Curated list of prokaryote viruses with fully sequenced genomes

Research in Microbiology

Volumn 158, Issue 7, 2007, Pages 555-566

  Ackermann, Hans W ^a   Kropinski, Andrew M ^b  

^a Faculty of Medicine   (Canada)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

Author keywords

Archaevirus; Bacteriophage; Sequenced prokaryote virus genomes

Indexed keywords

ACINETOBACTER; ALPHAPROTEOBACTERIA; BACILLUS; BACTERIOPHAGE; BORDETELLA; BREVIBACTERIUM; BURKHOLDERIA; CLOSTRIDIUM; ENTEROBACTERIACEAE; ESCHERICHIA; GENE SEQUENCE; HAEMOPHILUS; HALORUBRUM; HOST PATHOGEN INTERACTION; KLEBSIELLA; LACTOBACILLUS; LACTOCOCCUS; LEPTOSPIRA; LISTERIA; LISTONELLA; MANNHEIMIA; METHANOBACTERIUM; MYCOBACTERIUM; MYCOBACTERIUM SMEGMATIS; NONHUMAN; ORTHOMYXOVIRUS; PRIORITY JOURNAL; PROKARYOTE; PSEUDOMONAS; RHODOBACTER; RHODOTHERMUS; SALMONELLA; SHIGELLA; SHORT SURVEY; STAPHYLOCOCCUS; STREPTOCOCCUS; STREPTOMYCES; TAXON; THERMUS; VIBRIO; VIRUS GENOME; XANTHOMONAS; YERSINIA;

ARCHAEA; ARCHAEAL VIRUSES; BACTERIA; BACTERIOPHAGES; GENOME, VIRAL;

ARCHAEA; CAUDOVIRALES; CORYNEBACTERINEAE; ENTEROBACTERIACEAE; LACTOCOCCUS; PROKARYOTA;

EID: 34748891057     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2007.07.006     Document Type: Short Survey

References (234)

1. Ackermann H.-W. 5500 bacteriophages examined in the electron microscope. Arch. Virol. 152 (2006) 227-243
2. Adhin, M.R. (1989). A comparative analysis of RNA coliphages. Structural and regulatory features. Ph.D. thesis, Rijksuniversiteit Leiden, Leiden, The Netherlands.
3. Adhin M.R., Hirashima A., and van Duin J. Nucleotide sequence from the ssRNA bacteriophage JP34 resolves the discrepancy between serological and biophysical classification. Virology 170 (1989) 238-242
4. Ahn D.-G., Kim S.I., Rhee J.-K., Kim K.-P., Pan J.G., and Oh J.V. TTSV1, a new virus-like particle isolated from the hyperthermophilic crenarchaeote Thermoproteus tenax. Virology 351 (2006) 280-290
5. Allison G.E., Angeles D., Tran-Dinh N., and Verma N.K. Complete genomic sequence of SfV, a serotype-converting bacteriophage of Shigella flexneri. J. Bacteriol. 184 (2002) 1974-1987
6. Alonso J.C., Lüder G., Stiege A.C., Chai S., Weise F., and Trautner T.A. The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 204 (1997) 201-212
7. Altermann J., Klein E.R., and Henrich B. Primary structure and features of the genome of the Lactobacillus gasseri temperate bacteriophage φ{symbol}adh. Gene 236 (1999) 333-346
8. Ball A. The Universal Taxonomy of Viruses In Theory and Practice. In: Fauquet C.M., Mayo M.A., Maniloff J., Desselberger U., and Ball L.A. (Eds). Virus Taxonomy. VIIIth Report of the International Committee on Taxonomy of Viruses (2006), Elsevier Academic Press 3-7
9. Bamford D.H., Ravantti J.J., Rönnholm G., Laurinavicius S., Kukkaro P., Dyall-Smith M., Somerharju P., Kalkkinen N., and Bamford J.K.H. Constituents of SH1, a novel lipid-containing virus infecting the halophilic euryarchaeon Haloarcula hispanica. J. Virol. 79 (2005) 9097-9107
10. Bamford J.K.H., Hänninen A.-L., Pakula T.M., Ojala P.M., Kalkkinen N., Frilander M., and Bamford D.H. Genome organization of membrane-containing bacteriophage PRD1. Virology 183 (1991) 658-676
11. Barrangou R., Fremaux C., Deveau H., Richards M., Boyaval P., Moineau S., Romero D.A., and Horvath P. CRISPR provides acquired resistance against viruses in prokaryotes. Science 315 (2007) 1709-1712
12. Bath C., Cukalac T., Porter K., and Dyall-Smith M.L. His1 and His2 are distantly related, spindle-shaped haloviruses belonging to the novel virus group, Salterprovirus. Virology 350 (2006) 228-239
13. Beekwilder J., Nieuwenhuizen R., Poot R., and van Duin J. Secondary structure model for the first three domains of Qβ RNA. Control of A-protein synthesis. J. Mol. Biol. 256 (1996) 8-19
14. Beck E., and Zink B. Nucleotide sequence and genome organization of filamentous RT bacteriophages f1 and fd. Gene 16 (1981) 35-58
15. Bettstetter M., Peng X., Rachel R., Garrett R.A., and Prangishvili D. AFV1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Virology 315 (2003) 68-79
16. Blatny J.M., Godager L., Lunde M., and Nes I.F. Complete genome sequence of the Lactococcus lactis temperate phage φ{symbol}LC3: comparative analysis of φ{symbol}LC3 and its relatives in lactococci and streptococci. Virology 318 (2004) 231-244
17. Blondal T., Hjorleifsdottir S., Fridjonsson O.F., Aevarsson A., Skirnisdottir S., Hermannsdottir A.G., Hreggvidsson G.O., Smith A.V., and Kristjansson J.K. Discovery and characterization of a thermostable bacteriophage RNA ligase homologous to T4 RNA ligase 1. Nucleic Acids Res. 31 (2003) 7247-7254
18. Bourhy P., Frangeul L., Couvé E., Glaser P., Saint Girons I., and Picardeau M. Complete nucleotide sequence of the LE1 prophage from the spirochete Leptospira biflexa and characterization of its replication and partition functions. J. Bacteriol. 187 (2005) 3931-3940
19. Braid M.D., Silhavy J.L., Kitts C.L., Cano R.J., and Howe M.M. Complete genomic sequence of bacteriophage B3, a Mu-like phage of Pseudomonas aeruginosa. J. Bacteriol. 186 (2004) 6560-6574
20. Brentlinger K.L., Hafenstein S., Novak C.R., Fane B.A., Borgon R., McKenna R., and Agbandje-McKenna M. Microviridae, a family divided: isolation, characterization, and genome sequence of φ{symbol}MH2K, a bacteriophage of the obligate intracellular parasitic bacterium Bdellovibrio bacteriovorus. J. Bacteriol. 184 (2002) 1089-1094
21. Brondsted L., Ostergaard S., Pedersen M., Hammer K., and Vogensen F.K. Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: evolution, structure, and genome organization of lactococcal bacteriophages. Virology 283 (2001) 93-109
22. Bukovska G., Klucar L., Vlcek C., Adamovic J., Turna J., and Timko J. Complete nucleotide sequence and genome analysis of bacteriophage BFK20-A lytic phage of the industrial producer Brevibacterium flavum. Virology 348 (2006) 57-71
23. Campoy S., Aranda J., Alvarez G., Barbé J., and Llagostera M. Isolation and sequencing of a temperate transducing phage for Pasteurella multocida. Appl. Environ. Microbiol. 72 (2006) 3154-3160
