Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

BMC Genomics

Volumn 7, Issue , 2006, Pages

  Doddapaneni, Harshavardhan ^a   Yao, Jiqiang ^b   Lin, Hong ^c   Walker, M Andrew ^a   Civerolo, Edwin L ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Citrus Research Board   (United States)

^c AGRICULTURAL RESEARCH SERVICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; CYTOSINE; GLUTAMIC ACID;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CODON; CONTROLLED STUDY; GENE CLUSTER; GENE FREQUENCY; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; TANDEM REPEAT; XYLELLA FASTIDIOSA;

ANALYSIS OF VARIANCE; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; FIMBRIAE, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; MULTIGENE FAMILY; MUTATION; PLANT DISEASES; PLANTS; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECIES SPECIFICITY; XYLELLA;

BACTERIA (MICROORGANISMS); CITRUS; NEGIBACTERIA; VITIS; XYLELLA FASTIDIOSA;

EID: 33749136401     PISSN: 14712164     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-7-225     Document Type: Article

References (50)

1. Moller WJ, Sanborn RR, Mircetich SM, Williams HE, Beutel JA: A newly recognized leaf scorch disease of almond. Plant Dis Rep 1974, 58:99-101.
2. Mircetich SM, Lowe SL, Moller WJ, Nyland G: Etiology of almond leaf scorch disease and transmission of the causal agent. Phytopathology 1976, 66:17-24.
3. Purcell AH, Hopkins DL: Fastidious xylem-limited bacterial plant pathogens. Ann Rev Phytopathol 1996, 34:131-151.
4. USDA-APHIS select agent list [http://www.aphis.usda.gov/programs/ ag_selectagent/ag_bioterr_toxinslist.html]
5. Simpson AJ, Reinach FC, Arruda P, Abreu FA, Acencio M, Alvarenga R, Alves LM, Araya JE, Baia GS, Baptista CS, Barros MH, Bonaccorsi ED, Bordin S, Bove JM, Briones MR, Bueno MR, Camargo AA, Camargo LE, Carraro DM, Carrer H, Colauto NB, Colombo C, Costa FF, Costa MC, Costa-Neto CM, Coutinho LL, Cristofani M, Dias-Neto E, Docena C, El-Dorry H, Facincani AP, Ferreira AJ, Ferreira VC, Ferro JA, Fraga JS, Franca SC, Franco MC, Frohme M, Furlan LR, Garnier M, Goldman GH, Goldman MH, Gomes SL, Gruber A, Ho PL, Hoheisel JD, Junqueira ML, Kemper EL, Kitajima JP, Krieger JE, Kuramae EE, Laigret F, Lambais MR, Leite LC, Lemos EG, Lemos MV, Lopes SA, Lopes CR, Machado JA, Machado MA, Madeira AM, Madeira HM, Marino CL, Marques MV, Martins EA, Martins EM, Matsukuma AY, Menck CF, Miracca EC, Miyald CY, Monteriro-Vitorello CB, Moon DH, Nagai MA, Nascimento AL, Netto LE, Nhani A Jr, Nobrega FG, Nunes LR, Oliveira MA, de Oliveira MC, de Oliveira RC, Palmieri DA, Paris A, Peixoto BR, Pereira GA, Pereira HA Jr, Pesquero JB, Quaggio RB, Roberto PG, Rodrigues V, de M, Rosa AJ, de Rosa VE Jr, de Sa RG, Santelli RV, Sawasaki HE, da Silva AC, da Silva AM, da Silva FR, et al. The genome sequence of the plant pathogen Xylella fastidiosa Nature 2000 406 151-157
6. Bhattacharyya A, Stilwagen S, Ivanova N, D'Souza M, Bernal A, Lykidis A, Kapatral V, Anderson I, Larsen N, Los T, Reznik G, Selkov E Jr, Walunas TL, Feil H, Feil WS, Purcell A, Lassez JL, Hawkins TL, Haselkom R, Overbeek R, Predki PF, Kyrpides NC: Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc Natl Acad Sci USA 2002, 99:12403-8.
