Genomic characterization of the Yersinia genus

Genome Biology

Volumn 11, Issue 1, 2010, Pages

  Chen, Peter E ^a   Cook, Christopher ^a   Stewart, Andrew C ^a   Nagarajan, Niranjan ^b,f   Sommer, Dan D ^b   Pop, Mihai ^b   Thomason, Brendan ^a   Kiley Thomason, Maureen P ^a   Lentz, Shannon ^a   Nolan, Nichole ^a   Sozhamannan, Shanmuga ^a   Sulakvelidze, Alexander ^c   Mateczun, Alfred ^a   Du, Lei ^d   Zwick, Michael E ^a,e   Read, Timothy D ^a,e  

^a NAVAL MEDICAL RESEARCH CENTER   (United States)

^b Bldg 142   (United States)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

^d 454 Life Sciences Corporation   (United States)

^e EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; COBALAMIN; HYDROGENASE; UREASE;

ARTICLE; BACTERIAL GENETICS; BACTERIAL STRAIN; BACTERIAL VIRULENCE; DNA SEQUENCE; ENTEROBACTERIACEAE; EVOLUTIONARY ADAPTATION; FISH DISEASE; GENETIC ANALYSIS; GENETIC VARIABILITY; GENUS; NONHUMAN; ORTHOLOGY; PATHOGENESIS; PROTEIN FUNCTION; SEQUENCE ANALYSIS; SOIL MICROFLORA; SPECIES DIFFERENCE; SPECIES HABITAT; YERSINIA; YERSINIA ALDOVAE; YERSINIA BERCOVIERI; YERSINIA ENTEROCOLITICA; YERSINIA FREDERIKSENII; YERSINIA INTERMEDIA; YERSINIA KRISTENSENII; YERSINIA MOLLARETII; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS; YERSINIA ROHDEI; YERSINIA RUCKERI; BACTERIAL GENOME; CHROMOSOME MAP; CLUSTER ANALYSIS; GENETIC PROCEDURES; GENETICS; METHODOLOGY; MULTIGENE FAMILY; PHYLOGENY; VIRULENCE;

BACTERIA (MICROORGANISMS); ENTEROBACTERIACEAE; YERSINIA; YERSINIA ALDOVAE; YERSINIA BERCOVIERI; YERSINIA ENTEROCOLITICA; YERSINIA FREDERIKSENII; YERSINIA INTERMEDIA; YERSINIA KRISTENSENII; YERSINIA MOLLARETII; YERSINIA PESTIS; YERSINIA PSEUDOTUBERCULOSIS; YERSINIA ROHDEI; YERSINIA RUCKERI;

CHROMOSOME MAPPING; CLUSTER ANALYSIS; GENETIC TECHNIQUES; GENETIC VARIATION; GENOME, BACTERIAL; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VIRULENCE; YERSINIA; YERSINIA ENTEROCOLITICA; YERSINIA PESTIS;

EID: 77349121865     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2010-11-1-r1     Document Type: Article

References (107)