24. Canchaya C., Proux C., Fournous G., Bruttin A., and Brüssow H. Prophage genomics. Microbiol. Mol. Biol. Rev. 67 (2003) 238-276
25. Carlton R.M., Noordman W.H., Biswas B., de Meester E.D., and Loessner M.J. Bacteriophage P100 for control of Listeria monocytogenes in foods: genome sequence, bioinformatic analyses, oral toxicity study, and application. Regul. Toxicol. Pharmacol. 43 (2005) 301-312
26. Casjens S.R., Gilcrease E.B., Huang W.M., Bunny K.L., Pedulla M.L., Ford M.E., Houtz J.M., Hatfull G.F., and Hendrix R.W. The pKO2 linear plasmid prophage of Klebsiella oxytoca. J. Bacteriol. 186 (2004) 1818-1832
27. Casjens S.R., Gilcrease E.B., Winn-Stapley D.A., Schicklmaier P., Schmieger H., Pedulla M.L., Ford M.E., Houtz J.M., Hatfull G.F., and Hendrix R.W. The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J. Bacteriol. 187 (2005) 1091-1104
28. Casjens S., Winn-Stapley D.A., Gilcrease E.B., Morona R., Kühlewein C., Chua J.E., Manning P.A., Inwood W., and Clark A.J. The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging. J. Mol. Biol. 339 (2004) 379-394
29. Ceyssens P.J., Lavigne R., Mattheus W., Chibeu A., Hertveldt K., Mast J., Robben J., and Volckaert G. Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the φ{symbol}KMV subgroup within the T7 supergroup. J. Bacteriol. 188 (2006) 6924-6931
30. Chan B., Miyamoto H., Taniguchi H., and Yoshida S. Isolation and genetic characterization of a novel filamentous bacteriophage, a deleted form of phage f237, from a pandemic Vibrio haemolyticus O4:K68 strain. Microbiol. Immunol. 46 (2002) 565-569
31. Chandry P.S., Moore S.C., Boyce J.D., Davidson B.E., and Hillier A.J. Analysis of the DNA sequence, gene expression, origin of replication and modular structure of the Lactococcus lactis lytic bacteriophage sk1. Mol. Microbiol. 26 (1997) 49-64
32. Chang B., Taniguchi H., Miyamoto H., and Yoshida S.I. Filamentous bacteriophages of Vibrio parahaemolyticus as a possible clue to genetic transmission. J. Bacteriol. 180 (1998) 5094-5101
33. Chauvatcharin N., Ahantarig A., Baimai V., and Kittayapong P. Bacteriophage WO-B and Wolbachia in natural mosquito hosts: infection incidence, transmission mode and relative density. Mol. Ecol. 15 (2006) 2451-2461
34. Chen F., and Lu J. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68 (2002) 2589-2594
35. Chibani-Chennoufi S., Dillmann M.L., Marvin-Guy L., Rami-Shojaei S., and Brüssow H. Lactobacillus plantarum bacteriophage LP65: a new member of the SPO1-like genus of the family Myoviridae. J. Bacteriol. 186 (2004) 7069-7083
36. Chopin M.-C., Rouault A., Ehrlich S.D., and Gautier M. Filamentous phage active on the gram-positive bacterium Propionibacterium freudenreichii. J. Bacteriol. 184 (2002) 2030-2033
37. Christie G.E., Temple L.M., Bartlett B.A., and Goodwin T.S. Programmed translational frameshift in the bacteriophage P2 FETUD tail gene operon. J. Bacteriol. 184 (2002) 6522-6531
38. Clark A.J., Inwood W.B., Cloutier T., and Dhillon T.S. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. J. Mol. Biol. 311 (2001) 657-679
39. Comeau A.-M., Bertrand C., Letarov A., Tétart F., and Krisch H.M. Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Virology 362 (2007) 384-396
40. Crutz-Le Coq A.-M., Cesselin B., Commissaire J., and Anba J. Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Microbiology 148 (2002) 985-1001
41. Daniel A., Bonnen P.E., and Fischetti V.A. First complete genome sequence of two Staphylococcus epidermidis bacteriophages. J. Bacteriol. 189 (2007) 2086-2100
42. Davies R.L., and Lee I. Diversity of temperate bacteriophages induced in bovine and ovine Mannheimia haemolytica isolates and identification of a new P2-like phage. FEMS Microbiol. Lett. 260 (2006) 162-170
43. DeShazer D. Genomic diversity of Burkholderia pseudomallei clinical isolates: substractive hybridization reveals a Burkholderia mallei-specific prophage in B. pseudomallei 1026b. J. Bacteriol. 186 (2004) 3938-3950
44. Dobbins A.T., George M., Basham D.A., Ford M.E., Houtz J.M., Pedulla M.L., Lawrence J.G., Hatfull G.F., and Hendrix R.W. Complete genomic sequence of the virulent Salmonella bacteriophage SP6. J. Bacteriol. 186 (2004) 1933-1944
45. Dunn J.J., and Studier F.W. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J. Mol. Biol. 166 (1983) 477-535
46. Esposito D., Fitzmaurice W.P., Benjamin R.C., Goodman S.D., and Scocca J.J. The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids Res. 24 (1996) 2360-2368
47. Faruque S.M., Bin Naser I., Fujihara K., Diraphat P., Chowdhury N., Kamruzzarnan A., Qadri F., Yamasaki S., Ghosh A.N., and Mekalanos J.J. Genomic sequence and receptor for the Vibrio cholerae phage KSF-1Φ: evolutionary divergence among filamentous vibriophages mediating lateral gene transfer. J. Bacteriol. 187 (2005) 4095-4103
48. Fiers W., Contreras R., Duerinck D., Haegeman G., Iserentant D., Merregaert J., Min Jou W., Molemans F., Raeymaekers F., van den Berghe A., Volckaert G., and Ysebaert M. Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260 (1976) 500-507
49. Ford M.E., Sarkis G.J., Belanger A.E., Hendrix R.W., and Hatfull G.F. Genome structure of mycobacteriophage D29: implications for phage evolution. J. Mol. Biol. 279 (1998) 143-164
50. Ford M.E., Stenström C., Hendrix R.W., and Hatfull G.F. Mycobacteriophage TM4: genome structure and gene expression. Tuber. Lung Dis. 79 (1998) 63-73
51. Fortier L.-C., Bransi A., and Moineau S. Genome sequence and global gene expression of Q54, a new phage species linking the 936 and c2 phage species of Lactococcus lactis. J. Bacteriol. 188 (2006) 6101-6114
52. Fouts D.E., Rasko D.A., Cer R.Z., Jiang L., Federova N.B., Shvartsbeyn A., Vamathevan J.J., Tallon L., Althoff R., Arbogast T.S., Fadrosh D.W., Read T.D., and Gill S.R. Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry. J. Bacteriol. 188 (2006) 3402-3408
53. Fujii Y., Kubo T., Ishikawa H., and Sasaki T. Isolation and characterization of the bacteriophage WO from Wolbachia, an arthropod endosymbiont. Biochem. Biophys. Res. Commun. 317 (2004) 1183-1188