7. Van Sluys MA, de Oliveira MC, Monteiro-Vitorello CB, Miyaki CY, Furlan LR, Camargo LE, da Silva AC, Moon DH, Takita MA, Lemos EG, Machado MA, Ferro MI, da Silva FR, Goldman MH, Goldman GH, Lemos MV, El-Dorry H, Tsai SM, Carrer H, Carraro DM, de Oliveira RC, Nunes LR, Siqueira WJ, Coutinho LL, Kimura ET, Ferro ES, Harakava R, Kuramae EE, Marino CL, Giglioti E, Abreu IL, Alves LM, do Amaral AM, Baia GS, Blanco SR, Brito MS, Cannavan FS, Celestino AV, da Cunha AF, Fenille RC, Ferro JA, Formighieri EF, Kishi LT, Leoni SG, Oliveira AR, Rosa VE Jr, Sassaki FT, Sena JA, de Souza AA, Truffi D, Tsukumo F, Yanai GM, Zaros LG, Civerolo EL, Simpson AJ, Almeida NF Jr, Setubal JC, Kitajima JP; Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 2003, 185:1018-1026.
8. Hendson M, Purcell AH, Chen D, Smart C, Guilhabert M, Kirkpatrick B: Genetic diversity of Pierce's disease strains and other pathotypes of Xylella fastidiosa. Appl Environ Microbiol 2001, 67:895-903.
9. Coletta-Filho HD, Takita MA, de Souza AA, Aguilar-Vildoso CI, Machado MA: Differentiation of strains of Xylella fastidiosa by a variable number of tandem repeat analysis. Appl Environ Microbiol 2001, 67:4091-4095.
10. Lin H, Civerolo EL, Hu R, Barros S, Francis M, Walker MA. Multilocus simple sequence repeat markers for differentiating strains and evaluating genetic diversity of Xylella fastidiosa. Appl Environ Microbiol 2005, 71:4888-4892.
11. Aimeida RPP, Purcell AH: Biological traits of Xylella fastidiosa strains from grapes and almonds. Appl Environ Microbiol 2003, 69:7447-7452.
12. Britten RJ, Rowen L, Williams J, Cameron RA. Majority of divergence between closely related DNA samples is due to INDELs. Proc Natl Acad Sci USA 2003, 100:4661-5.
13. Golding B: Evolution: when was life's first branch point? Curr Biol 1996, 6:679-682.
14. Gupta RS: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiol Mol Biol Rev 1998, 62:1435-1491.
15. Brosch R, Pym AS, Gordon SV, Cole ST: The evolution of mycobacterial pathogenicity: clues from comparative genomics. Trends Microbiol 2001, 9:452-458.
16. Pearson T, Busch JD, Ravel J, Read TD, Rhoton SD, U'Ren JM, Simonson TS, Kachur SM, Leadem RR, Cardon ML, Van Ert MN, Huynh LY, Fraser CM, Keim P: Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc Natl Acad Sci USA 2004, 101:13536-13541.
17. Monot M, Honore N, Garnier T, Araoz R, Coppee JY, Lacroix C, Sow S, Spencer JS, Truman RW, Williams DL, Gelber R, Virmond M, Flageul B, Cho SN, Ji B, Paniz-Mondolfi A, Convit J, Young S, Fine PE, Rasolofo V, Brennan PJ, Cole ST. On the origin of leprosy. Science 2005, 308:1040-1042.
18. Stermann M, Sedlacek L, Maass S, Bange FC: A promoter mutation causes differential nitrate reductase activity of Mycobacterium, tuberculosis and Mycobacterium bovis. J Bacteriol 2004, 186:2856-2861.
19. Levy DD, Sharma B, Cebula TA. Single-nucleotide polymorphism mutation spectra and resistance to quinolones in Salmonella enterica serovar Enteritidis with a mutator phenotype. Antimicrob Agents Chemother 2004, 48:2355-2363.
20. Ochman H, Lawrence JG, Groisman EA. Lateral gene transfer and the nature of bacterial innovation. Nature 2000, 405:299-304.
21. Redfield RJ: Do bacteria have sex. Nat Rev Genet 2001, 2:634-639.
22. Lan R, Reeves PR: Gene transfer is a major factor in bacterial evolution. Mol Biol Evol 1996, 13:47-55.
23. Lawrence JG: Gene transfer, speciation, and the evolution of bacterial genomes. Curr Opin Microbiol 1999, 2:519-523.
24. Lawrence JG, Ochman H: Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 1998, 95:9413-9417.
25. Karlin S: Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol 2001, 9:335-343.
26. Munich Information Center for Protein Sequences (MIPS), PEDANT database [http://pedant.gsf.de/#1]
27. Organization for Nucleotide Sequencing and Analysis(ONSA), 9a5c genome database [http://aeg.lbi.ic.unicamp.br/xf//]