1. Ecker DJ, Sampath R, Willett P, Wyatt JR, Samant V, Massire C, Hall TA, Hari K, McNeil JA, Buchen-Osmond C, Budowle B: The Microbial Rosetta Stone Database: a compilation of global and emerging infectious microorganisms and bioterrorist threat agents. BMC Microbiol 2005, 5:19.
2. Achtman M, Zurth K, Morelli G, Torrea G, Guiyoule A, Carniel E: Yersinia pestis, the cause of plague, is a recently emerged clone of Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 1999, 96:14043-14048.
3. van Baarlen P, van Belkum A, Summerbell RC, Crous PW, Thomma BP: Molecular mechanisms of pathogenicity: how do pathogenic microorganisms develop cross-kingdom host jumps? FEMS Microbiol Rev 2007, 31:239-277
4. Van Ert MN, Easterday WR, Huynh LY, Okinaka RT, Hugh-Jones ME, Ravel J, Zanecki SR, Pearson T, Simonson TS, U'Ren JM, Kachur SM, Leadem-Dougherty RR, Rhoton SD, Zinser G, Farlow J, Coker PR, Smith KL, Wang B, Kenefic LJ, Fraser-Liggett CM, Wagner DM, Keim P: Global Genetic Population Structure of Bacillus anthracis. PLoS ONE 2007, 2:e461.
5. Zwick ME, McAfee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A: Microarray-based resequencing of multiple Bacillus anthracis isolates. Genome Biol 2005, 6:R10.
6. Ahmed N, Dobrindt U, Hacker J, Hasnain SE: Genomic fluidity and pathogenic bacteria: applications in diagnostics, epidemiology and intervention. Nat Rev Microbiol 2008, 6:387-394.
7. Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 2008, 24:133-141.
8. Shendure J, Ji H: Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145.
9. 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. Deng W, Burland V, Plunkett G, 3rd, Boutin A, Mayhew GF, Liss P, Perna NT, Rose DJ, Mau B, Zhou S, Schwartz DC, Fetherston JD, Lindler LE, Brubaker RR, Plano GV, Straley SC, McDonough KA, Nilles ML, Matson JS, Blattner FR, Perry RD: Genome sequence of Yersinia pestis KIM. J Bacteriol 2002, 184:4601-4611.
11. Song Y, Tong Z, Wang J, Wang L, Guo Z, Han Y, Zhang J, Pei D, Zhou D, Qin H, Pang X, Han Y, Zhai J, Li M, Cui B, Qi Z, Jin L, Dai R, Chen F, Li S, Ye C, Du Z, Lin W, Wang J, Yu J, Yang H, Wang J, Huang P, Yang R: Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans. DNA Res 2004, 11:179-197.
12. Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL: Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol 2006, 188:4453-4463.
13. Chain PS, Carniel E, Larimer FW, Lamerdin J, Stoutland PO, Regala WM, Georgescu AM, Vergez LM, Land ML, Motin VL, Brubaker RR, Fowler J, Hinnebusch J, Marceau M, Medigue C, Simonet M, Chenal-Francisque V, Souza B, Dacheux D, Elliott JM, Derbise A, Hauser LJ, Garcia E: Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proc Natl Acad Sci U S A 2004, 101:13826-13831.
14. Eppinger M, Rosovitz MJ, Fricke WF, Rasko DA, Kokorina G, Fayolle C, Lindler LE, Carniel E, Ravel J: The complete genome sequence of Yersinia pseudotuberculosis IP31758, the causative agent of Far East scarlet-like fever. PLoS Genet 2007, 3:e142.
15. 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.
16. Rollins SE, Rollins SM, Ryan ET: Yersinia pestis and the plague. Am J Clin Pathol 2003, 119 Suppl:S78-85.
17. Wren BW: The yersiniae--a model genus to study the rapid evolution of bacterial pathogens. Nat Rev Microbiol 2003, 1:55-64.
18. Cornelis GR: The Yersinia Ysc-Yop virulence apparatus. Int J Med Microbiol 2002, 291:455-462.
19. Juris SJ, F. Shao, and J.E. DIxon: Yersinia effectors target mammalian signaling pathways. Cell Microbiol 2002, 4:201-211.
20. Viboud GI, and Bliska, J.B.: Yersinia outer proteins: role in modulation of host cell signaling responses and pathogenesis. Annu Rev Microbiol 2005, 59:69-89.
