1887

Abstract

CAIM 1792 is a marine bacterial strain that causes mortality in farmed shrimp in north-west Mexico, and the identification of virulence genes in this strain is important for understanding its pathogenicity. The aim of this work was to compare the CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions that differentiate this strain from other strains. Twenty-one newly sequenced genomes were compared against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to those of other strains (78 %) than to those of the other closely related species (67 %), (63 %) and (59 %). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DNA–DNA hybridization and multi-locus sequence analysis of 11 concatenated housekeeping genes. SNP analysis clustered 34/38 genomes within their accepted species. The pangenomic and SNP trees showed that is the most conserved of the four species studied and may be divided into at least three subspecies, supported by intergenomic distance analysis. atlases were created to identify unique regions among the genomes most related to CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems and a transcriptional regulator, LysR, reported to be involved in virulence, metabolism, quorum sensing and motility.

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2015-09-01
2019-12-12
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References

  1. Amaral G. R. S. , Silva B.S.D.O. , Santos E. O. , Dias G. M. , Lopes R. M. , Edwards R. A. , Thompson C. C. , Thompson F. L. . ( 2012;). Genome sequence of the bacterioplanktonic, mixotrophic Vibrio campbellii strain PEL22A, isolated in the Abrolhos Bank. J Bacteriol 194: 2759–2760 [CrossRef] [PubMed].
    [Google Scholar]
  2. Amaral G. R. S. , Dias G. M. , Wellington-Oguri M. , Chimetto L. , Campeão M. E. , Thompson F. L. , Thompson C. C. . ( 2014;). Genotype to phenotype: identification of diagnostic vibrio phenotypes using whole genome sequences. Int J Syst Evol Microbiol 64: 357–365 [CrossRef] [PubMed].
    [Google Scholar]
  3. Ayala-Castro C. , Saini A. , Outten F. W. . ( 2008;). Fe-S cluster assembly pathways in bacteria. Microbiol Mol Biol Rev 72: 110–125 [CrossRef] [PubMed].
    [Google Scholar]
  4. Babu M. M. , Luscombe N. M. , Aravind L. , Gerstein M. , Teichmann S. A. . ( 2004;). Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14: 283–291 [CrossRef] [PubMed].
    [Google Scholar]
  5. Baker K. R. , Postle K. . ( 2013;). Mutations in Escherichia coli ExbB transmembrane domains identify scaffolding and signal transduction functions and exclude participation in a proton pathway. J Bacteriol 195: 2898–2911 [CrossRef] [PubMed].
    [Google Scholar]
  6. Baldi P. , Brunak S. , Chauvin Y. , Krogh A. . ( 1996;). Naturally occurring nucleosome positioning signals in human exons and introns. J Mol Biol 263: 503–510 [CrossRef] [PubMed].
    [Google Scholar]
  7. Bassler B. L. , Greenberg E. P. , Stevens A. M. . ( 1997;). Cross-species induction of luminescence in the quorum-sensing bacterium Vibrio harveyi . J Bacteriol 179: 4043–4045 [PubMed].
    [Google Scholar]
  8. Bolshoy A. , McNamara P. , Harrington R. E. , Trifonov E. N. . ( 1991;). Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc Natl Acad Sci U S A 88: 2312–2316 [CrossRef] [PubMed].
    [Google Scholar]
  9. Brenner S. E. , Hubbard T. , Murzin A. , Chothia C. . ( 1995;). Gene duplications in H. influenzae . Nature 378: 140 [CrossRef] [PubMed].
    [Google Scholar]
  10. Cano-Gomez A. , Bourne D. G. , Hall M. R. , Owens L. , Høj L. . ( 2009;). Molecular identification, typing and tracking of Vibrio harveyi in aquaculture systems: current methods and future prospects. Aquaculture 287: 1–10 [CrossRef].
    [Google Scholar]
  11. Cano-Gómez A. , Goulden E. F. , Owens L. , Høj L. . ( 2010;). Vibrio owensii sp. nov., isolated from cultured crustaceans in Australia. FEMS Microbiol Lett 302: 175–181 [CrossRef] [PubMed].
