The Complete Genome and Phenome of a Community-Acquired Acinetobacter baumannii

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Farrugia, Daniel N ^a   Elbourne, Liam D H ^a   Hassan, Karl A ^a   Eijkelkamp, Bart A ^b   Tetu, Sasha G ^a   Brown, Melissa H ^b   Shah, Bhumika S ^a   Peleg, Anton Y ^c,d   Mabbutt, Bridget C ^a   Paulsen, Ian T ^a  

^a MACQUARIE UNIVERSITY   (Australia)

^b FLINDERS UNIVERSITY   (Australia)

^c MONASH UNIVERSITY   (Australia)

^d ALFRED HOSPITAL   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

4 HYDROXYBENZOIC ACID; BETA LACTAM; CARBON; NITROGEN; POLYSACCHARIDE; SACCHARIC ACID; SULFONAMIDE; TETRACYCLINE;

ACINETOBACTER BAUMANNII; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; CARBOHYDRATE SYNTHESIS; CARBON METABOLISM; COMMUNICABLE DISEASE; CONCENTRATION RESPONSE; DNA RESTRICTION; GENE CLUSTER; GENE DOSAGE; GENE SEQUENCE; GENE STRUCTURE; GENETIC CODE; GENOME ANALYSIS; HOSPITAL INFECTION; MOLECULAR PHYLOGENY; NITROGEN METABOLISM; NONHUMAN; PHENOTYPE;

ACINETOBACTER BAUMANNII; ACINETOBACTER INFECTIONS; CHROMOSOME MAPPING; COMMUNITY-ACQUIRED INFECTIONS; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; DRUG RESISTANCE, BACTERIAL; GENOME, BACTERIAL; HUMANS; MULTIGENE FAMILY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PYLORIC ANTRUM;

EID: 84875103753     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058628     Document Type: Article

References (103)

