Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Genome Biology

Volumn 10, Issue 5, 2009, Pages

  Silby, Mark W ^a   Cerdeño Tárraga, Ana M ^b   Vernikos, Georgios S ^b   Giddens, Stephen R ^c   Jackson, Robert W ^c,d   Preston, Gail M ^c   Zhang, Xue Xian ^e   Moon, Christina D ^c,k   Gehrig, Stefanie M ^c   Godfrey, Scott A C ^c,l   Knight, Christopher G ^c,m   Malone, Jacob G ^c,n   Robinson, Zena ^c   Spiers, Andrew J ^c,o   Harris, Simon ^b   Challis, Gregory L ^f   Yaxley, Alice M ^g   Harris, David ^b   Seeger, Kathy ^b   Murphy, Lee ^b   Rutter, Simon ^b   Squares, Rob ^b   Quail, Michael A ^b   Saunders, Elizabeth ^h   Mavromatis, Konstantinos ⁱ   Brettin, Thomas S ^h   Bentley, Stephen D ^b   Hothersall, Joanne ^j   Stephens, Elton ^j   Thomas, Christopher M ^j   Parkhill, Julian ^b   Levy, Stuart B ^a   Rainey, Paul B ^e   Thomson, Nicholas R ^b   more..

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF READING   (United Kingdom)

^e MASSEY UNIVERSITY   (New Zealand)

^f UNIVERSITY OF WARWICK   (United Kingdom)

^g UNIVERSITY OF WARWICK   (United Kingdom)

^h LOS ALAMOS NATIONAL LABORATORY   (United States)

ⁱ DOE JOINT GENOME INSTITUTE   (United States)

^j UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^k AGRESEARCH GRASSLANDS   (New Zealand)

^l UNIVERSITY OF THE WEST OF ENGLAND   (United Kingdom)

^m UNIVERSITY OF MANCHESTER   (United Kingdom)

ⁿ UNIVERSITY OF BASEL   (Switzerland)

^o UNIVERSITY OF ABERTAY DUNDEE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

CHEY PROTEIN; GENE PRODUCT; NON RIBOSOMAL PEPTIDE SYNTHETASE; PROTEIN HISTIDINE KINASE; TRANSPOSASE; UNCLASSIFIED DRUG;

AMINO ACID ANALYSIS; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; DNA BASE COMPOSITION; DNA REPLICATION ORIGIN; DNA SEQUENCE; FUSION GENE; GENE EXPRESSION; GENE FUNCTION; GENE LOCATION; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GENOME ANALYSIS; IN VIVO STUDY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLANT MICROORGANISM INTERACTION; PSEUDOMONAS FLUORESCENS; SEQUENCE ALIGNMENT; SPECIES DIVERSITY; TRANSPOSON; CLASSIFICATION; ECOSYSTEM; GENETICS; METABOLISM; MICROBIOLOGY; PLANT;

ACARI; PSEUDOMONAS; PSEUDOMONAS FLUORESCENS; PSEUDOMONAS FLUORESCENS PF-5;

ECOSYSTEM; GENOME, BACTERIAL; PLANTS; PSEUDOMONAS FLUORESCENS;

EID: 67649653746     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-5-r51     Document Type: Article

References (75)