54. García E., Elliott J.M., Ramanculov E., Chain P.S.G., Chu M.C., and Molineux I.J. The genome sequence of Yersinia pestis bacteriophage φ{symbol}A1122 reveals an intimate with the coliphage T3 and T7 genomes. J. Bacteriol. 185 (2003) 5248-5262
55. García P., Ladero V., and Suárez J.E. Analysis of the morphogenetic cluster of the temperate Lactobacillus casei bacteriophage A2. Arch. Virol. 148 (2003) 1051-1070
56. Garner S.A., Everson J.S., Lambden P.R., Fane B.A., and Clarke I.N. Isolation, molecular characterisation and genome sequence of a bacteriophage (Chp3) from Chlamydophila pecorum. Virus Genes 28 (2004) 207-214
57. Godson G.N., Barrell B.G., Staden R., and Fiddes F.C. Nucleotide sequence of bacteriophage G4 DNA. Nature 276 (1978) 236-247
58. Gottlieb P., Potgieter C., Wei H., and Toporovsky I. Characterization of φ{symbol}12, a bacteriophage related to φ{symbol}6: nucleotide sequence of the large double-stranded RNA. Virology 295 (2002) 266-271
59. Gottlieb P., Wei H., Potgieter C., and Toporovsky I. Characterization of φ{symbol}12, a bacteriophage related to φ{symbol}6: nucleotide sequence of the small and middle double-stranded DNA. Virology 293 (2002) 118-124
60. Groeneveld H., Oudot F., and van Duin J. RNA phage KU1 has an insertion of 18 nucleotides in the start codon of its lysis gene. Virology 218 (1996) 141-147
61. Govind R., Fralick J.A., and Rolfe R.D. Genomic organization and molecular characterization of Clostridium difficile bacteriophage ΦCD119. J. Bacteriol. 188 (2006) 2568-2577
62. Halling C., Calendar R., Christie G.E., Dale E.C., Dehò G., Finkel S., Flensburg J., Ghisotti D., Kahn M.L., Lane K.B., Lin C.S., Lindqvist B.H., Pierson III L.S., Six E.W., Sunshine M.G., and Ziermann R. DNA sequence of satellite bacteriophage P4. Nucleic Acids Res. 18 (1990) 1649
63. Hardies S.C., Comeau A.M., Serwer P., and Suttle C.A. The complete sequence of marine bacteriophage VpV262 infecting Vibrio parahaemolyticus indicates that an ancestral component of a T7 viral supergroup is widespread in the marine environment. Virology 310 (2003) 359-371
64. Häring M., Peng X., Brügger K., Rachel R., Stetter K.O., Garrett R.A., and Prangishvili D. Morphology and genome organization of the virus PSV of the hyperthermophilic archaeal genera Pyrobaculum and Thermoproteus: a novel virus family, the Globuloviridae. Virology 323 (2004) 233-242
65. Häring M., Vestergaard G., Brügger K., Rachel R., Garrett R.A., and Prangishvili D. Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. J. Bacteriol. 187 (2005) 3855-3858
66. Hatfull G.F., and Sarkis G.J. DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol. Microbiol. 7 (1993) 395-405
67. Hertveldt K., Lavigne R., Pleteneva E., Sernova N., Kurochkina L., Korchevskii R., Robben J., Mesyanzhinov V., Krylov V.N., and Volckaert G. Genome comparison of Pseudomonas aeruginosa large phages. J. Mol. Biol. 354 (2005) 536-545
68. Hertwig S., Klein I., Lurz R., Lanka E., and Appel B. PY54, a linear plasmid prophage of Yersinia enterocolitica with covalently closed ends. Mol. Microbiol. 48 (2003) 989-1003
69. Highlander S.K., Weissenberger S., Alvarez L.A., Weinstock G.M., and Berget P.B. Complete nucleotide sequence of a P2 family lysogenic bacteriophage, φ{symbol}MhaA1-PHL101, from Mannheimia haemolytica serotype A1. Virology 350 (2006) 79-89
70. Hill D.F., and Petersen G.B. Nucleotide sequence of bacteriophage f1 DNA. J. Virol. 44 (1982) 32-46
71. Hill D.F., Short N.J., Perham N., and Petersen B. DNA sequence of the filamentous bacteriophage Pf1. J. Mol. Biol. 218 (1991) 349-364
72. Hirashima A., Inokuchi Y., Harigai H., Furuse K., and Watanabe I. Biochemical characterization of RNA coliphage MX1. J. Gen. Virol. 64 (1983) 939-946
73. Honma Y., Ikema M., Toma C., Ehara M., and Iwanaga M. Molecular analysis of a filamentous phage (fs1) of Vibrio cholerae O139. Biochim. Biophys. Acta 1362 (1997) 109-115
74. Hoogstraten D., Qiao X., Sun Y., Hu A., Onodera S., and Mindich L. Characterization of φ{symbol}8, a bacteriophage containing three double-stranded RNA genomic segments and distantly related to φ{symbol}6. Virology 272 (2000) 218-224
75. Hsia R.C., Ting L.M., and Bavoil P.M. Microvirus of Chlamydia psittaci strain Guinea pig inclusion conjunctivitis: isolation and molecular characterization. Microbiology 146 (2000) 1651-1660
76. Iandolo J.J., Worrell V., Groicher K.H., Qian Y., Tian R., Kenton S., Dorman A., Ji H., Lin S., Loh P., Qi S., Zhu H., and Roe B.A. Comparative analysis of the genomes of the temperate bacteriophages φ{symbol}11, φ{symbol}12 and φ{symbol}13 of Staphylococcus aureus 8325. Gene 289 (2002) 109-118
77. Ikema M., and Honma A. A novel filamentous phage, fs-2, of Vibrio cholerae O139. Microbiology 144 (1998) 1901-1906
78. Inokuchi Y., Jacobson A.B., Hirose T., Inayama S., and Hirashima A. Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP. Nucleic Acids Res. 16 (1988) 6205-6221
79. Inokuchi Y., Takahashi R., Hirose T., Inayama S., Jacobson A.B., and Hirashima A. The complete nucleotide sequence of group II RNA coliphage GA. J. Biochem. 99 (1986) 1169-1180
80. Jaeger F., and Klotz G. Cited in J. Maniloff and K. Dybvig, Mycoplasma phages. In: Calendar R. (Ed). The Bacteriophages. second ed. (2006), Oxford University Press, New York, NY 636-653
81. Jarling M., Bartkowiak K., Pape H., and Meinhardt F. The genome of φ{symbol}Asp2, an Actinoplanes infecting phage. Virus Genes 29 (2004) 117-129
82. Juhala R.J., Ford M.E., Duda R.L., Youlton A., Hatfull G.F., and Hendrix R.W. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299 (2000) 27-51
83. Kaneko J., Kimura T., Narita S., Tomita T., and Kamio Y. Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage φ{symbol}PVL carrying Panton-Valentine leukocidin genes. Gene 215 (1998) 57-67
84. Kapfhammer D., Blass J., Evers S., and Reidl J. Vibrio cholerae phage K139: complete genome sequence and comparative genomics of related phages. J. Bacteriol. 184 (2002) 6592-6601