1. Roca I, Espinal P, Vila-Farres X, Vila J, (2012) The Acinetobacter baumannii oxymoron: commensal hospital dweller turned pan-drug-resistant menace. Front Microbiol 3: 148.
2. Fournier PE, Vallenet D, Barbe V, Audic S, Ogata H, et al. (2006) Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet 2: 62-72.
3. Vila J, Marti S, Sanchez-Cespedes J, (2007) Porins, efflux pumps and multidrug resistance in Acinetobacter baumannii. J Antimicrob Chemoth 59: 1210-1215.
4. Wendt C, Dietze B, Dietz E, Ruden H, (1997) Survival of Acinetobacter baumannii on dry surfaces. J Clin Microbiol 35: 1394-1397.
5. Jawad A, Seifert H, Snelling AM, Heritage J, Hawkey PM, (1998) Survival of Acinetobacter baumannii on dry surfaces: comparison of outbreak and sporadic isolates. J Clin Microbiol 36: 1938-1941.
6. Neely AN, Maley MP, Warden GD, (1999) Computer keyboards as reservoirs for Acinetobacter baumannii in a burn hospital. Clin Infect Dis 29: 1358-1359.
7. Park JY, Kim S, Kim S-M, Cha SH, Lim S-K, et al. (2011) Complete genome sequence of multidrug-resistant Acinetobacter baumannii strain 1656-2, which forms sturdy biofilm. J Bacteriol 193: 6393-6394.
8. Adams MD, Goglin K, Molyneaux N, Hujer KM, Lavender H, et al. (2008) Comparative genome sequence analysis of multidrug-resistant Acinetobacter baumannii. J Bacteriol 190: 8053-8064.
9. Iacono M, Villa L, Fortini D, Bordoni R, Imperi F, et al. (2008) Whole-genome pyrosequencing of an epidemic multidrug-resistant Acinetobacter baumannii strain belonging to the European clone II group. Antimicrob Agents Chemother 52: 2616-2625.
10. Smith MG, Gianoulis TA, Pukatzki S, Mekalanos JJ, Ornston LN, et al. (2007) New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis. Gene Dev 21: 601-614.
11. Vallenet D, Nordmann P, Barbe V, Poirel L, Mangenot S, et al. (2008) Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One 3: e1805.
12. Gao F, Wang Y, Liu Y-J, Wu X-M, Lv X, et al. (2011) Genome sequence of Acinetobacter baumannii MDR-TJ. J Bacteriol 193: 2365-2366.
13. Zhou H, Zhang T, Yu D, Pi B, Yang Q, et al. (2011) Genomic analysis of the multidrug-resistant Acinetobacter baumannii strain MDR-ZJ06 widely spread in China. Antimicrob Agents Chemother 55: 4506-4512.
14. Chen C-C, Lin Y-C, Sheng W-H, Chen Y-C, Chang S-C, et al. (2011) Genome sequence of a dominant, multidrug-resistant Acinetobacter baumannii strain, TCDC-AB0715. J Bacteriol 193: 2361-2362.
15. Adams MD, Chan ER, Molyneaux ND, Bonomo RA, (2010) Genomewide analysis of divergence of antibiotic resistance determinants in closely related isolates of Acinetobacter baumannii. Antimicrob Agents Chemother 54: 3569-3577.
16. La Scola B, Raoult D, (2004) Acinetobacter baumannii in human body louse. Emerg Infect Dis 10: 1671-1673.
17. Bouvresse S, Socolovshi C, Berdjane Z, Durand R, Izri A, et al. (2011) No evidence of Bartonella quintana but detection of Acinetobacter baumannii in head lice from elementary schoolchildren in Paris. Comp Immunol Microb 34: 475-477.
18. Sarma PM, Bhattacharya D, Krishnan S, Lal B, (2004) Assessment of intra-species diversity among strains of Acinetobacter baumannii isolated from sites contaminated with petroleum hydrocarbons. Can J Microbiol 50: 405-414.
19. Chang LK, Ibrahim D, Omar IC, (2011) A laboratory scale bioremediation of Tapis crude oil contaminated soil by bioaugmentation of Acinetobacter baumannii T30C. Afr J Microbiol Res 5: 2609-2615.
20. Berg G, Roskot N, Steidle A, Eberl L, Zock A, et al. (2002) Plant-dependent genotypic and phenotypic diversity of antagonistic rhizobacteria isolated from different Verticillium host plants. Appl Environ Microb 68: 3328-3338.
21. Sachdev D, Nema P, Dhakephalkar P, Zinjarde S, Chopade B, (2010) Assessment of 16S rRNA gene-based phylogenetic diversity and promising plant growth-promoting traits of Acinetobacter community from the rhizosphere of wheat. Microbiol Res 165: 627-638.
22. Girlich D, Poirel L, Nordmann P, (2010) First isolation of the blaOXA-23 carbapenemase gene from an environmental Acinetobacter baumannii isolate. Antimicrob Agents Chemother 54: 578-579.
23. Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, et al. (2011) Metagenomics of the water column in the pristine upper course of the Amazon River. PLoS One 6: e23785.
24. Chu YW, Leung CM, Houang ET, Ng KC, Leung CB, et al. (1999) Skin carriage of Acinetobacters in Hong Kong. J Clin Microbiol 37: 2962-2967.
