Classification of plant associated bacteria using RIF, a computationally derived DNA marker

PLoS ONE

Volumn 6, Issue 4, 2011, Pages

  Schneider, Kevin L ^a   Marrero, Glorimar ^a   Alvarez, Anne M ^a   Presting, Gernot G ^a  

^a UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA MARKER; REPLICATION INITIATOR PROTEIN DNAA; SPACER DNA; BACTERIAL DNA;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CLAVIBACTER; COMPUTER MODEL; CONTROLLED STUDY; DICKEYA; ENTEROBACTERIACEAE; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PANTOEA; PECTOBACTERIUM; RALSTONIA; RALSTONIA SOLANACEARUM; SPECIES DIFFERENTIATION; XANTHOMONAS; XANTHOMONAS AXONOPODIS; XANTHOMONAS CAMPESTRIS; CLASSIFICATION; GENETIC MARKER; GENETICS; HORIZONTAL GENE TRANSFER; MICROBIOLOGY; MOLECULAR GENETICS; PLANT; SEQUENCE HOMOLOGY;

BACTERIA (MICROORGANISMS); CLAVIBACTER; DICKEYA; ENTEROBACTERIACEAE; PANTOEA; PECTOBACTERIUM; RALSTONIA; RALSTONIA SOLANACEARUM; XANTHOMONAS; XANTHOMONAS AXONOPODIS; XANTHOMONAS CAMPESTRIS;

BASE SEQUENCE; DNA, BACTERIAL; GENE TRANSFER, HORIZONTAL; GENETIC MARKERS; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PLANTS; SEQUENCE HOMOLOGY, NUCLEIC ACID; XANTHOMONAS;

EID: 79955437071     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0018496     Document Type: Article

References (62)