85. Kazmierczak K.M., and Rothman-Denes L.B. Bacteriophage N4. In: Calendar R. (Ed). The Bacteriophages. second ed. (2006), Oxford University Press, New York, NY 302-314
86. Kirs M., and Smith D.C. Multiplex quantitative real-time reverse transcriptase PCR for F+-specific RNA coliphages: a method for use in microbial source tracking. Appl. Environ. Microbiol. 73 (2007) 808-814
87. Klein R., Baranyi U., Rössler N., Greineder B., Scholz H., and Witte A. Natrialba magadii virus φ{symbol}Ch1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol. Microbiol. 45 (2002) 851-863
88. Klovins J., Tsareva N.A., de Smit M.H., Berzins V., and van Duin J. Rapid evolution of translational control mechanisms in RNA genomes. J. Mol. Biol. 265 (1997) 372-384
89. Kodaira K.-I., Nakano K., Okada S., and Taketo A. Nucleotide sequence of the genome of the bacteriophage α3: interrelationship of the genome structure and the gene products with those of the phages φ{symbol}X174, G4, and φ{symbol}K. Biochim. Biophys. Acta 1130 (1992) 277-288
90. Kodaira K.-I., Oki M., Kakikawa M., Kimoto H., and Taketo A. The virion proteins encoded by bacteriophage φ{symbol}K and its host range mutant φ{symbol}KhT: host range determination and DNA binding properties. J. Biochem. 119 (1996) 1062-1069
91. Kodaira K.-I., Oki M., Kakikawa M., Watanabe N., Hirakawa M., Yamada K., and Taketo A. Genome structure of the Lactobacillus temperate phage φ{symbol}g1e: the whole genome sequence and the putative promoter/repressor system. Gene 187 (1997) 45-53
92. Kotsonis S.E., Powell I.B., Hillier A.J., Limsowtin G.K.Y., and Davidson B.E. Analysis of asccφ{symbol}28, a Lactococcus lactis phage of a rare morphotype. Aust. J. Dairy Technol. 53 (1998) 132
93. Kovalyova I.V., and Kropinski A.M. The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida - evidence for close relationship to the T7 group. Virology 311 (2003) 305-315
94. Kropinski A.M. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J. Bacteriol. 182 (2000) 6066-6074
95. Kropinski A.M., Hayward M., Agnew M.D., and Jarrell K.F. The genome of BCJA1c: a bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii. Extremophiles 9 (2005) 99-109
96. Kuo T.T., Tan M.S., Su M.T., and Yang M.K. Complete nucleotide sequence of filamentous phage Cf1c from Xanthomonas campestris pv. citri. Nucleic Acids Res. 19 (1991) 2488
97. Kwan T., Liu J., DuBow M., Gros P., and Pelletier J. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 5174-5179
98. Kwan T., Liu J., DuBow M., Gros P., and Pelletier J. Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J. Bacteriol. 188 (2006) 1184-1187
99. Labrie S., and Moineau S. Complete genomic sequence of bacteriophage ul36: demonstration of phage heterogeneity within the P335 quasi-species of lactococcal phages. Virology 296 (2002) 308-320
100. Lang A.S., Taylor T.A., and Beatty J.T. Evolutionary implications of phylogenetic analyses of the gene transfer agent (GTA) of Rhodobacter capsulatus. J. Mol. Evol. 55 (2002) 534-543
101. Lau P.C.K., and Spencer J.H. Nucleotide sequence and genome organization of bacteriophage S13 DNA. Gene 40 (1985) 273-284
102. Lavigne R., Bourkaltseva M.V., Robben J., Sykilinda N.N., Kurochkina L.P., Grymonprez B., Jonckx B., Krylov V.N., Mesyanzhinov V., and Volckaert G. The genome of bacteriophage φ{symbol}KMV, a T7-like virus infecting Pseudomonas aeruginosa. Virology 312 (2003) 49-59
103. Lazarevic V. Ribonucleotide reductase genes of Bacillus prophages: a refuge to introns and intein coding sequences. Nucleic Acids Res. 29 (2001) 3212-3218
104. Lévesque C., Duplessis M., Labonté J., Labrie S., Fremaux C., Tremblay D., and Moineau S. Genomic organization and molecular analysis of virulent bacteriophage 2972 infecting an exopolysaccharide-producing Streptococcus thermophilus strain. Appl. Environ. Microbiol. 71 (2005) 4057-4068
105. Liu B.L., Everson J.S., Fane B., Giannikopoulou P., Vretou E., Lambden P.R., and Clarke I.N. Molecular characterization of a bacteriophage (Chp2) from Chlamydia psittaci. J. Virol. 74 (2000) 3464-3469
106. Liu M., Gingery M., Doulatov S.R., Liu Y., Hodes A., Baker S., Davis P., Simmonds M., Churcher C., Mungall K., Quail M.A., Preston A., Harvill E.T., Maskell D.J., Eiserling F.A., Parkhill J., and Miller J.F. Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes. J. Bacteriol. 186 (2004) 1503-1517
107. Lo T.-C., Shih T.-C., Lin C.-F., Chen H.-W., and Lin T.H. Complete genomic sequence of the temperate bacteriophage ΦAT3 isolated from Lactobacillus casei ATCC 393. Virology 339 (2005) 42-55
108. Lobocka M.B., Rose D.J., Plunkett III G., Rusin M., Samojedny A., Lehnherr H., Yarmolinsky M.B., and Blattner F.R. The genome of bacteriophage P1. J. Bacteriol. 186 (2004) 7032-7068
109. Loessner M.J., Inman R.B., Lauer P., and Calendar R. Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol. Microbiol. 35 (2000) 324-340
110. Lohr J.E., Chen F., and Hill R.T. Genomic analysis of bacteriophage ΦJL001: insights into its interaction with a sponge-associated alpha-proteobacterium. Appl. Environ. Microbiol. 71 (2005) 1598-1609
111. Lu Z., Altermann E., Breidt F., Predki P., Fleming H.P., and Klaenhammer T.R. Sequence analysis of the Lactobacillus plantarum bacteriophage φ{symbol}JL-1. Gene 348 (2005) 45-54
112. Lubbers M.W., Waterfield N.R., Beresford T.P.J., Le Page R.W.F., and Jarvis A.W. Sequencing and analysis of the prolate-headed lactococcal bacteriophage c2 genome and identification of the structural genes. Appl. Environ. Microbiol. 61 (1995) 4348-4356
113. Lucchini S., Desiere F., and Brüssow H. The genetic relationship between virulent and temperate Streptococcus thermophilus bacteriophages: whole genome comparison of cos-site phages Sfi19 and Sfi21. Virology 260 (1999) 232-243
114. Luiten R.G., Putterman D.G., Schoenmakers J.G., Konings R.N., and Day L.A. Nucleotide sequence of the genome of Pf3, an IncP-1 plasmid-specific filamentous bacteriophage of Pseudomonas aeruginosa. J. Virol. 56 (1985) 268-276