25. Anstey NM, Currie BJ, Hassell M, Palmer D, Dwyer B, et al. (2002) Community-acquired bacteremic Acinetobacter pneumonia in tropical Australia is caused by diverse strains of Acinetobacter baumannii, with carriage in the throat in at-risk groups. J Clin Microbiol 40: 685-686.
26. Zeana C, Larson E, Sahni J, Bayuga SJ, Wu F, et al. (2003) The epidemiology of multidrug-resistant Acinetobacter baumannii: Does the community represent a reservoir? Infect Cont Hosp Ep 24: 275-279.
27. Chen HP, Chen TL, Lai CH, Fung CP, Wong WW, et al. (2005) Predictors of mortality in Acinetobacter baumannii bacteremia. J Microbiol Immunol Infect 38: 127-136.
28. Falagas ME, Karveli EA, Kelesidis I, Kelesidis T, (2007) Community-acquired Acinetobacter infections. Eur J Clin Microbiol 26: 857-868.
29. Elliott JH, Anstey NM, Jacups SP, Fisher DA, Currie BJ, (2005) Community-acquired pneumonia in northern Australia: low mortality in a tropical region using locally-developed treatment guidelines. Int J Infect Dis 9: 15-20.
30. Leung AS, Chu CM, Tsang KY, Lo FH, Lo KF, et al. (2006) Fulminant community-acquired Acinetobacter baumannii pneumonia as a distinct clinical syndrome. Chest 129: 102-109.
31. Wang JT, McDonald LC, Chang SC, Ho M, (2002) Community-acquired Acinetobacter baumannii bacteremia in adult patients in Taiwan. J Clin Microbiol 40: 1526-1529.
32. Ong CWM, Lye DCB, Khoo KL, Chua GSW, Yeoh SF, et al. (2009) Severe community-acquired Acinetobacter baumannii pneumonia: An emerging highly lethal infectious disease in the Asia-Pacific. Respirology 14: 1200-1205.
33. Chong YP, Jung K-S, Lee KH, Kim M-N, Moon SM, et al. (2010) The bacterial etiology of community-acquired pneumonia in Korea: a nationwide prospective multicenter study. Infect Chemother 42: 397-403.
34. Anstey NM, Currie BJ, Withnall KM, (1992) Community-acquired Acinetobacter pneumonia in the Northern Territory of Australia. Clin Infect Dis 14: 83-91.
35. Gradon JD, Chapnick EK, Lutwick LI, (1992) Infective endocarditis of a native valve due to Acinetobacter: case report and review. Clin Infect Dis 14: 1145-1148.
36. Bick JA, Semel JD, (1993) Fulminant community-acquired Acinetobacter pneumonia in a healthy woman. Clin Infect Dis 17: 820-821.
37. Reindersma P, Nohlmans L, Korten JJ, (1993) Acinetobacter, an infrequent cause of community acquired bacterial meningitis. Clin Neurol Neurosurg 95: 71-73.
38. Ozaki T, Nishimura N, Arakawa Y, Suzuki M, Narita A, et al. (2009) Community-acquired Acinetobacter baumannii meningitis in a previously healthy 14-month-old boy. J Infect Chemother 15: 322-324.
39. Moreira Silva G, Morais L, Marques L, Senra V, (2012) Acinetobacter community-acquired pneumonia in a healthy child. Rev Port Pneumol 18: 96-98.
40. Einsiedel LJ, Woodman RJ, (2010) Two nations: racial disparities in bloodstream infections recorded at Alice Springs Hospital, central Australia, 2001-2005. Med J Aust 192: 567-571.
41. Chevreux B, Wetter T, Suhai S, (1999) Genome sequence assembly using trace signals and additional sequence information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99: 45-56.
42. Darling ACE, Mau B, Blattner FR, Perna NT, (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14: 1394-1403.
43. van Hijum SAFT, Zomer AL, Kuipers OP, Kok J, (2005) Projector 2: contig mapping for efficient gap-closure of prokaryotic genome sequence assemblies. Nucleic Acids Res 33: W560-W566.
44. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
45. Hall TA, (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
46. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75.
47. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
48. Okonechnikov K, Golosova O, Fursov M, (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28: 1166-1167.
49. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
50. Paulsen IT, Seshadri R, Nelson KE, Eisen JA, Heidelberg JF, et al. (2002) The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts. Proc Natl Acad Sci USA 99: 13148-13153.
51. Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, et al. (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci USA 105: 3100-3105.
52. Ogier J-C, Calteau A, Forst S, Goodrich-Blair H, Roche D, et al. (2010) Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus. BMC Genomics 11: 568.
53. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M, (2006) ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 34: D32-D36.
54. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
