Microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens

PLoS Computational Biology

Volumn 5, Issue 8, 2009, Pages

  Pritchard, Leighton ^a   Liu, Hui ^a   Booth, Clare ^a   Douglas, Emma ^a   François, Patrice ^b   Schrenzel, Jacques ^b   Hedley, Peter E ^a   Birch, Paul R J ^a,c   Toth, Ian K ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b GENEVA UNIVERSITY HOSPITALS   (Switzerland)

^c UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; DNA SEQUENCES; ENCODING (SYMBOLS); GENE ENCODING; HIDDEN MARKOV MODELS;

COMPARATIVE GENOMIC HYBRIDIZATIONS; ENTEROBACTERIA; GENOMIC APPLICATIONS; GENOMIC ORGANIZATION; HYBRIDISATION; HYBRIDIZATION ANALYSIS; PECTOBACTERIUM ATROSEPTICUM; PLANT PATHOGEN; RELATIVE ABUNDANCE; SPATIAL INFORMATIONS;

NITROGEN FIXATION;

PLANT TOXIN;

ARTICLE; BACTERIAL GENOME; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; DICKEYA DADANTII; ENTEROBACTER; GENUS; HOST RANGE; LACTOCOCCUS LACTIS; MICROARRAY ANALYSIS; MULTIDRUG RESISTANCE; NITROGEN FIXATION; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PECTOBACTERIUM ATROSEPTICUM; PLANT PATHOGEN INTERACTION; PROBABILITY; SEQUENCE ANALYSIS; STATISTICAL MODEL; CLUSTER ANALYSIS; COMPUTER SIMULATION; DNA MICROARRAY; ENTEROBACTERIACEAE; GENETIC VARIABILITY; GENETICS; GENOMIC ISLAND; HORIZONTAL GENE TRANSFER; METHODOLOGY; MICROBIOLOGY; NORMAL DISTRIBUTION; PLANT DISEASE; REPRODUCIBILITY;

BACTERIA (MICROORGANISMS); DICKEYA DADANTII; ENTEROBACTERIACEAE; LACTOCOCCUS LACTIS SUBSP. LACTIS IL1403; PECTOBACTERIUM ATROSEPTICUM;

CLUSTER ANALYSIS; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER SIMULATION; ENTEROBACTERIACEAE; GENE TRANSFER, HORIZONTAL; GENETIC VARIATION; GENOME, BACTERIAL; GENOMIC ISLANDS; MARKOV CHAINS; MODELS, STATISTICAL; NORMAL DISTRIBUTION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANT DISEASES; REPRODUCIBILITY OF RESULTS;

EID: 70049109965     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000473     Document Type: Article

References (71)