115. Lute S., Aranha A., Tremblay D., Liang D., Ackermann H.W., Chu B., Moineau S., and Brorson K. Characterization of coliphage PR772 and evaluation of its use for filter performance testing. Appl. Environ. Microbiol. 70 (2004) 4864-4871
116. Mahanivong C., Boyce J.D., Davidson B.E., and Hillier A.J. Sequence analysis and molecular characterization of the Lactococcus lactis temperate bacteriophage BK5-T. Appl. Environ. Microbiol. 67 (2001) 3564-3576
117. Mahony J., Deveau H., McGrath S., Ventura M., Canchaya C., Moineau S., Fitzgerald G.F., and van Sinderen D. Sequence and comparative genomic analysis of lactococcal bacteriophages jj50, 712 and P008: evolutionary insights into the 936 phage species. FEMS Microbiol. Lett. 261 (2006) 253-261
118. Maniloff J., Kampo G.J., and Dascher C.C. DNA sequence analysis of a unique temperate phage: mycoplasma virus L2. Gene 141 (1994) 1-8
119. Mann N.H., Clokie M.R.J., Millard A., Cook A., Wilson W.H., Wheatley J., Letarov A., and Krisch H.M. The genome of S-PM2, a photosynthetic T4-type bacteriophage that infects marine Synechococcus. J. Bacteriol. 187 (2005) 3188-3200
120. Männistö R.H., Kivelä H.M., Paulin H., Bamford D.H., and Bamford J.K. The complete genome sequence of PM2, the first lipid-containing bacterial virus to be isolated. Virology 262 (1999) 355-363
121. Martín A.C., López R., and García P. Analysis of the complete nucleotide sequence and functional organization of the genome of Streptococcus pneumoniae bacteriophage Cp-1. J. Virol. 70 (1996) 3678-3687
122. McGrath S., Fitzgerald G.F., and van Sinderen D. The impact of bacteriophage genomics. Curr. Opin. Biotechnol. 15 (2004) 94-99
123. Mediavilla J., Jain S., Kriakov J., Ford M.E., Duda R.L., Jacobs W.R., Hendrix R.W., and Hatfull G.F. Genome organization and characterization of mycobacteriophage Bxb1. Mol. Microbiol. 38 (2000) 955-970
124. Meijer W.J., Horcajadas J.A., and Salas M. φ{symbol}29 Family of phages. Microbiol. Mol. Biol. Rev. 65 (2001) 261-287
125. Mekler, P. (1981) Determination of nucleotide sequences of the bacteriophage Qβ genome: organization and evolution of an RNA virus. Ph.D. thesis, University of Zürich, Zürich, Switzerland.
126. Mesyanzhinov V.V., Robben J., Grymonprez B., Kostyuchenko V.A., Bourkaltseva M.V., Sykilinda N.N., Krylov V.N., and Volckaert G. The genome of bacteriophage φ{symbol}KZ of Pseudomonas aeruginosa. J. Mol. Biol. 317 (2002) 1-19
127. Mikkonen, M. (1996) Genes and genome of Lactobacillus phage LL-H. Ph.D. thesis, University of Oulu, Finland; Acta Univ. Ouluensis A 281, pp. 1-55.
128. Mikkonen M., Räisänen L., and Alatossava T. The early gene region completes the nucleotide sequence of Lactobacillus delbrueckii subsp. lactis phage LL-H. Gene 175 (1996) 49-57
129. Miller E.S., Heidelberg J.F., Eisen J.A., Nelson W.C., Durkin A.S., Ciecko A., Feldblyum T.V., White O., Paulson I.T., Nierman W.C., Lee J., Szczypinski B., and Fraser C.M. Complete genome sequence of the broad-host range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. J. Bacteriol. 185 (2003) 5220-5233
130. Miller E., Kutter E., Mosig G., Arisaka F., Kunisawa T., and Rüger W. The bacteriophage T4 genome. Microbiol. Mol. Biol. Rev. 67 (2003) 86-156
131. Mindich L., and Bamford D.H. Lipid-containing bacteriophages. In: Calendar R. (Ed). The Bacteriophages 2 (1988), Plenum Press, New York, NY 475-520
132. Mindich L., Qiao X., Qiao K., Onodera S., Romantchuk M., and Hoogstraten D. Isolation of additional bacteriophages with genomes of segmented double-stranded RNA. J. Bacteriol. 181 (1999) 4505-4508
133. Mmolawa P.T., Schmieger H., and Heuzenroeder M.W. Bacteriophage ST64B, a genetic mosaic of genes from diverse sources isolated from Salmonella enterica serovar Typhimurium DT 64. J. Bacteriol. 185 (2003) 6481-6485
134. Mmolawa P.T., Schmieger H., Tucker C.P., and Heuzenroeder M.W. Genomic structure of the Salmonella enterica serovar Typhimurium DT64 bacteriophage ST64T: evidence for modular genetic architecture. J. Bacteriol. 185 (2003) 3473-3475
135. Morgan G.J., Hatfull G.F., Casjens S., and Hendrix R.W. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J. Mol. Biol. 317 (2000) 337-359
136. Myrne M., and Kropinski A.M. The genome of the Pseudomonas aeruginosa generalized transducing bacteriophage F116. Gene 346 (2005) 187-194
137. Nakayama K., Kanaya S., Ohnishi M., Terawaki Y., and Hayashi T. The complete nucleotide sequence of φ{symbol}CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol. Microbiol. 31 (1999) 399-419
138. Narita S., Kaneko J., Chiba J., Piémont Y., Jarraud S., Etienne J., and Kamio Y. Phage conversion of Panton-Valentine leukocidin in Staphylococcus aureus: molecular analysis of a PVL-converting phage, φ{symbol}SLT. Gene 268 (2001) 195-206
139. Naryshkina T., Liu J., Florens L., Swanson S.K., Pavlov A.R., Pavlova N.V., Inman R., Minakhin L., Kozyavkin S.A., Washburn M., Mushegian A., and Severinov K. Thermus thermophilus bacteriophage φ{symbol}YS40 genome and proteomic characterization of virions. J. Mol. Biol. 364 (2006) 667-677
140. Nelson D. Phage taxonomy: we agree to disagree. J. Bacteriol. 186 (2004) 7029-7031
141. Nelson D., Schuch R., Zhu S., Tscherne D., and Fischetti V.A. Genomic sequence of C1, the first streptococcal phage. J. Bacteriol. 185 (2003) 3325-3332
142. Nolan J.M., Petrov V., Bertrand C., Krisch H.M., and Karam J.D. Genetic diversity among five T4-like bacteriophages. Virol. J (2006) 10.1186/1743-422X-3-30
143. Oakey H.J., Cullen B.R., and Owens L. The complete nucleotide sequence of the Vibrio harveyi bacteriophage VHML. J. Appl. Microbiol. 93 (2002) 1089-1098
144. Obregón V., García J.L., García E., López R., and García J.L. Genome organization and molecular analysis of the temperate phage MM1 of Streptococcus pneumoniae. J. Bacteriol. 185 (2003) 2362-2368
145. O'Flaherty S., Coffey A., Edwards R., Meaney W., Fitzgerald G.F., and Ross R.P. Genome of staphylococcal phage K: a new lineage of Myoviridae infecting gram-positive bacteria with a low G + C content. J. Bacteriol. 186 (2004) 2862-2871