55. Diancourt L, Passet V, Nemec A, Dijkshoorn L, Brisse S, (2010) The population structure of Acinetobacter baumannii: expanding multiresistant clones from an ancestral susceptible genetic pool. PLoS One 5: e10034.
56. Bochner BR, Gadzinski P, Panomitros E, (2001) Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res 11: 1246-1255.
57. Keseler IM, Collado-Vides J, Santos-Zavaleta A, Peralta-Gil M, Gama-Castro S, et al. (2011) EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Res 39: D583-D590.
58. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40: D742-D753.
59. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M, (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-D280.
60. Bertini A, Poirel L, Mugnier PD, Villa L, Nordmann P, et al. (2010) Characterization and PCR-based replicon typing of resistance plasmids in Acinetobacter baumannii. Antimicrob Agents Chemother 54: 4168-4177.
61. Dorsey CW, Tomaras AP, Actis LA, (2006) Sequence and organization of pMAC, an Acinetobacter baumannii plasmid harboring genes involved in organic peroxide resistance. Plasmid 56: 112-123.
62. Eijkelkamp BA, Stroeher UH, Hassan KA, Papadimitrious MS, Paulsen IT, et al. (2011) Adherence and motility characteristics of clinical Acinetobacter baumannii isolates. FEMS Microbiol Lett 323: 44-51.
63. Srivatsan A, Tehranchi A, MacAlpine DM, Wang JD, (2010) Co-orientation of replication and transcription preserves genome integrity. PLoS Genetics 6: e1000810.
64. Hill CW, Harnish BW, (1981) Inversions between ribosomal RNA genes of Escherichia coli. Proc Natl Acad Sci USA 78: 7069-7072.
65. Klockgether J, Munder A, Neugebauer J, Davenport CF, Stanke F, et al. (2010) Genome diversity of Pseudomonas aeruginosa PAO1 laboratory strains. J Bacteriol 192: 1113-1121.
66. Abadjieva A, Patel J, Webb M, Zinkevich V, Firman K, (1993) A Deletion Mutant of the Type-IC Restriction-Endonuclease EcoR124I Expressing a Novel DNA Specificity. Nucleic Acids Res 21: 4435-4443.
67. Meister J, MacWilliams M, Hubner P, Jutte H, Skrzypek E, et al. (1993) Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition. EMBO J 12: 4585-4591.
68. Adamczyk-Poplawska M, Lower M, Piekarowicz A, (2011) Deletion of one nucleotide within the homonucleotide tract present in the hsdS gene alters the DNA sequence specificity of type I restriction-modification system NgoAV. J Bacteriol 193: 6750-6759.
69. Kobayashi I (2004) Restriction-modification systems as minimal forms of life. In: Pingoud AM, editor. Restriction Endonucleases: Springer Berlin Heidelberg. pp. 19-62.
70. Waldron DE, Lindsay JA, (2006) Sau1: a novel lineage-specific type I restriction-modification system that blocks horizontal gene transfer into Staphylococcus aureus and between S. aureus isolates of different lineages. J Bacteriol 188: 5578-5585.
71. Schneider BL, Kiupakis AK, Reitzer LJ, (1998) Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J Bacteriol 180: 4278-4286.
72. Sakurada K, Ohta T, Fujishiro K, Hasegawa M, Aisaka K, (1996) Acetylpolyamine amidohydrolase from Mycoplana ramosa: gene cloning and characterization of the metal-substituted enzyme. J Bacteriol 178: 5781-5786.
73. Agarwal R, Burley SK, Swaminathan S, (2007) Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics. J Mol Biol 368: 450-463.
74. Permina EA, Mironov AA, Gelfand MS, (2002) Damage-repair error-prone polymerases of eubacteria: association with mobile genome elements. Gene 293: 133-140.
75. Beceiro A, Llobet E, Aranda J, Bengoechea JA, Doumith M, et al. (2011) Phosphoethanolamine modification of lipid A in colistin-resistant variants of Acinetobacter baumannii mediated by the pmrAB two-component regulatory system. Antimicrob Agents Chemother 55: 3370-3379.
76. Bonnin RA, Poirel L, Nordmann P, (2012) AbaR-type transposon structures in Acinetobacter baumannii. J Antimicrob Chemoth 67: 234-236.
77. Post V, White PA, Hall RM, (2010) Evolution of AbaR-type genomic resistance islands in multiply antibiotic-resistant Acinetobacter baumannii. J Antimicrob Chemoth 65: 1162-1170.
78. Krizova L, Dijkshoorn L, Nemec A, (2011) Diversity and evolution of AbaR genomic resistance islands in Acinetobacter baumannii strains of European clone I. Antimicrob Agents Chemother. 55: 3201-3206.
79. Park SH, Kim JW, Yun SH, Leem SH, Kahng HY, et al. (2006) Characterization of β-ketoadipate pathway from multi-drug resistance bacterium, Acinetobacter baumannii DU202 by proteomic approach. J Microbiol 44: 632-640.