    [Google Scholar]
  12. Cano-Gomez A. , Høj L. , Owens L. , Andreakis N. . ( 2011;). Multilocus sequence analysis provides basis for fast and reliable identification of Vibrio harveyi-related species and reveals previous misidentification of important marine pathogens. Syst Appl Microbiol 34: 561–565 [CrossRef] [PubMed].
    [Google Scholar]
  13. Chen Y. , Stine O. C. , Badger J. H. , Gil A. I. , Nair G. B. , Nishibuchi M. , Fouts D. E. . ( 2011;). Comparative genomic analysis of Vibrio parahaemolyticus: serotype conversion and virulence. BMC Genomics 12: 294 [CrossRef] [PubMed].
    [Google Scholar]
  14. Chimetto L. A. , Cleenwerck I. , Alves N. Jr , Silva B. S. , Brocchi M. , Willems A. , De Vos P. , Thompson F. L. . ( 2011;). Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei . Int J Syst Evol Microbiol 61: 362–368 [CrossRef] [PubMed].
    [Google Scholar]
  15. Conant G. C. , Wolfe K. H. . ( 2008;). Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet 9: 938–950 [CrossRef] [PubMed].
    [Google Scholar]
  16. Das B. , Bischerour J. , Barre F. X. . ( 2011;). Molecular mechanism of acquisition of the cholera toxin genes. Indian J Med Res 133: 195–200 [PubMed].
    [Google Scholar]
  17. Dias G. M. , Thompson C. C. , Fishman B. , Naka H. , Haygood M. G. , Crosa J. H. , Thompson F. L. . ( 2012;). Genome sequence of the marine bacterium Vibrio campbellii DS40M4, isolated from open ocean water. J Bacteriol 194: 904 [CrossRef] [PubMed].
    [Google Scholar]
  18. Espinoza-Valles I. , Soto-Rodríguez S. , Edwards R. A. , Wang Z. , Vora G. J. , Gómez-Gil B. . ( 2012;). Draft genome sequence of the shrimp pathogen Vibrio harveyi CAIM 1792. J Bacteriol 194: 2104 [CrossRef] [PubMed].
    [Google Scholar]
  19. Gelfand M. S. . ( 2006;). Evolution of transcriptional regulatory networks in microbial genomes. Curr Opin Struct Biol 16: 420–429 [CrossRef] [PubMed].
    [Google Scholar]
  20. Gomez-Gil B. , Thompson F. L. , Thompson C. C. , Swings J. . ( 2003;). Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis. Int J Syst Evol Microbiol 53: 239–243 [CrossRef] [PubMed].
    [Google Scholar]
  21. Gomez-Gil B. , Soto-Rodríguez S. , Lozano R. , Betancourt-Lozano M. . ( 2014;). Draft Genome sequence of Vibrio parahaemolyticus strain M0605, which causes severe mortalities of shrimps in Mexico. Genome Announc 2: e0005514 [CrossRef] [PubMed].
    [Google Scholar]
  22. Grimes D. J. , Stemmler J. , Hada H. , May E. B. , Maneval D. , Hetrick F. M. , Jones R. T. , Stoskopf M. , Colwell R. R. . ( 1984;). Vibrio species associated with mortality of sharks held in captivity. Microb Ecol 10: 271–282 [CrossRef] [PubMed].
    [Google Scholar]
  23. Hadjifrangiskou M. , Koehler T. M. . ( 2012;). Intrinsic curvature associated with the coordinately regulated anthrax toxin gene promoters. NIH Public Access 29: (6), 997–1003 [CrossRef] [PubMed].
    [Google Scholar]
  24. Harris L. J. , Owens L. . ( 1999;). Production of exotoxins by two luminous Vibrio harveyi strains known to be primary pathogens of Penaeus monodon larvae. Dis Aquat Organ 38: 11–22 [CrossRef].
    [Google Scholar]
  25. Hoang T. T. , Sullivan S. A. , Cusick J. K. , Schweizer H. P. . ( 2002;). Beta-ketoacyl acyl carrier protein reductase (FabG) activity of the fatty acid biosynthetic pathway is a determining factor of 3-oxo-homoserine lactone acyl chain lengths. Microbiology 148: 3849–3856 [PubMed].[CrossRef]
    [Google Scholar]
  26. Hoffmann M. , Monday S. R. , McCarthy P. J. , Lopez J. V. , Fischer M. , Brown E. W. . ( 2013;). Cladistics Genetic and phylogenetic evidence for horizontal gene transfer among ecologically disparate groups of marine Vibrio . Cladistics 29: 46–64 [CrossRef].