1. Hu J, Gao J-B, Cao Y, Bottinger E, Zhang W (2007) Exploiting noise in array CGH data to improve detection of DNA copy number change. Nucleic Acids Res 35: e35. (Pubitemid 46603436)
2. Wang J, Mexa-Zepada LA, Kresse SH, Myklebost O (2004) M-CGH: analysing microarray-based CGH experiments. BMC Bioinformatics 5: 74. (Pubitemid 40195428)
3. Fitzgerald JR, Sturdevant DE, Mackie SM, Gill SR, Musser JM (2001) Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc Natl Acad Sci U S A 98: 8821-8826.
4. Porwollik S, Hong RM-Y, McClelland M (2002) Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc Natl Acad Sci U S A 99: 8956-8961. (Pubitemid 34693665)
5. Witney AA, Marsden GL, Holden MTG, Stabler RA, Husain SE, et al. (2005) Design, validation, and application of a seven-strain Staphylococcus aureus PCR product microarray for comparative genomics. Appl Environ Microbiol 71: 7504-7514.
6. Koessler T, François P, Charbonnier Y, Huyghe A, Bento M, et al. (2006) Use of oligoarrays for characterization of community-onset methicillin-resistant Staphylococcus aureus. J Clin Microbiol 44: 1040-1048.
7. Lepage E, Brinster S, Caron C, Ducroix-Crepy C, Rigottier-Gois L, et al. (2006) Comparative genomic hybridization analysis of Enterococcus faecalis: identification of genes absent from food strains. J Bacteriol 188: 6858-6868. (Pubitemid 44497899)
8. Ben Zakour NL, Sturdevant DE, Even S, Guinane CM, Barbey C, et al. (2008) Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome. J Bacteriol 190: 6302-6317.
9. Sim SH, Yu Y, Lin CH, Karuturi RKM, Wuthiekanun V, et al. (2008) The core and accessory genomes of Burkholderia pseudomallei: Implications for human melioidosis. PLoS Pathog 4: e1000178.
10. Carter B, Wu G, Woodward MJ, Anjum MF (2008) A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes. BMC Genomics 9: 53. (Pubitemid 351344694)
11. Sarkar SF, Gordon JS, Martin GB, Guttman DS (2006) Comparative Genomics of Host-Specific Virulence in Pseudomonas syringae. Genetics 174: 1041-1056.
12. Aittamaa M, Somervuo P, Pirhonen M, Mattinen L, Nissinen R, et al. (2008) Distinguishing bacterial pathogens of potato using a genome-wide microarray approach. Mol Plant Pathol 9: 705-717.
13. van Hijum SAFT, Baerends RJS, Zomer AL, Karsens HA, Martin-Requena V, et al. (2008) Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. BMC Bioinformatics 9: 93.
14. Chain FJJ, Ilieve D, Evans BJ (2008) Single-species microarrays and comparative transcriptomics. PLoS ONE 3: e3279.
15. Kim CC, Joyce EA, Chan K, Falkow S (2002) Improved analytical methods for microarray-based genome-composition analysis. Genome Biol 3: RESEARCH0065.1-0065.17.
16. Davey R, Savva G, Dicks J, Roberts IN (2007) MPP: a microarray-to- phylogeny pipeline for analysis of gene and marker content datasets. Bioinformatics 23: 1023-1025. (Pubitemid 47050590)
17. Pin C, Reuter M (2007) Use of genomic DNA control features and predicted operon structure in microarray data analysis: ArrayLeaRNA - a Bayesian approach. BMC Bioinformatics 8: 455. (Pubitemid 351211051)
18. Fridlyand J, Snijders AM, Pinkel D, Albertson DG, Jain IN (2004) Hidden Markov models approach to the analysis of array CGH data. J Multivar Anal 90: 132-153. (Pubitemid 41137010)
19. Picard F, Robin S, LeBarbier E, Daudin J-J (2007) A segmentation/ clustering model for the analysis of array CGH data. Biometrics 63: 758-766 (Pubitemid 47352821)
20. Budinska E, Gelnarova E, Schimek MG (2009) MSMAD: A computationally efficient method for the analysis of noisy array CGH data. Bioinformatics 25: 703-713.
21. Perombelon MCM (2002) Potato diseases caused by soft rot erwinias: an overview of pathogenesis. Plant Pathol 51: 1-12.
22. Bell KS, Sebaihia M, Pritchard L, Holden MTG, Hyman LJ, et al. (2004) Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors. Proc Natl Acad Sci U S A 101: 11105-11110. (Pubitemid 38989591)
23. Barras F, van Gijsegem F, Chatterjee AK (1994) Extracellular enzymes and pathogenesis of soft-rot Erwinia. Annu Rev Phytopathol 32: 201-234. (Pubitemid 2151433)
24. Py B, Barras F, Harris S, Robson N, Salmond GPC (1998) Extracellular enzymes and their role in Erwinia virulence. Method Microbiol 27: 157-168. (Pubitemid 128142249)
25. Toth IK, Bell KS, Holeva MC, Birch PRJ (2003) Soft rot erwiniae: from genes to genomes. Mol Plant Pathol 4: 17-30.
26. Hugouvieux-Cotte-Pattat N, Condemine G, Nasser W, Reverchon S (1996) Regulation of pectinolysis in Erwinia chrysanthemi. Ann. Rev. Microbiol 50: 213-257.
