., Jaenicke, S., Rezzonico, F., Kamber, T., Goesmann, A., Frey, J. E., and Duffy, B. (2010). Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics 11.
Smits, T.H.M., et al., 2010. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics, 11(1).
T.H.M. Smits, et al., “Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity”, BMC Genomics, vol. 11, 2010.
Smits, T.H.M., Jaenicke, S., Rezzonico, F., Kamber, T., Goesmann, A., Frey, J.E., Duffy, B.: Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity. BMC Genomics. 11, (2010).
Smits, Theo H. M., Jaenicke, Sebastian, Rezzonico, Fabio, Kamber, Tim, Goesmann, Alexander, Frey, Jürg E, and Duffy, Brion. “Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163(T) and comparative genomic insights into plant pathogenicity”. BMC Genomics 11.1 (2010).
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PMID: 26992913
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PMID: 25073650
PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data.
Cosentino S, Voldby Larsen M, Moller Aarestrup F, Lund O., PLoS ONE 8(10), 2013
PMID: 24204795
Comparative genome analysis of Enterobacter cloacae.
Liu WY, Wong CF, Chung KM, Jiang JW, Leung FC., PLoS ONE 8(9), 2013
PMID: 24069314
Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics.
Smits TH, Rezzonico F, Lopez MM, Blom J, Goesmann A, Frey JE, Duffy B., Syst. Appl. Microbiol. 36(7), 2013
PMID: 23726521
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Mann RA, Smits TH, Buhlmann A, Blom J, Goesmann A, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B., PLoS ONE 8(2), 2013
PMID: 23409014
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Buhlmann A, Pothier JF, Rezzonico F, Smits TH, Andreou M, Boonham N, Duffy B, Frey JE., J. Microbiol. Methods 92(3), 2013
PMID: 23275135
Genome sequence of Pectobacterium carotovorum subsp. carotovorum strain PCC21, a pathogen causing soft rot in Chinese cabbage.
Park TH, Choi BS, Choi AY, Choi IY, Heu S, Park BS., J. Bacteriol. 194(22), 2012
PMID: 23105077
Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis.
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PMID: 22747707
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Malnoy M, Martens S, Norelli JL, Barny MA, Sundin GW, Smits TH, Duffy B., Annu Rev Phytopathol 50(), 2012
PMID: 22702352
Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora.
Rezzonico F, Braun-Kiewnick A, Mann RA, Rodoni B, Goesmann A, Duffy B, Smits TH., Mol. Plant Pathol. 13(8), 2012
PMID: 22583486
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Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B., PLoS ONE 6(7), 2011
PMID: 21789243
Eop1 from a Rubus strain of Erwinia amylovora functions as a host-range limiting factor.
Asselin JE, Bonasera JM, Kim JF, Oh CS, Beer SV., Phytopathology 101(8), 2011
PMID: 21469934
Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants.
Powney R, Smits TH, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B., J. Bacteriol. 193(3), 2011
PMID: 21131493
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Park DH, Thapa SP, Choi BS, Kim WS, Hur JH, Cho JM, Lim JS, Choi IY, Lim CK., J. Bacteriol. 193(2), 2011
PMID: 21075933
Genome sequence of the biocontrol agent Pantoea vagans strain C9-1.
Smits TH, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B., J. Bacteriol. 192(24), 2010
PMID: 20952567
De novo assembly of short sequence reads.
Paszkiewicz K, Studholme DJ., Brief. Bioinformatics 11(5), 2010
PMID: 20724458

82 References

Data provided by Europe PubMed Central.

Erwinia tasmaniensis sp. nov., a non-phytopathogenic bacterium from apple and pear trees.
Geider K, Auling G, Du Z, Jakovljevic V, Jock S, Volksch B., Int. J. Syst. Evol. Microbiol. 56(Pt 12), 2006
PMID: 17159002
Reclassification of non-pigmented Erwinia herbicola strains from trees as Erwinia billingiae sp. nov.
Mergaert J, Hauben L, Cnockaert MC, Swings J., Int. J. Syst. Bacteriol. 49 Pt 2(), 1999
PMID: 10319458
De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.
Hernandez D, Francois P, Farinelli L, Osteras M, Schrenzel J., Genome Res. 18(5), 2008
PMID: 18332092
Development of joint application strategies for two microbial gene finders.
McHardy AC, Goesmann A, Puhler A, Meyer F., Bioinformatics 20(10), 2004
PMID: 14988122
Microbial gene identification using interpolated Markov models.
Salzberg SL, Delcher AL, Kasif S, White O., Nucleic Acids Res. 26(2), 1998
PMID: 9421513
CRITICA: coding region identification tool invoking comparative analysis.
Badger JH, Olsen GJ, Woese CR., Mol. Biol. Evol. 16(4), 1999
PMID: 10331277
The KEGG databases at GenomeNet.
Kanehisa M, Goto S, Kawashima S, Nakaya A., Nucleic Acids Res. 30(1), 2002
PMID: 11752249

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