21. Schubert S, Rakin A, Heesemann J: The Yersinia high-pathogenicity island (HPI): evolutionary and functional aspects. Int J Med Microbiol 2004, 294:83-94.
22. Carniel E: The Yersinia high-pathogenicity island: an iron-uptake island. Microbes Infect 2001, 3:561-569.
23. Darling AE, Miklos I, Ragan MA: Dynamics of genome rearrangement in bacterial populations. PLoS Genet 2008, 4:e1000128.
24. Anisimov AP, Lindler LE, Pier GB: Intraspecific diversity of Yersinia pestis. Clin Microbiol Rev 2004, 17:434-464.
25. Wang X, Han Y, Li Y, Guo Z, Song Y, Tan Y, Du Z, Rakin A, Zhou D, Yang R: Yersinia genome diversity disclosed by Yersinia pestis genome-wide DNA microarray. Can J Microbiol 2007, 53:1211-1221.
26. Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, Rasko DA, Mammel MK, Eppinger M, Rosovitz MJ, Wagner D, Rahalison L, Leclerc JE, Hinshaw JM, Lindler LE, Cebula TA, Carniel E, Ravel J: Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS ONE 2007, 2:e309.
27. Derbise A, Chenal-Francisque V, Pouillot F, Fayolle C, Prévost MC, Médigue C, Hinnebusch BJ, Carniel E: A horizontally acquired filamentous phage contributes to the pathogenicity of the plague bacillus. Mol Microbiol 2007, 63:1145-1157.
28. Sulakvelidze A: Yersiniae other than Y. enterocolitica, Y. pseudotuberculosis, and Y. pestis: the ignored species. Microbes Infect 2000, 2:497-513.
29. Bottone EJ, Bercovier H, Mollaret HH: Genus XLI. Yersinia Van Loghem 1944, 15AL. In: Bergey's Manual of Systematic Bacteriology. Edited by Garrity GM, vol. 2. New York, NY: Springer; 2005: 838-846.
30. Kotetishvili M, Kreger A, Wauters G, Morris JG, Jr., Sulakvelidze A, Stine OC: Multilocus sequence typing for studying genetic relationships among Yersinia species. J Clin Microbiol 2005, 43:2674-2684.
31. Noble MA, Barteluk RL, Freeman HJ, Subramaniam R, Hudson JB: Clinical significance of virulence-related assay of Yersinia species. J Clin Microbiol 1987, 25:802-807.
32. Robins-Browne RM, Cianciosi S, Bordun AM, Wauters G: Pathogenicity of Yersinia kristensenii for mice. Infect Immun 1991, 59:162-167.
33. Fukushima H, Gomyoda M, Kaneko S: Mice and moles inhabiting mountainous areas of Shimane Peninsula as sources of infection with Yersinia pseudotuberculosis. J Clin Microbiol 1990, 28:2448-2455.
34. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M et al: Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380.
35. Ewing B, Green P: Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998, 8:186-194.
36. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB: Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 2008, 18:763-770.
37. Phillippy AM, Schatz MC, Pop M: Genome assembly forensics: finding the elusive mis-assembly. Genome Biol 2008, 9:R55.
38. Samad AH, Cai WW, Hu X, Irvin B, Jing J, Reed J, Meng X, Huang J, Huff E, Porter B: Mapping the genome one molecule at a time--optical mapping. Nature 1995, 378:516-517.
39. Nagarajan N, Read TD, Pop M: Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics 2008, 24:1229-35.
40. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M: ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006, 34:D32-36.
41. Price AL, Jones NC, Pevzner PA: De novo identification of repeat families in large genomes. Bioinformatics 2005, 21 Suppl 1:i351-358.
42. Hulton CS, Higgins CF, Sharp PM: ERIC sequences: a novel family of repetitive elements in the genomes of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol 1991, 5:825-834.