146. Olsthoorn R.C.L., Garde G., Dayhuff T., Atkins J.F., and van Duin J. Nucleotide sequence of a single-stranded RNA phage from Pseudomonas aeruginosa: kinship to coliphages and conservation of regulatory RNA structures. Virology 206 (1995) 611-625
147. Paces V., Vlcek C., Smarda J., Zadrazil S., and Fucik V. Tolerated variations in a genome: the case of closely related Bacillus phages PZA, φ{symbol}29 and φ{symbol}15 - a review. Gene 54 (1987) 155-165
148. Pajunen M.I., Elizondo M.R., Skurnik M., Kieleczawa J., and Molineux I.J. Complete nucleotide sequence and likely recombinatorial origin of bacteriophage T3. J. Mol. Biol. 319 (2002) 1115-1132
149. Pajunen M.I., Kiljunen S.J., Söderholm S.M.-E., and Skurnik M. Complete genomic sequence of the lytic bacteriophage φ{symbol}YeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol. 183 (2001) 1928-1937
150. Palm P., Schleper C., Grampp B., Yeats S., McWilliam P., Reiter W.D., and Zillig W. Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185 (1991) 242-250
151. Paul J.H., Williamson S.J., Long A., Authement R.N., John D., Segall A.M., Rohwer F.R., Androlewicz M., and Patterson S. Complete genome sequence of φ{symbol}HSIC, a pseudotemperate marine phage of Listonella pelagica. J. Appl. Environ. Microbiol. 71 (2005) 3311-3320
152. Pecenkova T., Benes V., Paces J., Vlcek C., and Paces V. Bacteriophage B103: complete DNA sequence of its genome and relationship to other Bacillus phages. Gene 199 (1997) 157-163
153. Pedulla M.L., Ford M.E., Houtz J.M., Karthikeyan T., Wadsworth C., Lewis J.A., Jacobs-Sera D., Falbo J., Gross J., Pannunzio N.R., Brucker W., Kumar V., Kandasamy J., Keenan L., Bardarov V., Kriakov J., Lawrence J.G., Jacobs W.R., Hendrix R.W., and Hatfull G.F. Origin of highly mosaic mycobacteriophage genomes. Cell 113 (2003) 171-182
154. Pedulla M.L., Ford M., Karthikeyan T., Houtz J., Hendrix R.W., Hatfull G.F., Poteete A.R., Gilcrease E., Winn-Stapley D.A., and Casjens S. Corrected sequence of the bacteriophage P22 genome. J. Bacteriol. 185 (2003) 1475-1477
155. Peeters B.P.H., Peters R.M., Schoenmakers J.G.G., and Konings R.N.H. Nucleotide sequence and genetic organization of the genome of the N-specific filamentous bacteriophage IKe: comparison with the genome of the F-specific filamentous phages M13, fd and f1. J. Mol. Biol. 181 (1985) 27-39
156. Pelludat C., Mirold S., and Hardt W.D. The SopEΦ phage integrates into the ssrA gene of Salmonella enterica serovar Typhimurium A36 and is closely related to the Fels-2 prophage. J. Bacteriol. 185 (2003) 5182-5191
157. Peng X., Basta T., Häring M., Garrett R.A., and Prangishvili D. Genome of Acidianus bottle-shaped virus and insights into the replication and packaging mechanisms. Virology 364 (2007) 237-243
158. Peng X., Blum H., She Q., Mallok S., Brügger K., Garrett R.A., Zillig W., and Prangishvili D. Sequences and replication of genomes of the archaeal rudiviruses SIRV1 and SIRV2: relationships to the archaeal lipothrixvirus SIFV and some eukaryal viruses. Virology 291 (2001) 226-234
159. Petrov V.M., Nolan J.M., Bertrand C., Levy D., Desplats C., Krisch H.M., and Karam J.D. Plasticity of the gene functions for DNA replication in the T4-like phages. J. Mol. Biol. 361 (2006) 46-68
160. Pfister P., Wasserfallen A., Stettler R., and Leisinger T. Molecular analysis of Methanobacterium phage ψM2. Mol. Microbiol. 30 (1998) 233-244
161. Plunkett III G., Rose D.J., Durfee T.J., and Blattner F.R. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J. Bacteriol. 181 (1999) 1767-1778
162. Prangishvili D. Evolutionary insights from studies on viruses of hyperthermophilic archaea. Res. Microbiol. 154 (2003) 289-294
163. Prangishvili D., Vestergaard G., Häring M., Aramoyo R., Basta T., Rachel R., and Garrett T.A. Structural and genomic properties of the hyperthermophilic archaeal virus ATV with an extracellular stage of the reproductive cycle. J. Mol. Biol. 359 (2006) 1203-1216
164. Qiao X., Qiao J., Onodera S., and Mindich L. Characterization of Φ13, a bacteriophage related to Φ6, and containing three dsRNA genomic segments. Virology 275 (2000) 218-224
165. Raslik I., Bukovska G., Godany A., and Timko J. Analysis of the nucleotide sequence of the genome of Brevibacterium flavum CCM 251 bacteriophage BFK20. Chemicke Zvesti 52 (1998) 266-267
166. Ravantti J., Gaidelyte A., Bamford D.H., and Bamford J.K. Comparative analysis of bacterial viruses Bam35, infecting a gram-positive host, and PRD1, infecting gram-negative hosts, demonstrate a viral lineage. Virology 313 (2003) 401-414
167. Ravin V., Ravin N., Casjens S., Ford M.E., Hatfull G.F., and Hendrix R.W. Genomic sequence and analysis of the atypical temperate bacteriophage N15. J. Mol. Biol. 299 (2000) 53-73
168. Read T.D., Brunham R.C., Shen C., Gill S.R., Heidelberg J.F., White O., Hickey E.K., Peterson J., Utterback T., Berry K., Bass S., Linher K., Weidman J., Khouri H., Craven B., Bowman C., Dodson R., Gwinn M., Nelson W., DeBoy R., Kolonay J., McClarty G., Salzberg S.L., Eisen J., and Fraser C.M. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28 (2000) 1397-1406
169. Recktenwald J., and Schmidt H. The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage φ{symbol}P27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Infect. Immun. 70 (2002) 1896-1908
170. Renaudin J., Aullo P., Vignault J.C., and Bové J.M. Complete nucleotide sequence of Spiroplasma citri virus SpV1-R8A2B. Nucleic Acids Res. 18 (1990) 1293
171. Renaudin J., and Bové J.M. SpV1 and SpV4, spiroplasma viruses with circular, single-stranded DNA genomes, and their contribution to the molecular biology of spiroplasmas. Adv. Virus Res. 44 (1994) 429-463
172. Renaudin J., Pascarel M.-C., and Bové J.M. Cloning and sequencing of the genome of Spiroplasma virus 4. Isr. J. Med. Sci. 23 (1987) 427-428
173. Renaudin J., Pascarel M.-C., and Bové J.M. Spiroplasma virus 4: nucleotide sequence of the viral DNA, regulatory signals, and proposed genome organization. J. Bacteriol. 169 (1987) 4950-4961