1. Naseby DC Way JA Bainton NJ Lynch JM Biocontrol of Pythium in the pea rhizosphere by antifungal metabolite producing and non-producing Pseudomonas strains. J Appl Microbiol 2001, 90:421-429. 10.1046/ j.1365-2672.2001.01260.x 11298238
2. Rodriguez F Pfender WF Antibiosis and antagonism of Sclerotinia homoeocarpa and Drechslera poae by Pseudomonas fluorescens Pf-5 in vitro and in planta. Phytopathology 1997, 87:614-621. 10.1094/ PHYTO.1997.87.6.614 18945079
3. de Bruijn I de Kock MJ Yang M de Waard P van Beek TA Raaijmakers JM Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species. Mol Microbiol 2007, 63:417-428. 10.1111/j.1365-2958.2006.05525.x 17241198
4. Haas D Defago G Biological control of soil-borne pathogens by fluorescent pseudomonads. Nat Rev Microbiol 2005, 3:307-319. 10.1038/ nrmicro1129 15759041
5. Rainey PB Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1999, 1:243-257. 10.1046/ j.1462-2920.1999.00040.x 11207743
6. Gal M Preston GM Massey RC Spiers AJ Rainey PB Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol Ecol 2003, 12:3109-3121. 10.1046/j.1365-294X.2003.01953.x 14629390
7. Silby MW Levy SB Use of in vivo expression technology to identify genes important in growth and survival of Pseudomonas fluorescens Pf0-1 in soil: Discovery of expressed sequences with novel genetic organization. J Bacteriol 2004, 186:7411-7419. 523206 15489453 10.1128/ JB.186.21.7411-7419.2004
8. Yang S Perna NT Cooksey DA Okinaka Y Lindow SE Ibekwe AM Keen NT Yang CH Genome-wide identification of plant-upregulated genes of Erwinia chrysanthemi 3937 using a GFP-based IVET leaf array. Mol Plant Microbe Interact 2004, 17:999-1008. 10.1094/MPMI.2004.17.9.999 15384490
9. Rediers H Bonnecarrere V Rainey PB Hamonts K Vanderleyden J De Mot R Development and application of a dapB-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium Pseudomonas stutzeri A15. Appl Environ Microbiol 2003, 69:6864-6874. 262291 14602651 10.1128/ AEM.69.11.6864-6874.2003
10. Preston GM Bertrand N Rainey PB Type III secretion in plant growth-promoting Pseudomonas fluorescens SBW25. Mol Microbiol 2001, 41:999-1014. 10.1046/j.1365-2958.2001.02560.x 11555282
11. Jackson RW Preston GM Rainey PB Genetic characterization of Pseudomonas fluorescens SBW25 rsp gene expression in the phytosphere and in vitro. J Bacteriol 2005, 187:8477-8488. 1317024 16321952 10.1128/ JB.187.24.8477-8488.2005
12. Giddens SR Jackson RW Moon CD Jacobs MA Zhang XX Gehrig SM Rainey PB Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. Proc Natl Acad Sci USA 2007, 104:18247-18252. 2084328 17989226 10.1073/ pnas.0706739104
13. Zhang XX Rainey PB Regulation of copper homeostasis in Pseudomonas fluorescens SBW25. Environ Microbiol 2008, 10:3284-3294. 10.1111/ j.1462-2920.2008.01720.x 18707611
14. Zhang XX Scott K Meffin R Rainey PB Genetic characterization of psp encoding the DING protein in Pseudomonas fluorescens SBW25. BMC Microbiol 2007, 7:114. 2225411 18088430 10.1186/1471-2180-7-114
15. Zhang XX George A Bailey MJ Rainey PB The histidine utilization (hut) genes of Pseudomonas fluorescens SBW25 are active on plant surfaces, but are not required for competitive colonization of sugar beet seedlings. Microbiology 2006, 152:1867-1875. 10.1099/mic.0.28731-0 16735749
16. Howden AJ Harrison CJ Preston GM A conserved mechanism for nitrile metabolism in bacteria and plants. Plant J 2009, 57:243-253. 10.1111/ j.1365-313X.2008.03682.x 18786181
17. Moon CD Zhang XX Matthijs S Schafer M Budzikiewicz H Rainey PB Genomic, genetic and structural analysis of pyoverdine-mediated iron acquisition in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. BMC Microbiol 2008, 8:7. 2235872 18194565 10.1186/1471-2180-8-7
18. Paulsen IT Press CM Ravel J Kobayashi DY Myers GS Mavrodi DV DeBoy RT Seshadri R Ren Q Madupu R Dodson RJ Durkin AS Brinkac LM Daugherty SC Sullivan SA Rosovitz MJ Gwinn ML Zhou L Schneider DJ Cartinhour SW Nelson WC Weidman J Watkins K Tran K Khouri H Pierson EA Pierson LS 3rd Thomashow LS Loper JE Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nat Biotechnol 2005, 23:873-878. 10.1038/ nbt1110 15980861