1. Baker B, Zambryski P, Staskawicz B, Dinesh-Kumar SP, (1997) Signaling in plant-microbe interactions. Science 276: 726-723.
2. Gottwald T, Hughes G, Graham JH, Sun X, Riley T, (2001) The citrus canker epidemic in Florida: the scientific basis of regulatory eradication policy for an invasive species. Phytopathol 91: 30-34.
3. Hawks B, (2005) Agricultural Bioterrorism Protection Act of 2002: Possession, use, and transfer of biological agents and toxins; final rule. Fed Regist 70: 13241-13292.
4. Hayward AC, (1993) The hosts of Xanthomonas. In: Swings JG, Civerolo EL, editors. Xanthomonas London Chapman and Hall pp. 1-18.
5. Denny TP, (2006) Plant pathogenic Ralstonia species; In: Gnanamanickam SS, editors. Plant-associated Bacteria The Netherlands Springer pp. 573-644.
6. Eichenlaub R, Gartemann KH, Burger A, (2006) Clavibacter michiganensis, a group of gram-positive phytopathogenic bacteria; In: Gnanamanickam SS, editors. Plant-associated Bacteria The Netherlands Springer pp. 131-155; 195-351.
7. Simpson AJG, Reinach FC, Arruda P, Abreu FA, Acencio M, (2000) The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406: 151-159.
8. Bakker PAHM, Pieterse CMJ, van Loon LC, (2007) Induced systemic resistance by fluorescent Pseudomonas spp. Phytopathol 97: 239-243.
9. Samson R, Legendre JB, Christen R, Fischer-Le Saux M, Achouak W, et al. (2005) Transfer of Pectobacterium chrysanthemi (Burkholderet al. 1953) Brenneret al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. Int J Syst Evol Microbiol 55: 1415-1427.
10. Hauben L, Moore ER, Vauterin L, Steenackers M, Mergaert J, et al. (1998) Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst Appl Microbiol 21: 384-97.
11. Gavini F, Mergaert J, Beji A, Mielcarek C, Izard D, et al. (1989) Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing and Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and description of Pantoea dispersa sp. nov. Int J Syst Evol Microbiol 39: 337-345.
12. Garrity GM, Bell JA, Lilburn T, (2005) Phylum XIV. Proteobacteria phyl. nov. In: Brenner DJ, Krieger-Huber S, Stanley JT, editors. Bergey's manual of systematic bacteriology New York Springer pp. 1-912.
13. Vauterin L, Hoste B, Kersters K, Swings J, (1995) Reclassification of Xanthomonas. Int J Syst Bacteriol 45: 472-489.
14. Buddenhagen I, Kelman A, (1964) Biological and Physiological Aspects of Bacterial Wilt Caused by Pseudomonas solanacearum. Annu Rev Phytopathol 2: 203-230.
15. Jones JB, Lacy GH, Bouzar H, Stall RE, Schaad NW, (2004) Reclassification of the xanthomonads associated with bacterial spot disease of tomato and pepper. Syst Appl Microbiol 27: 755-762.
16. Schaad NW, Postnikova E, Lacy G, Sechler A, Agarkova I, et al. (2006) Emended classification of xanthomonad pathogens on citrus. Syst Appl Microbiol 29: 690-695.
17. Young JM, Bull CT, De Boer SH, Dirrao G, Gardan L, et al. (2001) Committee on the Taxonomy of Plant Pathogenic Bacteria. International Standards for Naming Pathovars of Phytopathogenic Bacteria. http://www.isppweb.org/about_tpbb_naming.asp.
18. Fegan M, Taghavi M, Sly LI, Hayward AC, (1998) Phylogeny, diversity, and molecular diagnostics of Ralstonia solanacearum; In: Prior P, Allen C, Elphinstone JG, editors. Bacterial Wilt Disease: Molecular and Ecological Aspects Berlin Springer-Verlag pp. 19-33.
19. Fegan M, Prior P, (2005) How complex is the "Ralstonia solanacearum species complex"? In: Allen C, Prior P, Hayward AC, editors. Bacterial wilt disease and the Ralstonia solanacearum species complex St. Paul, MN APS Press pp. 449-461.
20. Normand P, Ponsonnet C, Nesme X, Neyra M, Simonet P, (1996) ITS analysis of prokaryotes; In: Akkermans DL, van Elsas JD, de Bruijn EI, editors. Molecular Microbial Ecology Manual Dordrecht Kluwer Academic Publishers pp. 1-12.
21. Ma B, Hibbing ME, Kim H, Reedy RM, Yedidia I, et al. (2007) Host range and molecular phylogenies of the soft rot enterobacterial genera Pectobacterium and Dickeya. Phytopathol 97: 1150-1163.
22. Young JM, Park DC, (2007) Relationships of plant pathogenic enterobacteria based on partial atpD, carA, and recA as individual and concatenated nucleotide and peptide sequences. Syst Appl Microbiol 30: 343-354.
23. Prior P, Fegan M, (2005) Recent developments in the phylogeny and classification of Ralstonia solanacearum. Acta Hort 695: 127-136.
24. Castillo JA, Greenberg JT, (2007) Evolutionary Dynamics of Ralstonia solanacearum. Appl Environ Microbiol 73: 1225-1238.
25. Young JM, Park DC, Shearman HM, Fargier E, (2008) A multilocus sequence analysis of the genus Xanthomonas. Syst Appl Microbiol 31: 366-77.
26. Parkinson N, Aritua V, Heeney J, Cowie C, Bew J, et al. (2007) Phylogenetic analysis of Xanthomonas species by comparison of partial gyrase B gene sequences. Int J Syst Evol Microbiol 57: 2881-2887.