43. De Gregorio E, Silvestro G, Venditti R, Carlomagno MS, Di Nocera PP: Structural organization and functional properties of miniature DNA insertion sequences in yersiniae. J Bacteriol 2006, 188:7876-7884.
44. Phillippy AM, Mason JA, Ayanbule K, Sommer DD, Taviani E, Huq A, Colwell RR, Knight IT, Salzberg SL: Comprehensive DNA signature discovery and validation. PLoS Comput Biol 2007, 3:e98.
45. Darling AC, Mau B, Blattner FR, Perna NT: Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004, 14:1394-1403.
46. Enright AJ, Van Dongen S, Ouzounis CA: An efficient algorithm for largescale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
47. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N et al: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A 2005, 102:13950-13955.
48. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
49. Felsenstein J: PHYLIP: Phylogeny Inference Package, version 3.6. In. Seattle, WA, USA.: University of Washington; 2001.
50. Tatusov RL, Galperin MY, Natale DA, Koonin EV: The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 2000, 28:33-36.
51. Lepore LS, Roelvink PR, Granados RR: Enhancin, the granulosis virus protein that facilitates nucleopolyhedrovirus (NPV) infections, is a metalloprotease. J Invertebr Pathol 1996, 68:131-140.
52. Bowen D, Rocheleau TA, Blackburn M, Andreev O, Golubeva E, Bhartia R, ffrench-Constant RH: Insecticidal toxins from the bacterium Photorhabdus luminescens. Science 1998, 280:2129-2132.
53. Brussow H, Canchaya C, Hardt WD: Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol Mol Biol Rev 2004, 68:560-602.
54. Collyn F, Guy L, Marceau M, Simonet M, Roten CA: Describing ancient horizontal gene transfers at the nucleotide and gene levels by comparative pathogenicity island genometrics. 2006, 22:1072-1079.
55. Collyn F, Billault A, Mullet C, Simonet M, Marceau M: YAPI, a new Yersinia pseudotuberculosis pathogenicity island. Infect Immun 2004, 72:4784-4790.
56. Howard SL, Gaunt MW, Hinds J, Witney AA, Stabler R, Wren BW: Application of comparative phylogenomics to study the evolution of Yersinia enterocolitica and to identify genetic differences relating to pathogenicity. J Bacteriol 2006, 188:3645-3653.
57. Haller JC, Carlson S, Pederson KJ, Pierson DE: A chromosomally encoded type III secretion pathway in Yersinia enterocolitica is important in virulence. Mol Microbiol 2000, 36:1436-1446.
58. Hensel M, Shea JE, Baumler AJ, Gleeson C, Blattner F, Holden DW: Analysis of the boundaries of Salmonella pathogenicity island 2 and the corresponding chromosomal region of Escherichia coli K-12. J Bacteriol 1997, 179:1105-1111.
59. Shea JE, Hensel M, Gleeson C, Holden DW: Identification of a virulence locus encoding a second type III secretion system in Salmonella typhimurium. Proc Natl Acad Sci U S A 1996, 93:2593-2597.
60. Thomson NR, Howard S, Wren BW, Prentice MB: Comparative genome analyses of the pathogenic Yersiniae based on the genome sequence of Yersinia enterocolitica strain 8081. Adv Exp Med Biol 2007, 603:2-16.
61. Prentice MB, Cuccui J, Thomson N, Parkhill J, Deery E, Warren MJ: Cobalamin synthesis in Yersinia enterocolitica 8081. Functional aspects of a putative metabolic island. Adv Exp Med Biol 2003, 529:43-46.
62. Roth JR, Lawrence JG, Bobik TA: Cobalamin (coenzyme B12): synthesis and biological significance. Annu Rev Microbiol 1996, 50:137-181.
63. Kofoid E, Rappleye C, Stojiljkovic I, Roth J: The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 1999, 181:5317-5329.
64. Maier RJ: Use of molecular hydrogen as an energy substrate by human pathogenic bacteria. Biochem Soc Trans 2005, 33:83-85.
