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Genetics and Genomics of Bacteriophages

The Evolution of Bacteriophage Genomes and Genomic Research

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Bacteriophages

Abstract

In recent years, advancements in sequencing technology and genome analysis software have broadened the horizons for bacteriophage research. As the repository of data generated continues to grow, the fundamental principles of bacteriophages in terms of their population numbers, diversity, and composition have become increasingly apparent. Comparative genomic analyses have facilitated the definition of key concepts such as “mosaicism,” providing researchers with an insight into the highly complex nature of bacteriophage evolution, while the identification of “viral hallmark genes” has established an underpinning connection between bacteriophages throughout the virosphere. Furthermore, large-scale metagenomic research has confirmed bacteriophages as potential candidates for exploitation in a number of biological applications, including rapid detection of pathogens, as well as in the development of antimicrobials and repair enzymes. In order to exploit bacteriophages to their fullest capabilities, developments and improvements to the current collection of analysis software must be made in order to handle the expansive wealth of data that continues to be generated.

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References

  • Abedon ST (2000) The murky origin of snow white and her T-even dwarfs. Genetics 155(2):481–486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ackermann HW (2007) 5500 phages examined in the electron microscope. Arch Virol 152(2):227–243

    Article  CAS  PubMed  Google Scholar 

  • Ackermann HW (2011) Bacteriophage taxonomy. Microbiol Aust 32(2):90–94

    Article  Google Scholar 

  • Ainsworth S, Zomer A, Mahony J, van Sinderen D (2013) Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. Appl Environ Microbiol 79(16):4786–4798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Akhter S, Aziz RK, Edwards RA (2012) PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity-and composition-based strategies. Nucleic Acids Res 40(16):e126–e126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Angly FE, Felts B, Breitbart M, Salamon P, Edwards RA, Carlson C, Chan AM, Haynes M, Kelley S, Liu H (2006) The marine viromes of four oceanic regions. PLoS Biol 4(11):e368

    Article  PubMed  PubMed Central  Google Scholar 

  • Bhattacharya D, Cheng J (2013) 3Drefine: consistent protein structure refinement by optimizing hydrogen bonding network and atomic-level energy minimization. Proteins Struct Funct Bioinf 81(1):119–131

    Article  CAS  Google Scholar 

  • Bondy-Denomy J, Pawluk A, Maxwell KL, Davidson AR (2013) Bacteriophage genes that inactivate the CRISPR/Cas bacterial immune system. Nature 493(7432):429–432

    Article  CAS  PubMed  Google Scholar 

  • Botstein D (1980) A theory of modular evolution for bacteriophages. Ann NY Acad Sci 354(1):484–491

    Article  CAS  PubMed  Google Scholar 

  • Breitbart M (2012) Marine viruses: truth or dare. Mar Sci 4:425–448

    Article  Google Scholar 

  • Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F (2002) Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci 99(22):14250–14255

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Browning C, Shneider MM, Bowman VD, Schwarzer D, Leiman PG (2012) Phage pierces the host cell membrane with the iron-loaded spike. Structure 20(2):326–339

    Article  CAS  PubMed  Google Scholar 

  • Busby B, Kristensen DM, Koonin EV (2013) Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens. Environ Microbiol 15(2):307–312

    Article  CAS  PubMed  Google Scholar 

  • Casey A, Fox EM, Schmitz-Esser S, Coffey A, McAuliffe O, Jordan K (2014) Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility. Front Microbiol 5(68):1–10

    Google Scholar 

  • Casjens SR (2005) Comparative genomics and evolution of the tailed-bacteriophages. Curr Opin Microbiol 8(4):451–458

    Article  CAS  PubMed  Google Scholar 

  • Cavanagh D, Guinane CM, Neve H, Coffey A, Ross RP, Fitzgerald GF, McAuliffe O (2013) Phages of non-dairy lactococci: isolation and characterization of ΦL47, a phage infecting the grass isolate Lactococcus lactis ssp. cremoris DPC6860. Front Microbiol 4(417):1–15

    Google Scholar 

  • Comeau AM, Bertrand C, Letarov A, Tétart F, Krisch H (2007) Modular architecture of the T4 phage superfamily: a conserved core genome and a plastic periphery. Virology 362(2):384–396

    Article  CAS  PubMed  Google Scholar 

  • Comeau AM, Tremblay D, Moineau S, Rattei T, Kushkina AI, Tovkach FI, Krisch HM, Ackermann H-W (2012) Phage morphology recapitulates phylogeny: the comparative genomics of a new group of myoviruses. PLoS One 7(7):e40102

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • d’Herelle F (1917) Sur un microbe invisible antagoniste des bacilles dysentériques. CR Acad Sci Paris 165:373–375

    Google Scholar 

  • da Silva JL, Piuri M, Broussard G, Marinelli LJ, Bastos GM, Hirata RDC, Hatfull GF, Hirata MH (2013) Application of BRED technology to construct recombinant D29 reporter phage expressing EGFP. FEMS Microbiol Lett 344(2):166–172