    [Google Scholar]
  27. Huang Y. , Jian J. , Lu Y. , Cai S. , Wang B. , Tang J. , Pang H. , Ding Y. , Wu Z. . ( 2012;). Draft genome sequence of the fish pathogen Vibrio harveyi strain ZJ0603. J Bacteriol 194: 6644–6645 [CrossRef] [PubMed].
    [Google Scholar]
  28. Hurley J. M. , Woychik N. A. . ( 2009;). Bacterial toxin HigB associates with ribosomes and mediates translation-dependent mRNA cleavage at A-rich sites. J Biol Chem 284: 18605–18613 [CrossRef] [PubMed].
    [Google Scholar]
  29. Hyatt D. , Chen G. L. , Locascio P. F. , Land M. L. , Larimer F. W. , Hauser L. J. . ( 2010;). Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119 [CrossRef] [PubMed].
    [Google Scholar]
  30. Johnson F. H. , Shunk I.V . ( 1936;). An interesting new species of luminous bacteria. Journal of Bacteriology 31: 585–592.
    [Google Scholar]
  31. Jacobsen A. , Hendriksen R. S. , Aaresturp F. M. , Ussery D. W. , Friis C. . ( 2011;). The Salmonella enterica pan-genome. Microb Ecol 62: 487–504 [CrossRef] [PubMed].
    [Google Scholar]
  32. Kahlke T. , Goesmann A. , Hjerde E. , Willassen N. P. , Haugen P. . ( 2012;). Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation. BMC Genomics 13: 179 [CrossRef] [PubMed].
    [Google Scholar]
  33. Karsch-Mizrachi I. , Nakamura Y. , Cochrane G. , International Nucleotide Sequence Database Collaboration . ( 2012;). The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res 40: (D1), D33–D37 [CrossRef] [PubMed].
    [Google Scholar]
  34. Khalturin K. , Anton-Erxleben F. , Sassmann S. , Wittlieb J. , Hemmrich G. , Bosch T. C. G. . ( 2008;). A novel gene family controls species-specific morphological traits in Hydra . PLoS Biol 6: e278 [CrossRef] [PubMed].
    [Google Scholar]
  35. Kimura M. . ( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111–120 [CrossRef] [PubMed].
    [Google Scholar]
  36. Krüger D. H. , Bickle T. A. . ( 1983;). Bacteriophage survival: multiple mechanisms for avoiding the deoxyribonucleic acid restriction systems of their hosts. Microbiol Rev 47: 345–360 [PubMed].
    [Google Scholar]
  37. Lan S. F. , Huang C. H. , Chang C. H. , Liao W. C. , Lin I. H. , Jian W. N. , Wu Y. G. , Chen S. Y. , Wong H. C. . ( 2009;). Characterization of a new plasmid-like prophage in a pandemic Vibrio parahaemolyticus O3:K6 strain. Appl Environ Microbiol 75: 2659–2667 [CrossRef] [PubMed].
    [Google Scholar]
  38. Leekitcharoenphon P. , Kaas R. S. , Thomsen M. C. F. , Friis C. , Rasmussen S. , Aarestrup F. M. . ( 2012;). snpTree—a web-server to identify and construct SNP trees from whole genome sequence data. BMC Genomics 13: (Suppl. 7), S6 [CrossRef] [PubMed].
    [Google Scholar]
  39. Li N. , Kojima S. , Homma M. . ( 2011;). Sodium-driven motor of the polar flagellum in marine bacteria Vibrio . Genes Cells 16: 985–999 [CrossRef] [PubMed].
    [Google Scholar]
  40. Lin B. , Wang Z. , Malanoski A. P. , O'Grady E. A. , Wimpee C. F. , Vuddhakul V. , Alves N. Jr , Thompson F. L. , Gomez-Gil B. , Vora G. J. . ( 2010;). Comparative genomic analyses identify the Vibrio harveyi genome sequenced strains BAA-1116 and HY01 as Vibrio campbellii . Environ Microbiol Rep 2: 81–89 [CrossRef] [PubMed].