19. Rainey PB Bailey MJ Physical and genetic map of the Pseudomonas fluorescens SBW25 chromosome. Mol Microbiol 1996, 19:521-533. 10.1046/ j.1365-2958.1996.391926.x 8830243
20. Rainey PB Travisano M Adaptive radiation in a heterogeneous environment. Nature 1998, 394:69-72. 10.1038/27900 9665128
21. Bantinaki E Kassen R Knight CG Robinson Z Spiers AJ Rainey PB Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity. Genetics 2007, 176:441-453. 1893022 17339222 10.1534/genetics.106.069906
22. Compeau G Al-Achi BJ Platsouka E Levy SB Survival of rifampin-resistant mutants of Pseudomonas fluorescens and Pseudomonas putida in soil systems. Appl Environ Microbiol 1988, 54:2432-2438. 204279 3144244
23. Mathee K Narasimhan G Valdes C Qiu X Matewish JM Koehrsen M Rokas A Yandava CN Engels R Zeng E Olavarietta R Doud M Smith RS Montgomery P White JR Godfrey PA Kodira C Birren B Galagan JE Lory S Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 2008, 105:3100-3105. 2268591 18287045 10.1073/pnas.0711982105
24. Hughes D Evaluating genome dynamics: The constraints on rearrangements within bacterial genomes. Genome Biol 2000 1 REVIEWS0006. 138892 11380986 10.1186/gb-2000-1-6-reviews0006
25. Tett A Spiers AJ Crossman LC Ager D Ciric L Dow JM Fry JC Harris D Lilley A Oliver A Parkhill J Quail MA Rainey PB Saunders NJ Seeger K Snyder LA Squares R Thomas CM Turner SL Zhang XX Field D Bailey MJ Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet. ISME J 2007, 1:331-340. 2656933 18043644
26. Lilley AK Bailey MJ The acquisition of indigenous plasmids by a genetically marked pseudomonad population colonizing the sugar beet phytosphere is related to local environmental conditions. Appl Environ Microbiol 1997, 63:1577-1583. 1389558 16535580
27. Bentley SD Chater KF Cerdeño-Tárraga AM Challis GL Thomson NR James KD Harris DE Quail MA Kieser H Harper D Bateman A Brown S Chandra G Chen CW Collins M Cronin A Fraser A Goble A Hidalgo J Hornsby T Howarth S Huang CH Kieser T Larke L Murphy L Oliver K O'Neil S Rabbinowitsch E Rajandream MA Rutherford K et al Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002, 417:141-147. 10.1038/417141a 12000953
28. Daubin V Ochman H Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res 2004, 14:1036-1042. 419781 15173110 10.1101/gr.2231904
29. Dykhuizen DE Green L Recombination in Escherichia coli and the definition of biological species. J Bacteriol 1991, 173:7257-7268. 209233 1938920
30. Curran B Jonas D Grundmann H Pitt T Dowson CG Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa. J Clin Microbiol 2004, 42:5644-5649. 535286 15583294 10.1128/JCM.42.12.5644-5649.2004
31. Haubold B Rainey PB Genetic and ecotypic structure of a fluorescent Pseudomonas population. Mol Ecol 1996, 5:747-761. 10.1111/ j.1365-294X.1996.tb00371.x
32. Konstantinidis KT Tiedje JM Prokaryotic taxonomy and phylogeny in the genomic era: Advancements and challenges ahead. Curr Opin Microbiol 2007, 10:504-509. 10.1016/j.mib.2007.08.006 17923431
33. Goris J Konstantinidis KT Klappenbach JA Coenye T Vandamme P Tiedje JM DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007, 57:81-91. 10.1099/ ijs.0.64483-0 17220447
34. Yamamoto S Kasai H Arnold DL Jackson RW Vivian A Harayama S Phylogeny of the genus Pseudomonas: Intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 2000, 146:2385-2394. 11021915
35. van Passel MW Kuramae EE Luyf AC Bart A Boekhout T The reach of the genome signature in prokaryotes. BMC Evol Biol 2006, 6:84. 1621082 17040564 10.1186/1471-2148-6-84
36. Cases I de Lorenzo V Ouzounis CA Transcription regulation and environmental adaptation in bacteria. Trends Microbiol 2003, 11:248-253. 10.1016/S0966-842X(03)00103-3 12823939
37. Ren Q Paulsen IT Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol 2005, 1:e27. 1188273 16118665 10.1371/journal.pcbi.0010027
