Journal of Plant Pathology

, Volume 101, Issue 1, pp 39–49 | Cite as

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

  • Yufei Huang
  • Changyuan LiuEmail author
  • Hui Wang
  • Tianshu Guan
  • Li Liu
  • Shuyi Yu
Original Article


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.


P. carotovorum subsp. brasiliense Complete genome sequence Effector 



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


  1. 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:e1000376CrossRefGoogle Scholar
  2. Bard J, Winter R (2000) Gene ontology:tool for the unification of biology. Nat Genet 25:25–29CrossRefGoogle Scholar
  3. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580CrossRefGoogle Scholar
  4. Bent AF, Mackey D (2007) Elicitors, effectors, and R genes: the new paradigm and a lifetime supply of questions. Annu Rev Phytopathol 45:399–436CrossRefGoogle Scholar
  5. 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:e1001732CrossRefGoogle Scholar
  6. 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 50:425–449CrossRefGoogle Scholar
  7. Chisholm ST, Coaker G, Day B, Staskawicz BJ (2006) Host-microbe interactions: shaping the evolution of the plant immune response. Cell 124:803–814CrossRefGoogle Scholar
  8. Choi O, Kim J (2013) Pectobacterium carotovorum subsp. brasiliense, causing soft rot on paprika in Korea. J Phytopathol 161:125–127CrossRefGoogle Scholar
  9. Coburn B, Sekirov I, Finlay BB (2007) Type iii secretion systems and disease. Clin Microbiol Rev 20:535–549CrossRefGoogle Scholar
  10. Delcher AL, Bratke KA, Powers EC (2007) Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 23:673–679CrossRefGoogle Scholar
  11. 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:e56632CrossRefGoogle Scholar
  12. Dou D, Zhou JM (2012) Phytopathogen effectors subverting host immunity: different foes, similar battleground. Cell Host Microbe 12:484–495CrossRefGoogle Scholar
  13. 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 101:241–242CrossRefGoogle Scholar
  14. Gardiner L-J (2014) New technologies for high throughput genetic analysis of complex genomes.Ph.D. In: Thesis. University of Liverpool, LondonGoogle Scholar
  15. Gardner PP, Daub J, Tate JG (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37:D136–D140CrossRefGoogle Scholar
  16. 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 21:1549–1560CrossRefGoogle Scholar
  17. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280CrossRefGoogle Scholar
  18. Kent WJ (2002) Blat--the blast-like alignment tool. Genome Res 12:656–664CrossRefGoogle Scholar
  19. 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 24:773–786CrossRefGoogle Scholar
  20. Lagesen K, Hallin PF, Rødland E (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108CrossRefGoogle Scholar
  21. 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 101:830Google Scholar
  22. Li H.L., (2013) Identification of four pathogenic bacteria causing bacterial diseases in vegetables. Master Thesis, Chinese Academy of Agricultural SciencesGoogle Scholar
  23. Li L, Stoeckert CJ, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189CrossRefGoogle Scholar
  24. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefGoogle Scholar
  25. 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 97:1150CrossRefGoogle Scholar
  26. Magrane M., UniProt Consortium, (2011) UniProt knowledgebase: a hub of integrated protein data. Database : the journal of biological databases and curation, (Oxford), bar009Google Scholar
  27. 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 AfricaGoogle Scholar
  28. Meng X, Chai A, Li B, Ma Z, Shi Y, Xie X (2016) Emergence of bacterial soft rot in cucumber caused by Pectobacterium carotovorum subsp. brasiliense in China. Plant Dis 101:279–287CrossRefGoogle Scholar
  29. 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 113:904–913Google Scholar
  30. 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 39:275–287CrossRefGoogle Scholar
  31. Onkendi EM, Moleleki LN (2014) Characterization of Pectobacterium carotovorum, subsp. carotovorum, and brasiliense, from diseased potatoes in Kenya. Eur J Plant Pathol 139:557–566CrossRefGoogle Scholar
  32. 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:e01530-15CrossRefGoogle Scholar
  33. Pérombelon MCM (2002) Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol 51:1–12CrossRefGoogle Scholar
  34. Pérombelon MCM, Kelman A (1980) Ecology of the soft rot erwinias. Annu Rev Phytopathol 18:361–387CrossRefGoogle Scholar
  35. Tatusov RL, Fedorova ND (2003) The COG database: an updated version includes eukaryotes. BMC Bioinf 11:4–41Google Scholar
  36. Toth IK, Bell KS, Holeva MC, Birch PRJ (2003) Soft rot erwiniae: from genes to genomes. Mol Plant Pathol 4:17–30CrossRefGoogle Scholar
  37. Waldee EL (1945) Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State Coll J Sci 19:435–484Google Scholar
  38. 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 99:1271CrossRefGoogle Scholar
  39. Wang Y, Huang H, Sun M, Zhang Q, Guo D (2012a) T3db: an integrated database for bacterial type iii secretion system. BMC Bioinf 13:66CrossRefGoogle Scholar
  40. 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:e49CrossRefGoogle Scholar
  41. 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 101:830CrossRefGoogle Scholar
  42. Werra PD, Bussereau F, Keiser A, Ziegler D (2009) First report of potato blackleg caused by Pectobacterium carotovorum subsp. brasiliense in switzerland. Plant Dis 99:551CrossRefGoogle Scholar
  43. 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 14:576–588CrossRefGoogle Scholar
  44. Yang Z (2007) Paml 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591CrossRefGoogle Scholar
  45. Zhang S, Bo H, Xia XF, Sun ZR (2007) Bioinformatics research in subcellular localization of protein. Prog Biochem Biophys 34:573–579Google Scholar

Copyright information

© Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2018

Authors and Affiliations

  • Yufei Huang
    • 1
  • Changyuan Liu
    • 2
    Email author
  • Hui Wang
    • 2
  • Tianshu Guan
    • 2
  • Li Liu
    • 2
  • Shuyi Yu
    • 2
  1. 1.College of Plant ProtectionShenyang Agricultural UniversityShenyangChina
  2. 2.Institute of Plant ProtectionLiaoning Academy of Agricultural SciencesShenyangChina

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