    [Google Scholar]
  41. Lu J. , Holmgren A. . ( 2014;). The thioredoxin antioxidant system. Free Radic Biol Med 66: 75–87 [CrossRef] [PubMed].
    [Google Scholar]
  42. Lukjancenko O. , Ussery D. W. , Wassenaar T. M. . ( 2012;). Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera. Microb Ecol 63: 651–673 [CrossRef] [PubMed].
    [Google Scholar]
  43. Maddocks S. E. , Oyston P. C. F. . ( 2008;). Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology (Reading, England) 154: (Pt 12), 3609–23.[CrossRef]
    [Google Scholar]
  44. McLean M. J. , Wolfe K. H. , Devine K. M. . ( 1998;). Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J Mol Evol 47: 691–696 [CrossRef] [PubMed].
    [Google Scholar]
  45. Meier-Kolthoff J. P. , Auch A. F. , Klenk H.-P. , Göker M. . ( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60 [CrossRef] [PubMed].
    [Google Scholar]
  46. Mekalanos J. J. . ( 1983;). Duplication and amplification of toxin genes in Vibrio cholerae . Cell 35: 253–263 [CrossRef] [PubMed].
    [Google Scholar]
  47. Mey A. R. , Wyckoff E. E. , Oglesby A. G. , Rab E. , Taylor R. K. , Payne S. M. . ( 2002;). Identification of the Vibrio cholerae enterobactin receptors VctA and IrgA: IrgA is not required for virulence. Infect Immun 70: 3419–3426 [CrossRef] [PubMed].
    [Google Scholar]
  48. Ornstein R. L. , Rein R. , Breen D. L. , Macelroy R. D. . ( 1978;). An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking. Biopolymers 17: (10), 2341–2360 http://doi.org/doi: 10.1002/bip.1978.360171005.[CrossRef]
    [Google Scholar]
  49. Ogierman M. A. , Fallarino A. , Riess T. , Williams S. G. , Attridge S. R. , Manning P. A. . ( 1997;). Characterization of the Vibrio cholerae El Tor lipase operon lipAB and a protease gene downstream of the hly region. J Bacteriol 179: 7072–7080 [PubMed].
    [Google Scholar]
  50. Pascual J. , Macián M. C. , Arahal D. R. , Garay E. , Pujalte M. J. . ( 2010;). Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes. Int J Syst Evol Microbiol 60: 154–165 [CrossRef] [PubMed].
    [Google Scholar]
  51. Pedersen K. , Verdonck L. , Austin B. , Austin D. A. , Blanch A. R. , Grimont P. A. D. , Jofre J. , Koblavi S. , Larsen J. L. , other authors . ( 1998;). Taxonomic evidence that Vibrio carchariae Grimes et al. 1985 is a junior synonym of Vibrio harveyi (Johnson and Shunk 1936) Baumann et al. 1981. Int J Syst Bacteriol 48: 749–758 [CrossRef].
    [Google Scholar]
  52. Rattanama P. , Srinitiwarawong K. , Thompson J. R. , Pomwised R. , Supamattaya K. , Vuddhakul V. . ( 2009;). Shrimp pathogenicity, hemolysis, and the presence of hemolysin and TTSS genes in Vibrio harveyi isolated from Thailand. Dis Aquat Organ 86: 113–122 [CrossRef] [PubMed].
    [Google Scholar]
  53. Reichelt J. , Baumann P. . ( 1973;). Taxonomy of the marine lumi- nous bacteria. Arch Microbiol 94: 283–330 [CrossRef] [PubMed].
    [Google Scholar]
  54. Rivera-Posada J. A. , Pratchett M. , Cano-Gomez A. , Arango-Gomez J. D. , Owens L. . ( 2011;). Refined identification of Vibrio bacterial flora from Acanthasther planci based on biochemical profiling and analysis of housekeeping genes. Dis Aquat Organ 96: 113–123 [CrossRef] [PubMed].
    [Google Scholar]
  55. Ross J. A. , Plano G. V. . ( 2011;). A C-terminal region of Yersinia pestis YscD binds the outer membrane secretin YscC. J Bacteriol 193: 2276–2289 [CrossRef] [PubMed].
