Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031

Standards in Genomic Sciences

Volumn 11, Issue 1, 2016, Pages

  Guarischi Sousa, Rodrigo ^a   Puigvert, Marina ^b   Coll, Núria S ^b   Siri, María Inés ^c   Pianzzola, María Julia ^c   Valls, Marc ^b   Setubal, João C ^a,d  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

^b CENTRE FOR RESEARCH IN AGRICULTURAL GENOMICS CRAG   (Spain)

^c UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

^d VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

Bacterial plant pathogen; Bacterial wilt; Methylome; Ralstonia solanacearum; Short genome report; Uruguay

Indexed keywords

ENTEROTOXIN; GENOMIC DNA;

ARTICLE; DOWNSTREAM PROCESSING; FRAMESHIFT MUTATION; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; PATHOGENICITY; PROTEIN ASSEMBLY; RALSTONIA SOLANACEARUM;

EID: 84954158136     PISSN: None     EISSN: 19443277     Source Type: Journal    
DOI: 10.1186/s40793-016-0131-4     Document Type: Article

References (37)

1. Mansfield J, Genin S, Magori S, Citovsky V, Sriariyanum M, Ronald P, et al. Top 10 plant pathogenic bacteria in molecular plant pathology. Mol Plant Pathol. 2012;13(6):614-29.
2. Genin S, Denny TP. Pathogenomics of the Ralstonia solanacearum species complex. Annu Rev Phytopathol. 2012;50:67-89.
3. Fegan M, Prior P. How complex is the 'Ralstonia solanacearum' species complex? In: Allen CP, editor. Bacterial wilt: The disease and the ralstonia solanacearum species complex. Prior, Hayward AC. St. Paul, MN: American Phytopathological Society; 2005. p. 449-61.
4. Janse JD, van den Beld HE, Elphinstone J, Simpkins S, Tjou-Tam-Sin NNA, van Vaerenbergh J. Introduction to Europe of Ralstonia solanacearum biovar 2, race 3 in Pelargonium zonale cuttings. J Plant Pathol. 2004;86(2):147-55.
5. Siri MI, Sanabria A, Pianzolla MJ. Genetic diversity and aggressiveness of Ralstonia solanacearum strains causing bacterial wilt of potato in Uruguay. Plant Dis. 2011;95(10):1292-301.
6. Gabriel DW, Allen C, Schell M, Denny TP, Greenberg JT, Duan YP, et al. Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2. MPMI. 2006;19(1):69-79.
7. Guidot A, Elbaz M, Carrere S, Siri MI, Pianzzola MJ, Prior P, et al. Specific genes from the potato brown rot strains of Ralstonia solanacearum and their potential use for strain detection. Phytopathology. 2009;99(9):1105-12.
8. Yuan KX, Cullis J, Levesque CA, Tambong J, Chen W, Lewis CT, et al. Draft genome sequences of Ralstonia solanacearum race 3 biovar 2 strains with different temperature adaptations. Genome Announc. 2015;3(4).
9. Salanoubat M, Genin S, Artiguenave F, Gouzy J, Mangenot S, Arlat M, et al. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature. 2002;415(6871):497-502.
10. Xu J, Zheng HJ, Liu L, Pan ZC, Prior P, Tang B, et al. Complete genome sequence of the plant pathogen Ralstonia solanacearum strain Po82. J Bacteriol. 2011;193(16):4261-2.
11. Remenant B, Coupat-Goutaland B, Guidot A, Cellier G, Wicker E, Allen C, et al. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence. BMC Genomics. 2010;11:379.
12. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013;10(6):563-9.
13. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068-9.
14. Peeters N, Carrere S, Anisimova M, Plener L, Cazale AC, Genin S. Repertoire, unified nomenclature and evolution of the type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics. 2013;14:859.
15. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402.
16. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol. 2013;79(24):7696-701.
17. Li L, Stoeckert Jr CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;13(9):2178-89.
18. Flusberg BA, Webster DR, Lee JH, Travers KJ, Olivares EC, Clark TA, et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods. 2010;7(6):461-5.
19. Sanchez-Romero MA, Cota I, Casadesus J. DNA methylation in bacteria: from the methyl group to the methylome. Curr Opin Microbiol. 2015;25:9-16.
20. Garcia-Del Portillo F, Pucciarelli MG, Casadesus J. DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity. Proc Natl Acad Sci U S A. 1999;96(20):11578-83.
21. Heithoff DM, Sinsheimer RL, Low DA, Mahan MJ. An essential role for DNA adenine methylation in bacterial virulence. Science. 1999;284(5416):967-70.
22. Roberts RJ, Vincze T, Posfai J, Macelis D. REBASE--a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res. 2015;43(Database issue):D298-9.
23. Di Pierro M, Lu R, Uzzau S, Wang W, Margaretten K, Pazzani C, et al. Zonula occludens toxin structure-function analysis. Identification of the fragment biologically active on tight junctions and of the zonulin receptor binding domain. J Biol Chem. 2001;276(22):19160-5.
24. Murugaiyan S, Bae JY, Wu J, Lee SD, Um HY, Choi HK, et al. Characterization of filamentous bacteriophage PE226 infecting Ralstonia solanacearum strains. J Appl Microbiol. 2011;110(1):296-303.
25. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792-7.
26. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010;59(3):307-21.
27. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008;26(5):541-7.
28. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990;87(12):4576-9.
29. Garrity GM, Bell JA, Lilburn T. Phylum XIV. Proteobacteria phyl. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's manual of systematic bacteriology, vol. 2. Second ed. New York: Springer; 2005. p. Part B:1.
30. Garrity GM, Bell JA, Lilburn T. Class II. Betaproteobacteria class. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's manual of systematic bacteriology, vol. 2. Second ed. New York: Springer; 2005. p. 575. part C.
31. List Editor. Validation List Number 107. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol. 2006,56:1-6
32. Garrity GM, Bell JA, Lilburn T. Order I. Burkholderiales ord. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's manual of systematic bacteriology, vol. 2. Second ed. New York: Springer; 2005. p. 575. part C.
33. Garrity GM, Bell JA, Lilburn T. Family I. Burkholderiaceae fam. nov. In: Garrity GM, Brenner DJ, Krieg NR, Staley JT, editors. Bergey's manual of systematic bacteriology, vol. 2. Second ed. New York: Springer; 2005. p. 575. part C.
34. Yabuuchi E, Kosako Y, Yano I, Hotta H, Nishiuchi Y. Transfer of two Burkholderia and an Alcaligenes species to Ralstonia gen. Nov.: proposal of Ralstonia pickettii (Ralston, Palleroni and Doudoroff 1973) comb. nov., Ralstonia solanacearum (Smith 1896) comb. nov. and Ralstonia eutropha (Davis 1969) comb. Nov. Microbiol Immunol. 1995;39(11):897-904.
35. List Editor. Validation List No. 57. Validation of the publication of new names and new combinations previously effectively published outside the IJSB. Int J Syst Bacteriol. 1996,46:625-626
36. Denny TP, Hayward AC, Schaad NW, Jones JB, Chun W. II. Gram negative bacteria. F. Ralstonia. In: Laboratory guide for identification of plant pathogenic bacteria. Thirdth ed. St. Paul, MN, USA: American Phytopathological Society Press; 2001.
37. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet. 2000;25(1):25-9.