65. Ewing WH, Ross AJ, Brenner DJ, R. FG: Yersinia ruckeri sp. nov., the Redmouth (RM) Bacterium. Internation Journal of Systematic Bacteriology 1978, 28:37-44.
66. Sekowska A, Dénervaud V, Ashida H, Michoud K, Haas D, Yokota A, Danchin A: Bacterial variations on the methionine salvage pathway. BMC Microbiol 2004, 4:9.
67. Hiller NL, Janto B, Hogg JS, Boissy R, Yu S, Powell E, Keefe R, Ehrlich NE, Shen K, Hayes J, Barbadora K, Klimke W, Dernovoy D, Tatusova T, Parkhill J, Bentley SD, Post JC, Ehrlich GD, Hu FZ: Comparative Genomic Analyses of Seventeen Streptococcus pneumoniae Strains: Insights into the Pneumococcal Supragenome. J Bacteriol 2007, 189:8186-95.
68. Hogg JS, Hu FZ, Janto B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD: Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 2007, 8:R103.
69. 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.
70. Holt K, Parkhill J, Mazzoni C, Roumagnac P, Weill F, Goodhead I, Rance R, Baker S, Maskell D, Wain J, Dolecek C, Achtman M, Dougan G: Highthroughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet 2008:7.
71. Simmons S, Dibartolo G, Denef V, Goltsman D, Thelen M, Banfield J, Eisen J: Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation. Plos Biol 2008, 6:e177.
72. Rasko D, Rosovitz M, Myers G, Mongodin E, Fricke W, Gajer P, Crabtree J, Sperandio V, Ravel J: The pan-genome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. J Bacteriol 2008:44.
73. Read TD, Peterson SN, Tourasse N, Baillie LW, Paulsen IT, Nelson KE, Tettelin H, Fouts DE, Eisen JA, Gill SR, Holtzapple EK, Okstad OA, Helgason E, Rilstone J, Wu M, Kolonay JF, Beanan MJ, Dodson RJ, Brinkac LM, Gwinn M, DeBoy RT, Madpu R, Daugherty SC, Durkin AS, Haft DH, Nelson WC, Peterson JD, Pop M, Khouri HM, Radune D et al: The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003, 423:81-86.
74. Tettelin H, Masignani V, Cieslewicz MJ, Eisen JA, Peterson S, Wessels MR, Paulsen IT, Nelson KE, Margarit I, Read TD, Madoff LC, Wolf AM, Beanan MJ, Brinkac LM, Daugherty SC, DeBoy RT, Durkin AS, Kolonay JF, Madupu R, Lewis MR, Radune D, Fedorova NB, Scanlan D, Khouri H, Mulligan S, Carty HA, Cline RT, Van Aken SE, Gill J, Scarselli M et al: Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc Natl Acad Sci U S A 2002, 99:12391-12396.
75. Sprague LD, Neubauer H: Yersinia aleksiciae sp. nov. Int J Syst Evol Microbiol 2005, 55:831-835.
76. Sprague LD, Scholz HC, Amann S, Busse HJ, Neubauer H: Yersinia similis sp. nov. Int J Syst Evol Microbiol 2008, 58:952-958.
77. Merhej V, Adekambi T, Pagnier I, Raoult D, Drancourt M: Yersinia massiliensis sp. nov., isolated from fresh water. Int J Syst Evol Microbiol 2008, 58:779-784.
78. Delpino MV, Marchesini MI, Estein SM, Comerci DJ, Cassataro J, Fossati CA, Baldi PC: A bile salt hydrolase of Brucella abortus contributes to the establishment of a successful infection through the oral route in mice. Infect Immun 2007, 75:299-305.
79. Sherlock O, Vejborg RM, Klemm P: The TibA adhesin/invasin from enterotoxigenic Escherichia coli is self recognizing and induces bacterial aggregation and biofilm formation. Infect Immun 2005, 73:1954-1963.
80. Liu B, Pop M: ARDB--Antibiotic Resistance Genes Database. Nucleic Acids Res 2009, 37:D443-447.
81. Leplae R, Hebrant A, Wodak SJ, Toussaint A: ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res 2004, 32:D45-49.
82. Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M: Frameshift detection in prokaryotic genomic sequences. Int J Bioinform Res Appl 2009, 5:458-477.
83. Pop M, Phillippy A, Delcher AL, Salzberg SL: Comparative genome assembly. Brief Bioinform 2004, 5:237-248.
84. Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
85. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol 2004, 5:R12.
86. Stewart AC, Osborne B, Read TD: DIYA: A bacterial annotation pipeline for any genomics lab. Bioinformatics 2009, 25:962-3.
87. Salzberg SL, Delcher AL, Kasif S, White O: Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26:544-548.
88. Lowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997, 25:955-964.
89. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, Ussery DW: RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007, 35:3100-3108.
90. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH: UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 2007, 23:1282-1288.
91. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
92. Conserved Domain Database(CDD). In.
93. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
94. Cook CP, Stewart AC, Akmal A, Read TD. "MegaGenomic" Analysis: A Cluster Based Approach 2008 Roche/454 North American Users Group Meeting: 2008, Conference; New Haven, CT.
95. Talavera G, Castresana J: Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 2007, 56:564-577.
96. Langille MG, Brinkman FS: IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25:664-665.
97. Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J: DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 2009, 25:119-120.
98. MAUVE Aligner User Guide [http://asap.ahabs.wisc.edu/mauvealigner/ mauve-user-guide/]
99. Antibiotic Resistance Genes Database [http://ardb.cbcb.umd.edu/]
100. Read TD, Myers GS, Brunham RC, Nelson WC, Paulsen IT, Heidelberg J, Holtzapple E, Khouri H, Federova NB, Carty HA, Umayam LA, Haft DH, Peterson J, Beanan MJ, White O, Salzberg SL, Hsia RC, McClarty G, Rank RG, Bavoil PM, Fraser CM: Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res 2003, 31:2134-2147.
101. Rasko DA, Myers GS, Ravel J: Visualization of comparative genomic analyses by BLAST score ratio. BMC Bioinformatics 2005, 6:2.
102. Bercovier H, Steigerwalt AG, Guiyoule A, Huntley-Carter G, Brenner DJ: Yersinia aldovae (Formerly Yersinia enterocolitica-Like Group X2): a New Species of Enterobacteriaceae Isolated from Aquatic Ecosystems. International Journal of Systematic and Evolutionary Microbiology 1984, 34:166.
103. Wauters G, Janssens M, Steigerwalt AG, Brenner DJ: Yersinia mollaretii sp. nov. and Yersinia bercovieri sp. nov., Formerly Called Yersinia enterocolitica Biogroups 3A and 3B. International Journal of Systematic and Evolutionary Microbiology 1988, 38:424.
104. Ursing J, Brennert DJ, Bercovier H, Fanning GR, Steigerwalt AG, Brault J, Mollaret HH: Yersinia frederiksenii: A new species of enterobacteriaceae composed of rhamnose-positive strains (formerly called atypical yersinia enterocolitica or Yersinia enterocolitica -Like). Current Microbiology 1980, 4:213-217.
105. Brenner DJ, Bercovier HH, Ursing J, Alonso JM, Steigerwalt AG, Fanning GR, Carter GP, Mollaret HH: Yersinia intermedia: A new species of enterobacteriaceae composed of rhamnose-positive, melibiose-positive, raffinose-positive strains (formerly called Yersinia enterocolitica or Yersinia enterocolitica -like). Current Microbiology 1980, 4:207-212.
106. Bercovier H, Ursing J, Brenner DJ, Steigerwalt AG, Fanning GR, Carter GP, Mollaret HH: Yersinia kristensenii: A new species of enterobacteriaceae composed of sucrose-negative strains (formerly called atypical Yersinia enterocolitica or Yersinia enterocolitica -Like). Current Microbiology 1980, 4:219-224.
107. Aleksic S, Steigerwalt AG, Bockemuehl J: Yersinia rohdei sp. nov. isolated from human and dog feces and surface water. Int J Syst Bacteriol 1987.