174. Resch G., Kulik E.M., Dietrich F.S., and Meyer E. Complete genomic nucleotide sequence of the temperate bacteriophage AaΦ23 of Actinobacillus actinomycetemcomitans. J. Bacteriol. 186 (2004) 5523-5538
175. Rice G., Tang L., Stedman K., Roberto F., Spuhler J., Gillitzer E., Johnson J.E., Douglas T., and Young M. The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 7716-7720
176. Roberts M.D., Martin N.L., and Kropinski A.M. The genome and proteome of coliphage T1. Virology 318 (2004) 245-266
177. Rohwer F., and Edwards R. The phage proteomic tree: a genome-based taxonomy for phage. J. Bacteriol. 184 (2002) 4529-4535
178. Rohwer F., Segall A.M., Steward G., Seguritan V., Wolven F., Breitbart M., and Azam F. The complete genomic sequence of the marine phage roseophage SIO1 shares homology with nonmarine phages. Limnol. Oceanogr. 45 (2000) 408-418
179. Rokyta D.R., Burch C.L., Caudle S.B., and Wichman H.A. Horizontal gene transfer and the evolution of microvirid coliphage genomes. J. Bacteriol. 188 (2006) 1134-1142
180. Romero P., López R., and García E. Genomic organization and molecular analysis of the inducible prophage EJ-1, a mosaic myovirus from an inducible pneumococcus. Virology 322 (2004) 239-252
181. Ruokoranta T.M., Grahn A.M., Ravantti J.J., Poranen M.M., and Bamford D.H. Complete genome sequence of the broad host range single-stranded RNA phage PRR1 places it in the Levivirus genus with characteristics shared with alloleviviruses. J. Virol. 80 (2006) 9326-9330
182. Sakaguchi Y., Hayashi T., Kurokawa K., Nakayama K., Oshima K., Fujinaga Y., Ohnishi M., Ohtsubo E., Hattori M., and Oguma K. The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. Proc. Natl. Acad. Sci. U.S.A. 102 (2005) 17472-17477
183. Sanger F., Air G.M., Barrell B.G., Brown N.L., Coulson A.R., Fiddes J.C., Hutchison C.A., Slocombe P.M., and Smith M. Nucleotide sequence of bacteriophage φ{symbol}X174 DNA. Nature 265 (1977) 687-695
184. Sanger F., Coulson A.R., Hong G.F., Hill D.F., and Petersen G.B. Nucleotide sequence of bacteriophage λ DNA. J. Mol. Biol. 162 (1982) 729-773
185. Saren A.-M., Ravantti J.J., Benson S.D., Burnett R.M., Paulin L., Bamford D.H., and Bamford J.K.H. A snapshot of viral evolution from genome analysis of the Tectiviridae family. J. Mol. Biol. 350 (2005) 427-440
186. Scholl D., Kieleczawa J., Kemp P., Rush J., Richardson C.C., Merril C., Adhya S., and Molineux I.J. Genomic analysis of bacteriophages SP6 and K1-5, an estranged subgroup of the T7 supergroup. J. Mol. Biol. 335 (2004) 1151-1171
187. Scholl D., and Merril C. The genome of bacteriophage K1F, a T7-like phage that has acquired the ability to replicate on K1 strains of Escherichia coli. J. Bacteriol. 187 (2005) 8499-8503
188. Schouler C., Ehrlich S.D., and Chopin M.C. Sequence and organization of the lactococcal prolate-headed bIL67 phage genome. Microbiology 140 (1994) 3061-3069
189. Schuch R., and Fischetti V.A. Detailed genomic analysis of the Wß and γ phages infecting Bacillus anthracis: implications for evolution of environmental fitness and antibiotic resistance. J. Bacteriol. 188 (2006) 3037-3051
190. Seegers J.F.M.L., McGrath S., O'Connell-Motherway M., Arendt E.K., van de Guchte M., Creaven M., Fitzgerald G.F., and van Sinderen D. Molecular and transcriptional analysis of the temperate lactococcal bacteriophage Tuc2009. Virology 329 (2004) 40-52
191. Seguritan V., Feng L.-W., Rohwer F., Swift M., and Segall A.M. Genome sequences of two closely related Vibrio parahaemolyticus phages, VP16T and VP16C. J. Bacteriol. 185 (2003) 6434-6447
192. Sha Y., Melcher U., Davis R.E., and Fletcher J. Common elements of spiroplasma plectroviruses revealed by nucleotide sequence of SVTS2. Virus Genes 20 (2000) 47-56
193. Siboo I.R., Bensing B.A., and Sullam P.M. Genomic organization and molecular characterization of SM1, a temperate bacteriophage of Streptococcus mitis. J. Bacteriol. 185 (2003) 6968-6975
194. Smith M.C.M., Burns R.N., Wilson S.E., and Gregor M.A. The complete sequence of the Streptomyces temperate phage φ{symbol}C31: evolutionary relationships to other viruses. Nucleic Acids Res. 27 (1999) 2145-2155
195. Stanley E., Fitzgerald G.F., Le Marrec C., Fayard B., and van Sinderen D. Sequence analysis and characterization of φ{symbol}O1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology (UK) 143 (1997) 3417-3429
196. Stanley E., Walsh L., van der Zwet A., Fitzgerald G., and van Sinderen D. Identification of four loci isolated from two Streptococcus thermophilus phage genomes responsible for mediating bacteriophage resistance. FEMS Microbiol. Lett. 182 (2000) 271-277
197. Stassen A.P.M., Schoenmakers E.F.P.M., Yu M., Schoenmarkers J.G.G., and Konings R.N.H. Nucleotide sequence of the genome of the filamentous bacteriophage I2-2: module evolution of the filamentous phage genome. J. Mol. Evol. 34 (1992) 141-152
198. Stedman K.M., She Q., Phan H., Arnold H.P., Holz I., Garrett R.A., and Zillig W. Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res. Microbiol. 154 (2003) 295-302
199. Storey C.C., Lusher M., and Richmond S.J. Analysis of the complete nucleotide sequence of Chp1, a phage which infects avian Chlamydia psittaci. J. Gen. Virol. 70 (1989) 3381-3390
200. Strömsten N.J., Benson S.D., Burnett R.M., Bamford D.H., and Bamford J.K.H. The Bacillus thuringiensis linear double-stranded DNA phage Bam35, which is highly similar to the Bacillus cereus linear plasmid pBClin15, has a prophage state. J. Bacteriol. 185 (2003) 6985-6989
201. Stummeyer K., Schwarzer D., Claus H., Vogel U., Gerardy-Schahn R., and Mühlenhoff M. Evolution of bacteriophages infecting encapsulated bacteria: lessons from Escherichia coli K1-specific phages. Mol. Microbiol. 60 (2006) 1123-1135
202. Sullivan M.B., Coleman M., Weigele P., Rohwer F., and Chisholm S.W. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 3 (2005) 144
203. Summer E.J., Gonzalez C.F., Bomer M., Carlisle T., Embry A., Kucherka A.M., Lee J., Mebane L., Morrison W.C., Mark L., King M.D., LiPuma J.J., Vidaver A.K., and Young R. Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex. J. Bacteriol. 188 (2006) 255-268