80. Aghaie A, Lechaplais C, Sirven P, Tricot S, Besnard-Gonnet M, et al. (2008) New insights into the alternative D-glucarate degradation pathway. J Biol Chem 283: 15638-15646.
81. Henry R, Vithanage N, Harrison P, Seemann T, Coutts S, et al. (2012) Colistin-resistant, lipopolysaccharide-deficient Acinetobacter baumannii responds to lipopolysaccharide loss through increased expression of genes involved in the synthesis and transport of lipoproteins, phospholipids, and poly-β-1,6-N-acetylglucosamine. Antimicrob Agents Chemother 56: 59-69.
82. Bentancor LV, Camacho-Peiro A, Bozkurt-Guzel C, Pier GB, Maira-Litrán T, (2012) Identification of Ata, a multifunctional trimeric autotransporter of Acinetobacter baumannii. J Bacteriol 194: 3950-3960.
83. Loehfelm TW, Luke NR, Campagnari AA, (2008) Identification and characterization of an Acinetobacter baumannii biofilm-associated protein. J Bacteriol 190: 1036-1044.
84. Brossard KA, Campagnari AA, (2012) The Acinetobacter baumannii biofilm-associated protein plays a role in adherence to human epithelial cells. Infect Immun 80: 228-233.
85. Gaddy JA, Arivett BA, McConnell MJ, López-Rojas R, Pachón J, et al. (2012) Role of acinetobactin-mediated iron acquisition functions in the interaction of Acinetobacter baumannii strain ATCC 19606T with human lung epithelial cells, Galleria mellonella caterpillars, and mice. Infect Immun 80: 1015-1024.
86. Russo TA, Luke NR, Beanan JM, Olson R, Sauberan SL, et al. (2010) The K1 capsular polysaccharide of Acinetobacter baumannii strain 307-0294 is a major virulence factor. Infect Immun 78: 3993-4000.
87. Eijkelkamp B, Hassan K, Paulsen I, Brown M, (2011) Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions. BMC Genomics 12: 126.
88. Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M, (2010) Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing. PLoS Pathog 6: e1000834.
89. Jacobs AC, Hood I, Boyd KL, Olson PD, Morrison JM, et al. (2010) Inactivation of phospholipase D diminishes Acinetobacter baumannii pathogenesis. Infect Immun 78: 1952-1962.
90. Johnson DA, Tetu SG, Phillippy K, Chen J, Ren Q, et al. (2008) High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes. PLoS Genet 4: e1000211.
91. Bernards AT, Dijkshoorn L, Vandertoorn J, Bochner BR, Vanboven CPA, (1995) Phenotypic characterization of Acinetobacter strains of 13 DNA-DNA hybridization groups by means of the Biolog system. J Med Microbiol 42: 113-119.
92. Baumann P, Doudoroff M, Stanier RY, (1968) A study of the Moraxella group. II. oxidative-negative species (genus Acinetobacter). J Bacteriol 95: 1520-1541.
93. Nemec A, Krizova L, Maixnerova M, van der Reijden TJK, Deschaght P, et al. (2011) Genotypic and phenotypic characterization of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex with the proposal of Acinetobacter pittii sp nov (formerly Acinetobacter genomic species 3) and Acinetobacter nosocomialis sp nov (formerly Acinetobacter genomic species 13TU). Res Microbiol 162: 393-404.
94. Peekhaus N, Conway T, (1998) What's for dinner?: Entner-Doudoroff metabolism in Escherichia coli. J Bacteriol 180: 3495-3502.
95. Müller RH, Babel W, (1986) Glucose as an energy donor in acetate growing Acinetobacter calcoaceticus. Arch Microbiol 144: 62-66.
96. Lee-Peng FC, Hermodson MA, Kohlhaw GB, (1979) Transaminase B from Escherichia coli: quaternary structure, amino-terminal sequence, substrate specificity, and absence of a separate valine-alpha-ketoglutarate activity. J Bacteriol 139: 339-345.
97. Powell JT, Morrison JF, (1978) Role of the Escherichia coli aromatic amino acid aminotransferase in leucine biosynthesis. J Bacteriol 136: 1-4.
98. Nigro SJ, Hall RM, (2011) GIsul2, a genomic island carrying the sul2 sulphonamide resistance gene and the small mobile element CR2 found in the Enterobacter cloacae subspecies cloacae type strain ATCC 13047 from 1890, Shigella flexneri ATCC 700930 from 1954 and Acinetobacter baumannii ATCC 17978 from 1951. J Antimicrob Chemother 66: 2175-2176.
99. Tatusov RL, Koonin EV, Lipman DJ, (1997) A genomic perspective on protein families. Science 278: 631-637.
100. Stothard P, Wishart DS, (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21: 537-539.
101. Stover BC, Muller KF, (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11: 7.
102. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, et al. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
103. Darling AE, Mau B, Perna NT, (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5: e11147.