38. Zhang XX Lilley AK Bailey MJ Rainey PB The indigenous Pseudomonas plasmid pQBR103 encodes plant-inducible genes, including three putative helicases. FEMS Microbiol Ecol 2004, 51:9-17. 10.1016/ j.femsec.2004.07.006 16329852
39. Stover CK Pham XQ Erwin AL Mizoguchi SD Warrener P Hickey MJ Brinkman FS Hufnagle WO Kowalik DJ Lagrou M Garber RL Goltry L Tolentino E Westbrock-Wadman S Yuan Y Brody LL Coulter SN Folger KR Kas A Larbig K Lim R Smith K Spencer D Wong GK Wu Z Paulsen IT Reizer J Saier MH Hancock RE Lory S Olson MV Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 2000, 406:959-964. 10.1038/35023079 10984043
40. Silby MW Rainey PB Levy SB IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 2004, 150:518-520. 10.1099/mic.0.26871-0 14993298
41. Silby MW Levy SB Overlapping protein-encoding genes in Pseudomonas fluorescens Pf0-1. PLoS Genet 2008, 4:e1000094. 2396522 18551168 10.1371/ journal.pgen.1000094
42. Parkhill J Wren BW Thomson NR Titball RW Holden MT Prentice MB Sebaihia M James KD Churcher C Mungall KL Baker S Basham D Bentley SD Brooks K Cerdeño-Tárraga AM Chillingworth T Cronin A Davies RM Davis P Dougan G Feltwell T Hamlin N Holroyd S Jagels K Karlyshev AV Leather S Moule S Oyston PC Quail M Rutherford K et al Genome sequence of Yersinia pestis, the causative agent of plague. Nature 2001, 413:523-527. 10.1038/ 35097083 11586360
43. Parkhill J Sebaihia M Preston A Murphy LD Thomson N Harris DE Holden MT Churcher CM Bentley SD Mungall KL Cerdeño-Tárraga AM Temple L James K Harris B Quail MA Achtman M Atkin R Baker S Basham D Bason N Cherevach I Chillingworth T Collins M Cronin A Davis P Doggett J Feltwell T Goble A Hamlin N Hauser H et al Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet 2003, 35:32-40. 10.1038/ng1227 12910271
44. Wu M Sun LV Vamathevan J Riegler M Deboy R Brownlie JC McGraw EA Martin W Esser C Ahmadinejad N Wiegand C Madupu R Beanan MJ Brinkac LM Daugherty SC Durkin AS Kolonay JF Nelson WC Mohamoud Y Lee P Berry K Young MB Utterback T Weidman J Nierman WC Paulsen IT Nelson KE Tettelin H O'Neill SL Eisen JA Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: A streamlined genome overrun by mobile genetic elements. PLoS Biol 2004, 2:E69. 368164 15024419 10.1371/ journal.pbio.0020069
45. Delihas N Small mobile sequences in bacteria display diverse structure/ function motifs. Mol Microbiol 2008, 67:475-481. 2229807 18086200
46. Aranda-Olmedo I Tobes R Manzanera M Ramos JL Marques S Species-specific repetitive extragenic palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res 2002, 30:1826-1833. 113213 11937637 10.1093/nar/ 30.8.1826
47. Jordan IK Rogozin IB Wolf YI Koonin EV Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 2002, 12:962-968. 1383730 12045149
48. Shakhnovich BE Koonin EV Origins and impact of constraints in evolution of gene families. Genome Res 2006, 16:1529-1536. 1665636 17053091 10.1101/gr.5346206
49. Spiers AJ Bohannon J Gehrig SM Rainey PB Biofilm formation at the air-liquid interface by the Pseudomonas fluorescens SBW25 wrinkly spreader requires an acetylated form of cellulose. Mol Microbiol 2003, 50:15-27. 10.1046/j.1365-2958.2003.03670.x 14507360
50. Spiers AJ Kahn SG Bohannon J Travisano M Rainey PB Adaptive divergence in experimental populations of Pseudomonas fluorescens. I. Genetic and phenotypic bases of wrinkly spreader fitness. Genetics 2002, 161:33-46. 1462107 12019221
51. Lawrence JG Ochman H Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 1998, 95:9413-9417. 21352 9689094 10.1073/ pnas.95.16.9413
52. Mavrodi DV Loper JE Paulsen IT Thomashow LS Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5. BMC Microbiol 2009, 9:8. 2647930 19144133 10.1186/1471-2180-9-8
53. El-Sayed AK Hothersall J Cooper SM Stephens E Simpson TJ Thomas CM Characterization of the mupirocin biosynthesis gene cluster from Pseudomonas fluorescens NCIMB 10586. Chem Biol 2003, 10:419-430. 10.1016/ S1074-5521(03)00091-7 12770824
54. Burrus V Waldor MK Shaping bacterial genomes with integrative and conjugative elements. Res Microbiol 2004, 155:376-386. 10.1016/ j.resmic.2004.01.012 15207870