27. Boughammoura A, Matzanke BF, Böttger L, Reverchon S, Lesuisse E, et al. (2008) Differential role of ferritins in iron metabolism and virulence of the plant-pathogenic bacterium Erwinia chrysanthemi 3937. J Bacteriol 190: 1518-1530. (Pubitemid 351304005)
28. Desveaux D, Singer AU, Dangl JL (2006) Type III effector proteins: doppelgangers of bacterial virulence. Curr Opin Plant Biol 9: 376-382. (Pubitemid 43914530)
29. McCann HC, Guttman DS (2008) Evolution of the type III secretion system and its effectors in plant-microbe interactions. New Phytol 177: 33-47.
30. Block A, Li G, Fu ZQ, Alfano JR (2008) Phytopathogen type III effector weaponry and their plant targets. Curr Opin Plant Biol 11: 396-403.
31. Zhou J, Chai J (2008) Plant pathogenic bacterial type III effectors subdue host responses. Curr Opin Microbiol 11: 179-185.
32. Bauer DW, Wei ZM, Beer SV, Collmer A (1995) Erwinia chrysanthemi harpin (Ech) - an elicitor of the hypersensitive response that contributes to soft-rot pathogenesis. Mol Plant Microbe Interact 8: 484-491.
33. Yang C-H, Gavilanes-Ruiz M, Okinaka Y, Vedel R, Berthuy I, et al. (2002) hrp genes of Erwinia chrysanthemi 3937 are important virulence factors. Mol Plant Microbe Interact 15: 472-480. (Pubitemid 34523133)
34. Lehtimäki S, Rantakari A, Routtu J, Tuikkala A, Li J, et al. (2003) Characterization of the hrp pathogenicity cluster of Erwinia carotovora subsp. carotovora: high basal level expression in a mutant is associated with reduced virulence. Mol Genet Genomics 270: 263-272. (Pubitemid 37518629)
35. Holeva MC, Bell KS, Hyman LJ, Avrova AO, Whisson SC, et al. (2004) Use of a pooled transposon mutation grid to demonstrate roles in disease development for Erwinia carotovora subsp. atroseptica putative type III secreted effector (DspE/A) and helper (HrpN) proteins. Mol Plant Microbe Interact 17: 943-950.
36. Toth IK, Birch PRJ (2005) Rotting softly and stealthily. Curr Opin Plant Biol 8: 424-429.
37. Liu H, Coulthurst SJ, Pritchard L, Hedley PE, Ravensdale MR, et al. (2008) Quorum sensing coordinates brute force and stealth modes of infection in the plant pathogen Pectobacterium atrosepticum. PLoS Pathog 4: e1000093. (Pubitemid 351930625)
38. Toth IK, Pritchard L, Birch PRJ (2006) Comparative genomics reveals what makes an enterobacterial plant pathogen. Annu Rev Phytopathol 44: 305-336. (Pubitemid 44437547)
39. Lindeberg M, Myers CR, Collmer A, Schneider DJ (2008) Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization. Mol Plant Microbe Interact 21: 685-700. (Pubitemid 351929163)
40. Eswarappa SM, Janice J, Nagarajan AG, Balasundaram SV, Karnam G, et al. (2008) Differentially Evolved Genes of Salmonella Pathogenicity Islands: Insights into the Mechanism of Host Specificity in Salmonella. PLoS ONE 3: e3829.
41. Charbonnier Y, Gettler B, François P, Bento M, Renzoni A, et al. (2005) A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus. BMC Genomics 6: 95. (Pubitemid 41372181)
42. Vernikos GS, Parkhill J (2006) Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196-2203.
43. Dong Y, Glasner JD, Blattner FR, Triplett EW (2001) Genomic interspecies microarray hybridization: rapid discovery of three thousand genes in the maize endophyte, Klebsiella pneumoniae 342, by microarray hybridization with Escherichia coli K-12 open reading frames. Appl Environ Microbiol 67: 1911-1921. (Pubitemid 33644966)
44. Taboada EN, Acedillo RR, Luebbert CC, Findlay WA, Nash JHE (2005) A new approach for the analysis of bacterial microarray-based Comparative Genomic Hybridization: insights from an empirical study. BMC Genomics 6: 78.
45. Nash JHE, Findlay WA, Luebbert CC, Mykytczuk OL, Foote SJ, et al. (2006) Comparative genomics profiling of clinical isolates of Aeromonas salmonicida using DNA microarrays. BMC Genomics 7: 43.
46. Earl AM, Losick R, Kolter R (2007) Bacillus subtilis genome diversity. J Bacteriol 189: 1163-1170.
47. Kunin V, Goldovsky L, Darzentas N, Ouzounis CA (2005) The net of life: reconstructing the microbial phylogenetic network. Genome Res 15: 954-959. (Pubitemid 40994215)
48. Chan K, Baker S, Kim CC, Detweiler CS, Dougan G, et al. (2003) Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar typhimurium DNA microarray. J Bacteriol 185: 553-563. (Pubitemid 36070482)