28. Integrated Genomics website [http://www.integratedgenomics.com]
29. Scally M, Schuenzel EL, Stouthamer R, Nunney L: Multilocus sequence type system for the plant pathogen Xylella fastidiosa and relative contributions of recombination and point mutation to clonal diversity. Appl Environ Microbiol 2005, 71:8491-8499.
30. Schuenzel EL, Scally M, Stouthamer R, Nunney L: A multigene phylogenetic study of clonal diversity and divergence in North American strains of the plant pathogen Xylella fastidiosa. Appl Environ Microbiol 2005, 71:3832-3839.
31. Ludwig W, Schleifer KH: Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. FEMS Microbiol Rev 15: 155-173.
32. Meng YZ, Li YX, Galvani DG, Hao GX, Turner JN, Burr TJ, Hoch HC: Upstream migration of Xylella fastidiosa via pilus-driven twitching motility. J Bacteriol 2005, 187:5560-5567.
33. Sojar HT, Han Y, Hamada N, Sharma A, Genco RJ: Role of the amino-terminal region of Porphyromonas gingivalis fimbriae in adherence to epithelial cells. Infect Immun 1999, 7:6173-6176.
34. Koide T, Zaini PA, Moreira LM, Vencio RZ, Matsukuma AY, Durham AM, Teixeira DC, El-Dorry H, Monteiro PB, da Silva AC, Verjovski-Almeida S, da Silva AM, Gomes SL: DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence. J Bacteriol 2004, 186:5442-5449.
35. Saunders NJ, Boonmee P, Peden JF, Jarvis SA. Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori. BMC Genomics 2005, 6:9.
36. Daubin V, Lerat E, Perriere G: The source of laterally transferred genes in bacterial genomes. Genome Biol 2003, 4:R57.
37. Sharp PM, Li WH: The codon Adaptation Index a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987, 15:1281-1295.
38. Sueoka N: Intrastrand parity rules of DNA base composition and usage biases of synonymous codons. J Mol Evol 1995, 40:318-325.
39. Sueoka N: DNA G+C content of the third codon position and codon usage biases of human genes. Gene 2000, 261:53-62.
40. Gur-Arie R, Cohen CJ, Eitan Y, Shelef L, Hallerman EM, Kashi Y: Simple sequences repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res 2000, 10:62-71.
41. Web link to the Xfbase [http://fresno.ars.usda.gov/citrusdisease/ CVC_index.htm]
42. Web link to the Washington University BLAST(WU-BLAST) archive page [http://blast.wustl.edu/]
43. Web link to the RepeatMasker webpage [http://www.repeatmasker.org/]
44. Eernisse DJ, Kluge AG: Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology. Mol Biol Evol 1993, 10:1170-1195.
45. TanderRepeats Finder web page address [http://tandem.bu.edu/trf/trf.html]
46. Supek F, Vlahovicek K: INCA: Synonymous codon usage analysis and clustering by means of self-organizing map. Bioinformatics 2004, 20:2329-2330.
47. Okamoto S, Ohmori M: The cyanobacterial PilT protein responsible for cell motility and transformation hydrolyzes ATP. Plant Cell Physiol 2002, 43:1127-1136.
48. Hélaine S, Carbonnelle E, Prouvensier L, Beretti JL, Nassif X, Pelicic V: PilX, a pilus-associated protein essential for bacterial aggregation, is a key to pilus-facilitated attachment of Neisseria meningitidis to human cells. Mol Microbiol 2005, 55:65-77.
49. Alm RA, Hallinan JP, Watson AA, Mattick JS: Fimbrial biogenesis genes of Pseudomonas aeruginosa: pilW and pilX increase the similarity of type 4 fimbriae to the GSP protein-secretion systems and pilYI encodes a gonococcal PilC homologue. Mol Microbiol 1996, 22:161-73.
50. Andrewsa TD, Gojoborib T: Strong Positive Selection and Recombination Drive the Antigenic Variation of the PilE Protein of the Human Pathogen Neisseria meningitidis. Genetics 2004, 166:25-32.