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Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages
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Allison GE, Angeles D, Tran-Dinh N, Verma NK: Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri. J Bacteriol 2002, 184:1974-1987.
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The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved
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Recktenwald J, Schmidt H: The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Infect Immun 2002, 70:1896-1908.
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Proux C, van Sinderen D, Suarez J, Garcia P, Ladero V, Fitzgerald GF, Desiere F, Brussow H: The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J Bacteriol 2002, 184:6026-6036.
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Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR et al.: Origins of highly mosaic mycobacteriophage genomes. Cell 2003, 113:171-182. This paper presents a comparative analysis of 14 mycobacteriophage genome sequences, which are seen to be exuberantly mosaic. Some information is derived about relative rates of gene flow into, out of, and among this group of phages. There are examples presented of hypotheses about novel biological mechanisms that are generated from the comparative analysis and not obvious by other means.
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Jacobs-Sera, D.7
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Hendrix RW: Bacteriophages: evolution of the majority. Theor Popul Biol 2002, 61:471-480.
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Wagner PL, Neely MN, Zhang X, Acheson DW, Waldor MK, Friedman DI: Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain. J Bacteriol 2001, 183:2081-2085.
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Wagner, P.L.1
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Wagner PL, Livny J, Neely MN, Acheson DW, Friedman DI, Waldor MK: Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Mol Microbiol 2002, 44:957-970.
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Hendrix RW, Lawrence JG, Hatfull GF, Casjens S: The origins and ongoing evolution of viruses. Trends Microbiol 2000, 8:504-508.
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Jiang W, Li Z, Zhang Z, Baker ML, Prevelige PE Jr, Chiu W: Coat protein fold and maturation transition of bacteriophage P22 seen at subnanometer resolutions. Nat Struct Biol 2003, 10:131-135. This is the first demonstration for the tailed phages that virion proteins with no discernable sequence similarity nevertheless have the same protein fold and go through the same conformational dance, arguing for distant common ancestry.
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Nat Struct Biol
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Hendrix RW, Smith MC, Burns RN, Ford ME, Hatfull GF: Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 1999, 96:2192-2197.
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Lawrence JG, Hatfull GF, Hendrix RW: Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 2002, 184:4891-4905. This paper discusses the meaning of the concept 'virus species' and points out the problems for virus taxonomy that arise as a result of the rampant horizontal exchange of sequences seen, particularly, in the tailed phages. It attempts to reconcile the realities of phage evolution with the great intellectual traditions of biological taxonomy.
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J Bacteriol
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Lawrence, J.G.1
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Hertwig S, Klein I, Lurz R, Lanka E, Appel B: PY54, a linear plasmid prophage of Yersinia enterocolitica with covalently closed ends. Mol Microbiol 2003, 48:989-1003.
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Mol Microbiol
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Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F: Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 2002, 99:14250-14255. This is the most comprehensive attempt so far to compare an unbiased sample of the population of phage sequences in the environment to those in GenBank. The fraction of the environmental sequences that match known sequences is not dramatically different from the fraction of matches in many newly sequenced complete genomes. Some estimates of phage population diversity are derived.
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Proc Natl Acad Sci USA
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Breitbart, M.1
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Genome of Xanthomonas oryzae bacteriophage Xp10: An odd T-odd phage
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Yuzenkova J, Nechaev S, Berlin J, Rogulja D, Kuznedelov K, Inman R, Mushegian A, Severinov K: Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. J Mol Biol 2003, 330:735-748.
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Comparison of the genomes of two Xanthomonas pathogens with differing host specificities
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da Silva AC, Ferro JA, Reinach FC, Farah CS, Furlan LR, Quaggio RB, Monteiro-Vitorello CB, Van Sluys MA, Almeida NF, Alves LM et al.: Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 2002, 417:459-463.
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Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
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Nelson KE, Weinel C, Paulsen IT, Dodson RJ, Hilbert H, Martins dos Santos VA et al.: Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 2002, 4:799-808.
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Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Ruger W: Bacteriophage T4 genome. Microbiol Mol Biol Rev 2003, 67:86-156. This paper is only peripherally concerned with comparative genomics, but it is an exhaustive examination of the T4 genome sequence in the context of nearly 60 years worth of experimental data, and worth reading on those grounds alone.
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Microbiol Mol Biol Rev
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Miller, E.S.1
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A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2
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Hambly E, Tetart F, Desplats C, Wilson WH, Krisch HM, Mann NH: A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc Natl Acad Sci USA 2001, 98:11411-11416.
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The genome of bacteriophage phiKZ of Pseudomonas aeruginosa
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Mesyanzhinov W, Robben J, Grymonprez B, Kostyuchenko VA, Bourkaltseva MV, Sykilinda NN, Krylov VN, Volckaert G: The genome of bacteriophage phiKZ of Pseudomonas aeruginosa. J Mol Biol 2002, 317:1-19.
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J Mol Biol
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Rohwer F, Edwards R: The Phage Proteomic Tree: a genome-based taxonomy for phage. J Bacteriol 2002, 184:4529-4535. Genomic research shows that traditional phage taxonomy is incongruent with our current understanding of the biology of the phages. This paper presents one (somewhat controversial) approach to solving this problem, in which the number of shared genes between two genomes is used as a measure of taxonomic distance, from which a hierarchical tree is derived.
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J Bacteriol
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Microbiol Mol Biol Rev
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Nakayama K, Takashima K, Ishihara H, Shinomiya T, Kageyama M, Kanaya S, Ohnishi M, Murata T, Mori H, Hayashi T: The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol 2000, 38:213-231.
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Mol Microbiol
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Lang AS, Beatty JT: A bacterial signal transduction system controls genetic exchange and motility. J Bacteriol 2002, 184:913-918.
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J Bacteriol
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Lang AS, Beatty JT: Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus. Proc Natl Acad Sci USA 2000, 97:859-864.
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Newcomb WW, Juhas RM, Thomsen DR, Homa FL, Burch AD, Weller SK, Brown JC: The UL6 gene product forms the portal for entry of DNA into the herpes simplex virus capsid. J Virol 2001, 75:10923-10932.
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