27. Parkinson N, Cowie C, Heeney J, Stead D, (2009) Phylogenetic structure of Xanthomonas determined by comparison of gyrB sequences. Int J Syst Evol Microbiol 57: 2881-2887.
28. Yabuuchi E, Kosako Y, Yano I, Hotta H, Nishiuchi Y, (1995) 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 39: 897-904.
29. Frézal L, Leblois R, (2008) Four years of DNA barcoding: Current advances and prospects. Infect Genet and Evol 8: 727-736.
30. Hebert PDN, Cywinska A, Ball SL, DeWaard JR, (2003) Biological identifications through DNA barcodes. Proc R Soc London Ser 270: 313-321.
31. Presting GG, (2006) Identification of conserved regions in the plastid genome: implications for DNA barcoding and biological function. Can J Bot 84: 434-1443.
32. Sherwood AR, Presting GG, (2007) Universal primers amplify a 23S rDNA plastid marker in eukaryotic algae and cyanobacteria. J Phycol 43: 605-608.
33. Wang N, Sherwood A, Kurihara A, Conklin K, Sauvage T, et al. (2009) The Hawaiian Algal Database: a laboratory LIMS and online resource for biodiversity data. BMC Plant Biol 9: 117.
34. Sherwood AR, Chan YL, Presting GG, (2008) Application of universally amplifying plastid primers to environmental sampling of a stream periphyton community. Mol Ecol Resour 8: 1011-1014.
35. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
36. Benson DA, Boguski MS, Lipman DJ, Ostell J, Ouellette BF, et al. (1999) GenBank. Nucleic Acids Res 27: 12-17.
37. García-Martínez J, Acinas SG, Antón AI, Rodríguez-Valera F, (1999) Use of the 16S-23S ribosomal genes spacer region in studies of prokaryotic diversity. J Microbiol Methods 36: 55-64.
38. Gurtler V, Stanisich VA, (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiol 142: 3-16.
39. Kang YJ, Cheng J, Mai LJ, Hu J, Piao Z, (2010) Multiple copies of 16S rRNA gene affect the restriction patterns and DGGE profile revealed by analysis of genome database. Microbiol 79: 655-662.
40. Wilton SD, Lim L, Dye D, Laing N, (1997) Bandstab: a PCR-based alternative to cloning PCR products. BioTechniques 22: 642-645.
41. Urwin R, Maiden MCJ, (2003) Multi-locus sequence typing: a tool for global epidemiology. Trends Microbiol 11: 479-487.
42. Pascual J, Macián MC, Arahal DR, Garay E, Pujalte MJ, (2010) Multilocus sequence analysis of the central clade of the genus Vibrio using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int J Syst Evol Microbiol 60: 154-165.
43. Santos S, Ochman H, (2004) Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6: 754-759.
44. da Silva ACR, Ferro JA, Reinach FC, Farah CS, Furlan LR, et al. (2002) Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417: 459-463.
45. Qian W, Jia Y, Ren SX, He YQ, Feng JX, et al. (2005) Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris. Genome Res 15: 757-767.
46. Lee BM, Park YJ, Park DS, Kang HW, Kim JG, et al. (2005) The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Res 33: 577-86.
47. Thieme F, Koebnik R, Bekel T, Berger C, Boch J, et al. (2005) Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. J Bacteriol 187: 7254-7266.
48. Ewing A, (2008) A study on the phylogenetics of gene transfer: from pathways to kingdoms. MS Thesis, University of Hawaii at Manoa, Honolulu, Hi.
49. Ewing B, Green P, (1998a) Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
50. Ewing B, Hillier L, Wendl M, Green P, (1998b) Basecalling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
51. Nassar A, Darrasse A, Lemattre M, Kotoujansky A, Dervin C, et al. (1996) Characterization of Erwinia chrysanthemi by pectinolytic isozyme polymorphism and restriction fragment length polymorphism analysis of PCR-amplified fragments of pel genes. Appl Environ Microbiol 62: 2228-2235.
52. Kaguni J, (2006) DnaA: Controlling the Initiation of Bacterial DNA Replication and More. Annu Rev Microbiol 60: 351-371.
53. Mackiewicz P, Zakrzewska-Czerwiñska J, Zawilak A, Dudek MR, Cebrat S, (2004) Where does bacterial replication start? Rules for predicting the oriC region. NAR 32: 3781-3791.
54. Almeida N, Yan S, Cai R, Clarke CR, Morris CE, et al. (2010) PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. Phytopathology 100: 208-215.
55. Vitorino L, Chelo I, Bacellar F, Ze-Ze L, (2007) Rickettsiae phylogeny: a multigenic approach. Microbiology 153: 160-168.
56. Zmasek CM, Eddy SR, (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384.
57. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12.
58. Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497-3500.
59. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
60. de Lamballerie X, Zandotti C, Vignoli C, Bollet C, de Micco P, (1992) A one-step microbial DNA extraction method using "Chelex 100" suitable for gene amplification. Res Microbiol 143: 785-790.
61. Hall T, (1999) BioEdit 7. Nucleic Acids Symp Ser 41: 95-98.
62. Kumar S, Tamura K, Nei M, (2004) MEGA 3: Integrated Software for Molecular Evolutionary Genetics Analysis and Sequence Alignment. Brief Bioinform 5: 150-163.