    [Google Scholar]
  56. Roy Chowdhury P. , Boucher Y. , Hassan K. A. , Paulsen I. T. , Stokes H. W. , Labbate M. . ( 2011;). Genome sequence of Vibrio rotiferianus strain DAT722. J Bacteriol 193: 3381–3382 [CrossRef] [PubMed].
    [Google Scholar]
  57. Rybniker J. , Pojer F. , Marienhagen J. , Kolly G. S. , Chen J. M. , van Gumpel E. , Hartmann P. , Cole S. T. . ( 2014;). The cysteine desulfurase IscS of Mycobacterium tuberculosis is involved in iron-sulfur cluster biogenesis and oxidative stress defence. Biochem J 459: 467–478 [CrossRef] [PubMed].
    [Google Scholar]
  58. Sawabe T. , Kita-Tsukamoto K. , Thompson F. L. . ( 2007;). Inferring the evolutionary history of vibrios by means of multilocus sequence analysis. J Bacteriol 189: 7932–7936 [CrossRef] [PubMed].
    [Google Scholar]
  59. Sawabe T. , Ogura Y. , Matsumura Y. , Feng G. , Amin A. R. , Mino S. , Nakagawa S. , Sawabe T. , Kumar R. , other authors . ( 2013;). Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov. Front Microbiol 4: 414 [CrossRef] [PubMed].
    [Google Scholar]
  60. Shpigelman E. S. , Trifonov E. N. , Bolshoy A. . ( 1993;). curvature: software for the analysis of curved DNA. Comput Appl Biosci 9: 435–440 [PubMed].
    [Google Scholar]
  61. Snipen L. , Ussery D. W. . ( 2010;). Standard operating procedure for computing pangenome trees. Stand Genomic Sci 2: 135–141 [CrossRef] [PubMed].
    [Google Scholar]
  62. Soto-Rodriguez S. A. , Gomez-Gil B. , Lozano R. . ( 2010;). ‘Bright-red’ syndrome in Pacific white shrimp Litopenaeus vannamei is caused by Vibrio harveyi . Dis Aquat Organ 92: 11–19 [CrossRef] [PubMed].
    [Google Scholar]
  63. Stintzi A. , Evans K. , Meyer J. M. , Poole K. . ( 1998;). Quorum-sensing and siderophore biosynthesis in Pseudomonas aeruginosa: lasR/lasI mutants exhibit reduced pyoverdine biosynthesis. FEMS Microbiol Lett 166: 341–345 [CrossRef] [PubMed].
    [Google Scholar]
  64. Taguchi F. , Ogawa Y. , Takeuchi K. , Suzuki T. , Toyoda K. , Shiraishi T. , Ichinose Y. . ( 2006;). A homologue of the 3-oxoacyl-(acyl carrier protein) synthase III gene located in the glycosylation island of Pseudomonas syringae pv. tabaci regulates virulence factors via N-acyl homoserine lactone and fatty acid synthesis. J Bacteriol 188: 8376–8384 [CrossRef] [PubMed].
    [Google Scholar]
  65. Taguchi F. , Suzuki T. , Inagaki Y. , Toyoda K. , Shiraishi T. , Ichinose Y. . ( 2010;). The siderophore pyoverdine of Pseudomonas syringae pv. tabaci 6605 is an intrinsic virulence factor in host tobacco infection. J Bacteriol 192: 117–126 [CrossRef] [PubMed].
    [Google Scholar]
  66. Tamura K. , Peterson D. , Peterson N. , Stecher G. , Nei M. , Kumar S. . ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28: 2731–2739 [CrossRef] [PubMed].
    [Google Scholar]
  67. Teichmann S. A. , Babu M. M. . ( 2004;). Gene regulatory network growth by duplication. Nat Genet 36: 492–496 [CrossRef] [PubMed].
    [Google Scholar]
  68. Teichmann S. A. , Park J. , Chothia C. . ( 1998;). Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc Natl Acad Sci U S A 95: 14658–14663 [CrossRef] [PubMed].
    [Google Scholar]
  69. Tettelin H. , Masignani V. , Cieslewicz M. J. , Donati C. , Medini D. , Ward N. L. , Angiuoli S. V. , Crabtree J. , Jones A. L. , other authors . ( 2005;). Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 102: 13950–13955 [CrossRef] [PubMed].