204. Summer E.J., Gonzalez C.F., Carlisle T., Mebane L.M., Cass A.M., Savva C.G., LiPuma J.J., and Young R. Burkholderia cenocepacia phage BcepMu and a family of Mu-like phages encoding potential pathogenesis factors. J. Mol. Biol. 340 (2004) 49-65
205. Tan Y.L., Zhang K.B., Rao X.C., Jin X.L., Huang J.J., Zhu J.M., Chen Z.J., Hu X.M., Shen X.D., Wang L., and Hu F.Q. Whole genome sequencing of a novel temperate bacteriophage of P. aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome. Cell. Microbiol. 9 (2007) 479-491
206. Tang S.-L., Nuttall S., and Dyall-Smith M. Haloviruses HF1 and HF2 evidence for a recent and large recombination event. J. Bacteriol. 186 (2004) 2810-2817
207. Tang S.-L., Nuttall S., Ngui K., Fisher C., Lopez P., and Dyall-Smith M. HF2: a double-stranded DNA tailed haloarchaeal virus with a mosaic genome. Mol. Microbiol. 44 (2002) 283-296
208. Tremblay D.M., and Moineau S. Complete genomic sequence of the lytic bacteriophage DT1 of Streptococcus thermophilus. Virology 255 (1999) 63-76
209. Trotter M., McAuliffe O., Callanan M., Edwards R., Fitzgerald G.F., Coffey A., and Ross R.P. Genome analysis of the obligately lytic bacteriophage 4268 of Lactococcus lactic provides insight into its adaptable nature. Gene 366 (2006) 189-199
210. Tu A.-H.T., Voelker L.L., Shen X., and Dybvig K. Complete nucleotide sequence of the mycoplasma virus P1 genome. Plasmid 45 (2001) 122-126
211. Tuohimaa A., Riipinen K.A., Brandt K., and Alatossava T. The genome of the virulent phage Lc-Nu of probiotic Lactobacillus rhamnosus, and comparative genomics with Lactobacillus casei phages. Arch. Virol. 151 (2006) 947-965
212. Vander Byl C., and Kropinski A.M. Sequence of the genome of Salmonella bacteriophage P22. J. Bacteriol. 182 (2000) 6472-6481
213. van der Wilk F., Dullemans A.M., Verbeek M., and van den Heuvel J.F. Isolation and characterization of APSE-1, a bacteriophage infecting the secondary endosymbiont of Acyrthosiphon pisum. Virology 262 (1999) 104-113
214. van Dessel W., van Mellaert L., Liesegang H., Raasch C., de Keersmaeker S., Geukens N., Lammertyn E., Streit W., and Anné J. Complete genomic nucleotide sequence and analysis of the temperate bacteriophage VWB. Virology 331 (2005) 325-337
215. van Meerten D., and van Duin J. Levivirus. Leviviridae. In: Tidona C.A., Darai G., and Büchen-Osmond C. (Eds). The Springer Index of Viruses (2001), Springer, Berlin 495-498
216. van Sinderen D., Karsens H., Kok J., Terpstra P., Ruiter M.H., Venema G., and Nauta A. Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Mol. Microbiol. 19 (1996) 1343-1355
217. van Wezenbeek P.M.G.F., Hulsebos T.J.M., and Schoenmakers J.G.G. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome; comparison with phage fd. Gene 11 (1980) 129-148
218. Verheust C., Fornelos N., and Mahillon J. GIL16, a new Gram-positive tectiviral phage related to the Bacillus thuringiensis GIL01 and the Bacillus cereus pBClin15 elements. J. Bacteriol. 187 (2004) 1966-1973
219. Verheust C., Jensen G., and Mahillon J. pGIL01, a linear tectiviral plasmid prophage originating from Bacillus thuringiensis serovar israelensis. Microbiology 149 (2003) 2083-2092
220. Vestergaard G., Häring M., Peng X., Rachel R., Garrett R.A., and Prangishvili D. A novel rudivirus, ARV1, of the hyperthermophilic archaeal genus Acidianus. Virology 336 (2005) 83-92
221. Vybiral D., Takac M., Loessner M.J., Witte A., von Ahsen U., and Bläsi U. Complete nucleotide sequence and molecular characterization of two lytic Staphylococcus aureus phages: 44AHJD and P68. FEMS Microbiol. Lett. 219 (2003) 275-283
222. Waldor M.K., and Mekalanos J.J. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272 (1996) 1910-1914
223. Wang J., Jiang Y., Vincent M., Sun Y., Yu H., Wang J., Bao Q., Kong H., and Hu S. Complete genome sequence of bacteriophage T5. Virology 332 (2005) 45-55
224. Wang P.W., Chu L., and Guttman D.S. Complete sequence and evolutionary genomic analysis of the Pseudomonas aeruginosa transposable bacteriophage D3112. J. Bacteriol. 186 (2004) 400-410
225. Whichard, J.M. (2000) Bacteriophage Felix O1: genetic characterization and biomedical application. Ph.D. thesis, Virginia Polytechnic Institute and State University, Blacksburg, VA.
226. Wiedenheft B., Stedman K.M., Roberto F., Willits D., Gleske A., Zoeller L., Snyder S., Douglas T., and Young M. Comparative genomic analysis of hyperthermophilic archaeal Fuselloviridae viruses. J. Virol. 78 (2004) 1954-1961
227. Wietzorrek A., Schwarz H., Herrmann C., and Braun V. The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1. J. Bacteriol. 188 (2006) 1419-1436
228. Williams B.J., Golomb M., Phillips T., Brownlee J., Olson M.V., and Smith A.L. Bacteriophage HP2 of Haemophilus influenzae. J. Bacteriol. 184 (2002) 6893-6905
229. Woods D.E., Jeddeloh J.A., Fritz D.L., and DeShazer D. Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei. J. Bacteriol. 184 (2002) 4003-4017
230. Xiang X., Chen L., Huang X., Luo Y., She Q., and Huang L. Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J. Virol. 79 (2005) 8677-8686
231. Yamaguchi T., Hayashi T., Takami H., Nakasone K., Ohnishi M., Nakayama K., Yamada S., Komatsuzawa H., and Sugai M. Phage conversion of exfoliative toxin A production in Staphylococcus aureus. Mol. Microbiol. 38 (2000) 694-705
232. Yuzenkova J., Nechaev S., Berlin J., Rogulja D., Kuznedelov K., Inman R., Mushegian A., and Severinov K. Genome of Xanthomonas oryzae bacteriophage Xp10: an odd T-odd phage. J. Mol. Biol. 330 (2003) 735-748
233. Zimmer M., Sattelberger E., Inman R.B., Calendar R., and Loessner M.J. Genome and proteome of Listeria monocytogenes phage PSA: an unusual case for programmed +1 translational frame-shifting in structural protein synthesis. Mol. Microbiol. 50 (2003) 303-317
234. Zimmer M., Scherer S., and Loessner M.J. Genomic analysis of Clostridium perfringens bacteriophage φ{symbol}3626 which integrates into guaA and possibly affects sporulation. J. Bacteriol. 184 (2002) 4359-4368