55. Pitman AR Jackson RW Mansfield JW Kaitell V Thwaites R Arnold DL Exposure to host resistance mechanisms drives evolution of bacterial virulence in plants. Curr Biol 2005, 15:2230-2235. 10.1016/ j.cub.2005.10.074 16360685
56. Collyn F Billault A Mullet C Simonet M Marceau M YAPI, a new Yersinia pseudotuberculosis pathogenicity island. Infect Immun 2004, 72:4784-4790. 470613 15271940 10.1128/IAI.72.8.4784-4790.2004
57. Thomson NR Howard S Wren BW Holden MT Crossman L Challis GL Churcher C Mungall K Brooks K Chillingworth T Feltwell T Abdellah Z Hauser H Jagels K Maddison M Moule S Sanders M Whitehead S Quail MA Dougan G Parkhill J Prentice MB The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet 2006, 2:e206. 1698947 17173484 10.1371/journal.pgen.0020206
58. Pickard D Wain J Baker S Line A Chohan S Fookes M Barron A Gaora PO Chabalgoity JA Thanky N Scholes C Thomson N Quail M Parkhill J Dougan G Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7. J Bacteriol 2003, 185:5055-5065. 180996 12923078 10.1128/ JB.185.17.5055-5065.2003
59. Stanier RY Palleroni NJ Doudoroff M The aerobic pseudomonads: A taxonomic study. J Gen Microbiol 1966, 43:159-271. 5963505
60. Rainey PB Bailey MJ Thompson IP Phenotypic and genotypic diversity of fluorescent pseudomonads isolated from field-grown sugar beet. Microbiology 1994, 140:2315-2331. 7952185
61. Ravel J Cornelis P Genomics of pyoverdine-mediated iron uptake in pseudomonads. Trends Microbiol 2003, 11:195-200. 12781517
62. Parkhill J Achtman M James KD Bentley SD Churcher C Klee SR Morelli G Basham D Brown D Chillingworth T Davies RM Davis P Devlin K Feltwell T Hamlin N Holroyd S Jagels K Leather S Moule S Mungall K Quail MA Rajandream MA Rutherford KM Simmonds M Skelton J Whitehead S Spratt BG Barrell BG Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 2000, 404:502-506. 10.1038/35006655 10761919
63. Rutherford K Parkhill J Crook J Horsnell T Rice P Rajandream MA Barrell B Artemis: Sequence visualization and annotation. Bioinformatics 2000, 16:944-945. 10.1093/bioinformatics/16.10.944 11120685
64. Pierce E Xie G Barabote RD Saunders E Han CS Detter JC Richardson P Brettin TS Das A Ljungdahl LG Ragsdale SW The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 2008, 10:2550-2573. 2575129 18631365 10.1111/ j.1462-2920.2008.01679.x
65. Carver TJ Rutherford KM Berriman M Rajandream MA Barrell BG Parkhill J ACT: The Artemis Comparison Tool. Bioinformatics 2005, 21:3422-3423. 10.1093/bioinformatics/bti553 15976072
66. Carver T Thomson N Bleasby A Berriman M Parkhill J DNAPlotter: Circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120. 2612626 18990721 10.1093/bioinformatics/btn578
67. Edgar RC MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32:1792-1797. 390337 15034147 10.1093/nar/gkh340
68. Castresana J Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000, 17:540-552. 10742046
69. Stamatakis A RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006, 22:2688-2690. 10.1093/bioinformatics/btl446 16928733
70. Price AL Jones NC Pevzner PA De novo identification of repeat families in large genomes. Bioinformatics 2005, 21(Suppl 1):i351-358. 10.1093/ bioinformatics/bti1018 15961478
71. Higgins DG Sharp PM CLUSTAL: A package for performing multiple sequence alignment on a microcomputer. Gene 1988, 73:237-244. 10.1016/ 0378-1119(88)90330-7 3243435
72. Clamp M Cuff J Searle SM Barton GJ The Jalview Java alignment editor. Bioinformatics 2004, 20:426-427. 10.1093/bioinformatics/btg430 14960472
73. Schuster-Bockler B Schultz J Rahmann S HMM Logos for visualization of protein families. BMC Bioinformatics 2004, 5:7. 341448 14736340 10.1186/ 1471-2105-5-7
74. Vernikos GS Parkhill J Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22:2196-2203. 10.1093/ bioinformatics/btl369 16837528
75. Rainey PB Heithoff DM Mahan MJ Single-step conjugative cloning of bacterial gene fusions involved in microbe-host interactions. Mol Gen Genet 1997, 256:84-87. 10.1007/s004380050548 9341682