    [Google Scholar]
  70. Thompson F. L. , Gomez-Gil B. , Vasconcelos A. T. R. , Sawabe T. . ( 2007;). Multilocus sequence analysis reveals that Vibrio harveyi and V. campbellii are distinct species. Appl Environ Microbiol 73: 4279–4285 [CrossRef] [PubMed].
    [Google Scholar]
  71. Thompson J. D. , Higgins D. G. , Gibson T. J. . ( 1994;). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680 [CrossRef] [PubMed].
    [Google Scholar]
  72. Thompson F. L. , Iida T. , Swings J. . ( 2004;). Biodiversity of vibrios. Microbiol Mol Biol Rev 68: 403–431 [CrossRef] [PubMed].
    [Google Scholar]
  73. Thompson F. L. , Gevers D. , Thompson C. C. , Dawyndt P. , Naser S. , Hoste B. , Munn C. B. , Swings J. . ( 2005;). Phylogeny and molecular identification of vibrios on the basis of multilocus sequence analysis. Appl Environ Microbiol 71: 5107–5115 [CrossRef] [PubMed].
    [Google Scholar]
  74. Thompson C. C. , Vicente A. C. P. , Souza R. C. , Vasconcelos A. T. R. , Vesth T. , Alves N. Jr , Ussery D. W. , Iida T. , Thompson F. L. . ( 2009;). Genomic taxonomy of Vibrios . BMC Evol Biol 9: 258 [CrossRef] [PubMed].
    [Google Scholar]
  75. Troisfontaines P. , Cornelis G. R. . ( 2005;). Type III secretion: more systems than you think. Physiology (Bethesda) 20: 326–339 [CrossRef] [PubMed].
    [Google Scholar]
  76. UniProt Consortium ( 2014;). Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42: (D1), D191–D198 [CrossRef] [PubMed].
    [Google Scholar]
  77. Urbanczyk H. , Ogura Y. , Hayashi T. . ( 2013;). Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences. Int J Syst Evol Microbiol 63: 2742–2751 [CrossRef] [PubMed].
    [Google Scholar]
  78. Ussery D. W. , Borini S. , Wassenaar T. M. . ( 2009;). Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists (Computational Series vol. 8) London: Springer;.[CrossRef]
    [Google Scholar]
  79. Vesth T. , Wassenaar T. M. , Hallin P. F. , Snipen L. , Lagesen K. , Ussery D. W. . ( 2010;). On the origins of a Vibrio species. Microb Ecol 59: 1–13 [CrossRef] [PubMed].
    [Google Scholar]
  80. Vesth T. , Lagesen K. , Acar Ö. , Ussery D. . ( 2013;). CMG-biotools, a free workbench for basic comparative microbial genomics. PLoS One 8: e60120 [CrossRef] [PubMed].
    [Google Scholar]
  81. Yoshizawa S. , Wada M. , Kita-Tsukamoto K. , Ikemoto E. , Yokota A. , Kogure K. . ( 2009;). Vibrio azureus sp. nov., a luminous marine bacterium isolated from seawater. Int J Syst Evol Microbiol 59: 1645–1649 [CrossRef] [PubMed].
    [Google Scholar]
  82. Yu G. , Stoltzfus A. . ( 2012;). Population diversity of ORFan genes in Escherichia coli . Genome Biol Evol 4: 1176–1187 [CrossRef] [PubMed].
    [Google Scholar]
  83. Yu M. , Ren C. , Qiu J. , Luo P. , Zhu R. , Zhao Z. , Hu C. . ( 2013;). Draft genome sequence of the opportunistic marine pathogen Vibrio harveyi strain E385. Genome Announc 1: e00677–e00613 [CrossRef] [PubMed].
    [Google Scholar]
  84. Zhang X. H. , Meaden P. G. , Austin B. . ( 2001;). Duplication of hemolysin genes in a virulent isolate of Vibrio harveyi . Appl Environ Microbiol 67: 3161–3167 [CrossRef] [PubMed].
    [Google Scholar]
  85. Zhang H. , Zhu F. , Yang T. , Ding L. , Zhou M. , Li J. , Haslam S. M. , Dell A. , Erlandsen H. , Wu H. . ( 2014;). The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold. Nat Commun 5: 4339 [PubMed].
    [Google Scholar]
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