49. Hotopp JCD, Grifantini R, Kumar N, Tzeng YL, Fouts DE, et al. (2006) Comparative genomics of Neisseria meningitidis: core genome, islands of horizontal transfer and pathogen-specific genes. Microbiology 152: 3733-3749. (Pubitemid 46040693)
50. Peng J, Zhang X, Yang J, Wang J, Yang E, et al. (2006) The use of comparative genomic hybridization to characterize genome dynamics and diversity among the serotypes of Shigella. BMC Genomics 7: 218. (Pubitemid 44419883)
51. Pin C, Reuter M, Pearson B, Friis L, Overweg K, et al. (2006) Comparison of different approaches for comparative genetic analysis using microarray hybridization. Appl Microbiol Biotechnol 72: 852-859. (Pubitemid 44454951)
52. Paauw A, Caspers MPM, Schuren FHJ, Leverstein-van Hall MA, Delétoile A, et al. (2008) Genomic diversity within the Enterobacter cloacae complex. PLoS ONE 3: e3018.
53. Mohd-Zain Z, Turner SL, Cerdeno-Tarraga AM, Lilley AK, Inzana TJ, et al. (2004) Transferable antibiotic resistance elements in Haemophilus influenzae share a common evolutionary origin with a diverse family of syntenic genomic islands. J Bacteriol 186: 8114-8122. (Pubitemid 39552524)
54. Moreira LM, de Souza RF, Digiampietri LA, da Silva ACR, Setubal JC (2005) Comparative analyses of Xanthomonas and Xylella complete genomes. Omics 9: 43-76.
55. Dziejman M, Balon EL, Boyd DH, Fraser CM, Heidelberg JF, et al. (2002) Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc Natl Acad Sci U S A 99: 1556-1561. (Pubitemid 34136531)
56. Stabler RA, Marsden GL, Witney AA, Li Y, Bentley SD, et al. (2005) Identification of pathogen-specific genes through microarray analysis of pathogenic and commensal Neisseria species. Microbiology 151: 2907-2922. (Pubitemid 41309564)
57. Bender CL, Alarcón-Chaidez F, Gross DC (1999) Pseudomonas syringae phytotoxins: mode of action, regulation, and biosynthesis by peptide and polyketide synthetases. Microbiol Mol Biol Rev 63: 266-292. (Pubitemid 29264972)
58. Rojas CM, Ham JH, Deng W-L, Doyle JJ, Collmer A (2002) HecA, a member of a class of adhesins produced by diverse pathogenic bacteria, contributes to the attachment, aggregation, epidermal cell killing, and virulence phenotypes of Erwinia chrysanthemi EC16 on Nicotiana clevelandii seedlings. Proc Natl Acad Sci U S A 99: 13142-13147.
59. Rojas CM, Ham JH, Schechter LM, Kim JF, Beer SV, et al. (2004) The Erwinia chrysanthemi EC16 hrp/hrc gene cluster encodes an active Hrp type III secretion system that is flanked by virulence genes functionally unrelated to the Hrp system. Mol Plant Microbe Interact 17: 644-653.
60. Enard C, Diolex A, Expert D (1988) Systemic virulence of Erwinia chrysanthemi 3937 requires a functional iron assimilation system. J Bacteriol 170: 2419-2426.
61. Franza T, Mahém B, Expert D (2005) Erwinia chrysanthemi requires a second iron transport route dependent of the siderophore achromobactin for extracellular growth and plant infection. Mol Microbiol 55: 261-275. (Pubitemid 40127901)
62. Gurusiddaiah S, Weller DM, Sarkar A, Cook RJ (1986) Characterization of an antibiotic produced by a strain of Pseudomonas fluorescens inhibitory to Gaeumannomyces graminis var. tritici and Pythium spp.. Antimicrob Agents Chemother 29: 488-495. (Pubitemid 16143260)
63. Thomashow LS, Weller DM (1988) Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici. J Bacteriol 170: 3499-3508.
64. Coulthurst SJ, Barnard AML, Salmond GPC (2005) Regulation and biosynthesis of carbapenem antibiotics in bacteria. Nat Rev Micro 3: 295-306.
65. Zhu J, Oger PM, Schrammeijer B, Hooykaas PJ, Farrand SK, et al. (2000) The bases of crown gall tumorigenesis. J Bacteriol 182: 3885-3895.
66. Glasner JD, Marquez-Villavicencio M, Kim H-S, Jahn CE, Ma B, et al. (2008) Niche-Specificity and the Variable Fraction of the Pectobacterium Pan-Genome. Mol Plant Microbe Interact 21: 1549-1560.
67. 't Hoen PAC, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RHAM, et al. (2008) Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 36: e141.
68. Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24: 133-141.
69. Pop M, Salzberg S (2008) Bioinformatics challenges of new sequencing technology. Trends Genet 24: 142-149.
70. Coppée J-Y (2008) Do DNA microarrays have their future behind them? Microbes Infect 10: 1067-1071.
71. Pritchard L, White JA, Birch RJ, Toth IK (2006) GenomeDiagram: a python package for the visualization of large-scale genomic data. Bioinformatics 22: 616-617. (Pubitemid 43372824)