SpringerLink
Log in

Bioinformatic analysis of the complete genome sequence of Pectobacterium carotovorum subsp. brasiliense BZA12 and candidate effector screening

  • Original Article
  • Published:
Journal of Plant Pathology Aims and scope Submit manuscript

Abstract

Pectobacterium carotovorum subsp. brasiliense (Pcb) is a gram-negative, plant pathogenic bacterium of the soft rot Enterobacteriaceae (SRE) family. We present the complete genome sequence of Pcb strain BZA12, which reveals that Pcb strain BZA12 carries a single 4,924,809 bp chromosome with 51.97% GC content and comprises 4508 predicted protein-coding genes. Gene annotation of these genes utilized GO, KEGG, and COG databases. In comparison with three closely related soft-rot pathogens, strain BZA12 has 3797 gene families, among which 3107 gene families are identified as orthologous with those of both P. carotovorum subsp. carotovorum PCC21 and P. carotovorum subsp. odoriferum BCS7, as well as 36 putative Unique Gene Families. We selected five putative effectors from the BZA12 genome and transiently expressed them in Nicotiana benthamiana. Candidate effector A12GL002483 was localized in the cell nucleus and induced cell death. This study provides a foundation for a better understanding of the genomic structure and function of Pcb, particularly in the discovery of potential pathogenic factors and for the development of more effective strategies against this pathogen.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  • Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S (2009) Correction: sequence-based prediction of type iii secreted proteins. PLoS Pathog 5:e1000376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bard J, Winter R (2000) Gene ontology:tool for the unification of biology. Nat Genet 25:25–29

    Article  CAS  Google Scholar 

  • Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bent AF, Mackey D (2007) Elicitors, effectors, and R genes: the new paradigm and a lifetime supply of questions. Annu Rev Phytopathol 45:399–436

    Article  CAS  PubMed  Google Scholar 

  • Caillaud M, Asai S, Rallapalli G, Piquerez S, Fabro G, Jones JDG (2013) A downy mildew effector attenuates salicylic acid–triggered immunity in arabidopsis by interacting with the host mediator complex. PLoS Biol 11:e1001732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charkowski A, Blanco C, Condemine G, Expert D, Franza T, Hayes C (2012) The role of secretion systems and small molecules in soft-rot Enterobacteriaceae pathogenicity. Annu Rev Phytopathol 50:425–449

    Article  CAS  PubMed  Google Scholar 

  • Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: sha** the evolution of the plant immune response. Cell 124:803–814

    Article  CAS  PubMed  Google Scholar 

  • Choi O, Kim J (2013) Pectobacterium carotovorum subsp. brasiliense, causing soft rot on paprika in Korea. J Phytopathol 161:125–127

    Article  CAS  Google Scholar 

  • Coburn B, Sekirov I, Finlay BB (2007) Type iii secretion systems and disease. Clin Microbiol Rev 20:535–549

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Delcher AL, Bratke KA, Powers EC (2007) Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 23:673–679

    Article  CAS  PubMed  Google Scholar 

  • Dong X, Zhang YJ, Zhang Z (2013) Using weakly conserved motifs hidden in secretion signals to identify type-iii effectors from bacterial pathogen genomes. PLoS One 8:e56632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dou D, Zhou JM (2012) Phytopathogen effectors subverting host immunity: different foes, similar battleground. Cell Host Microbe 12:484–495

    Article  CAS  PubMed  Google Scholar 

  • Fujimoto T, Yasuoka S, Aono Y, Nakayama T, Ohki T, Sayama M, Maoka T (2016) First report of potato blackleg caused by Pectobacterium carotovorum subsp brasiliense in Japan. Plant Dis 101:241–242

    Article  Google Scholar 

  • Gardiner L-J (2014) New technologies for high throughput genetic analysis of complex genomes.Ph.D. In: Thesis. University of Liverpool, London

    Google Scholar 

  • Gardner PP, Daub J, Tate JG (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37:D136–D140

    Article  CAS  PubMed  Google Scholar 

  • Glasner JM, Kim HS, Jahn CE, Ma B, Biehl BS, Rissman AI (2008) Niche-specificity and the variable fraction of the Pectobacterium pan-genome. Mol Plant-Microbe Interact 21:1549–1560

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kent WJ (2002) Blat--the blast-like alignment tool. Genome Res 12:656–664

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HS, Thammarat P, Lommel SA, Hogan CS, Charkowski AO (2011) Pectobacterium carotovorum elicits plant cell death with dspe/f but the p. carotovorum dspe does not suppress callose or induce expression of plant genes early in plant-microbe interactions. Mol Plant-Microbe Interact 24:773–786

    Article  CAS  PubMed  Google Scholar 

  • Lagesen K, Hallin PF, Rødland E (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Laverde AJ, Davey CAH, López EDG (2017) First report of bacterial stem rot of tomatoes caused by Pectobacterium carotovorum subsp. brasiliense in Colombia. Plant Dis 101:830

    Google Scholar 

  • Li H.L., (2013) Identification of four pathogenic bacteria causing bacterial diseases in vegetables. Master Thesis, Chinese Academy of Agricultural Sciences

  • Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ma B, Hibbing ME, Kim HS, Reedy RM, Yedidia I, Breuer J (2007) Host range and molecular phylogenies of the soft rot enterobacterial genera pectobacterium and dickeya. Phytopathology 97:1150

    Article  PubMed  Google Scholar 

  • Magrane M., UniProt Consortium, (2011) UniProt knowledgebase: a hub of integrated protein data. Database : the journal of biological databases and curation, (Oxford), bar009

  • Mashavha M.L., (2013) Characterisation of Pectobacterium carotovorum subsp. brasiliense isolates causing blackleg and soft rot diseases of potato in south Africa Ph.D. Thesis. Pretoria University, South Africa

  • Meng X, Chai A, Li B, Ma Z, Shi Y, **e X (2016) Emergence of bacterial soft rot in cucumber caused by Pectobacterium carotovorum subsp. brasiliense in China. Plant Dis 101:279–287

    Article  PubMed  Google Scholar 

  • Nabhan S, de Boer SH, Maiss E, Wydra K (2012) Taxonomic relatedness between Pectobacterium carotovorum subsp. carotovorum, Pectobacterium carotovorum subsp. odoriferum and Pectobacterium carotovorum subsp. brasiliense subsp. nov. J Appl Microbiol 113:904–913

  • Ochiai H, Inoue Y, 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. Jpn Agric Res Q 39:275–287

    Article  CAS  Google Scholar 

  • Onkendi EM, Moleleki LN (2014) Characterization of Pectobacterium carotovorum, subsp. carotovorum, and brasiliense, from diseased potatoes in Kenya. Eur J Plant Pathol 139:557–566

    Article  Google Scholar 

  • Onkendi EM, Ramesh AM, Kwenda S, Naidoo S, Moleleki L (2016) Draft genome sequence of a virulent Pectobacterium carotovorum subsp. brasiliense isolate causing soft rot of cucumber. Genome Announc 4:e01530-15

    Article  PubMed  PubMed Central  Google Scholar 

  • Pérombelon MCM (2002) Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol 51:1–12

    Article  Google Scholar 

  • Pérombelon MCM, Kelman A (1980) Ecology of the soft rot erwinias. Annu Rev Phytopathol 18:361–387

    Article  Google Scholar 

  • Tatusov RL, Fedorova ND (2003) The COG database: an updated version includes eukaryotes. BMC Bioinf 11:4–41

    Google Scholar 

  • Toth IK, Bell KS, Holeva MC, Birch PRJ (2003) Soft rot erwiniae: from genes to genomes. Mol Plant Pathol 4:17–30

    Article  CAS  PubMed  Google Scholar 

  • Waldee EL (1945) Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State Coll J Sci 19:435–484

    Google Scholar 

  • Waleron M, Waleron K, Lojkowska E (2015) First report of Pectobacterium carotovorum subsp. brasiliense causing soft rot on potato and other vegetables in Poland. Plant Dis 99:1271

    Article  Google Scholar 

  • Wang Y, Huang H, Sun M, Zhang Q, Guo D (2012a) T3db: an integrated database for bacterial type iii secretion system. BMC Bioinf 13:66

    Article  CAS  Google Scholar 

  • Wang Y, Tang H, Debarry JD, Tan X, Li J, Wang X (2012b) Mcscanx: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res 40:e49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang J, Wang YH, Zhao T, Dai PG, Chen D, Li XL (2017) First report of tobacco bacterial leaf blight caused by Pectobacterium carotovorum. Subsp. brasiliense in China. Plant Dis 101:830

    Article  Google Scholar 

  • Werra PD, Bussereau F, Keiser A, Ziegler D (2009) First report of potato blackleg caused by Pectobacterium carotovorum subsp. brasiliense in switzerland. Plant Dis 99:551

    Article  Google Scholar 

  • Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K (2013) The noncanonical type iii secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection. Mol Plant Pathol 14:576–588

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Z (2007) Paml 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    Article  CAS  PubMed  Google Scholar 

  • Zhang S, Bo H, **a XF, Sun ZR (2007) Bioinformatics research in subcellular localization of protein. Prog Biochem Biophys 34:573–579

    Google Scholar 

Download references

Acknowledgements

This project was supported by the National Key R&D Program of China (2017YED0201100).

Author information

Authors and Affiliations

  1. College of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, China

    Yufei Huang

  2. Institute of Plant Protection, Liaoning Academy of Agricultural Sciences, Shenyang, 110161, China

    Changyuan Liu, Hui Wang, Tianshu Guan, Li Liu & Shuyi Yu

Authors
  1. Yufei Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Changyuan Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hui Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tianshu Guan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Li Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Shuyi Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Changyuan Liu.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Huang, Y., Liu, C., Wang, H. et al. Bioinformatic analysis of the complete genome sequence of Pectobacterium carotovorum subsp. brasiliense BZA12 and candidate effector screening. J Plant Pathol 101, 39–49 (2019). https://doi.org/10.1007/s42161-018-0126-7

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s42161-018-0126-7

Keywords

Search

Navigation