    Article  PubMed  Google Scholar 

  • De Paepe M, Hutinet G, Son O, Amarir-Bouhram J, Schbath S, Petit M-A (2014) Temperate phages acquire DNA from defective prophages by relaxed homologous recombination: the role of Rad52-like recombinases. PLoS Genet 10(3):e1004181

    Article  PubMed  PubMed Central  Google Scholar 

  • Dunn JJ, Studier FW, Gottesman M (1983) Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J Mol Biol 166(4):477–535

    Article  CAS  PubMed  Google Scholar 

  • Fallico V, Ross RP, Fitzgerald GF, McAuliffe O (2011) Genetic response to bacteriophage infection in Lactococcus lactis reveals a four-strand approach involving induction of membrane stress proteins, D-alanylation of the cell wall, maintenance of proton motive force, and energy conservation. J Virol 85(22):12032–12042

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fancello L, Desnues C, Raoult D, Rolain JM (2011) Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota. J Antimicrob Chemother 66(11):2448–2454

    Article  CAS  PubMed  Google Scholar 

  • Fokine A, Rossmann MG (2014) Molecular architecture of tailed double-stranded DNA phages. Bacteriophage 4(e28281):1–22

    Google Scholar 

  • Fouts DE (2006) Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res 34(20):5839–5851

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garneau JE, Dupuis M-È, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadán AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468(7320):67–71

    Article  CAS  PubMed  Google Scholar 

  • Gibbs AJ (2013) Viral taxonomy needs a spring clean; its exploration era is over. Virol J 10(1):254

    Article  PubMed  PubMed Central  Google Scholar 

  • Godson GN, Barrell BG, Staden R, Fiddes JC (1978) Nucleotide sequence of bacteriophage G4 DNA. Nature 276(5685):236–247

    Article  CAS  PubMed  Google Scholar 

  • Hatfull GF (2008) Bacteriophage genomics. Curr Opin Microbiol 11(5):447–453

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hatfull GF, Hendrix RW (2011) Bacteriophages and their genomes. Curr Opin Virol 1(4):298–303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hendrix RW (2002) Bacteriophages: evolution of the majority. Theor Popul Biol 61(4):471–480

    Article  PubMed  Google Scholar 

  • Hendrix RW (2009) Jumbo bacteriophages. Curr Top Microbiol Immunol 328:229–240.

    Google Scholar 

  • Hendrix RW, Smith MCM, Burns RN, Ford ME, Hatfull GF (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc Natl Acad Sci 96(5):2192–2197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hildebrand A, Remmert M, Biegert A, Söding J (2009) Fast and accurate automatic structure prediction with HHpred. Proteins Struct Funct Bioinf 77(S9):128–132

    Article  CAS  Google Scholar 

  • Holmes EC (2011) What does virus evolution tell us about virus origins? J Virol 85(11):5247–5251

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holmfeldt K, Solonenko N, Shah M, Corrier K, Riemann L, VerBerkmoes NC, Sullivan MB (2013) Twelve previously unknown phage genera are ubiquitous in global oceans. Proc Natl Acad Sci 110(31):12798–12803

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jacobs-Sera D, Marinelli LJ, Bowman C, Broussard GW, Guerrero Bustamante C, Boyle MM, Petrova ZO, Dedrick RM, Pope WH, Modlin RL (2012) On the nature of mycobacteriophage diversity and host preference. Virology 434(2):187–201

    Article  CAS  PubMed  Google Scholar 

  • Jakhetia R, Talukder KA, Verma NK (2013) Isolation, characterization and comparative genomics of bacteriophage SfIV: a novel serotype converting phage from Shigella flexneri. BMC Genomics 14(1):677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jansen R, Embden J, Gaastra W, Schouls L (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43(6):1565–1575

    Article  CAS  PubMed  Google Scholar 

  • Kim K-H, Bae J-W (2011) Amplification methods bias metagenomic libraries of uncultured single-stranded and double-stranded DNA viruses. Appl Environ Microbiol 77(21):7663–7668

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim M-S, Whon TW, Bae J-W (2013) Comparative viral metagenomics of environmental samples from Korea. Genome Inform 11(3):121–128

    Article  Google Scholar 

  • King AM, Adams MJ, Lefkowitz EJ, Carstens EB (2011) Virus taxonomy: IXth report of the international committee on taxonomy of viruses. Elsevier Academic Press, London

    Google Scholar 

  • Klumpp J, Fouts DE, Sozhamannan S (2013) Bacteriophage functional genomics and its role in bacterial pathogen detection. Brief Funct Genomics 12:354–365

    Article  PubMed  Google Scholar 

  • Koonin EV (2005) Virology: Gulliver among the Lilliputians. Curr Biol 15(5):R167–R169

    Article  CAS  PubMed  Google Scholar 

  • Koonin EV, Dolja VV (2013) A virocentric perspective on the evolution of life. Curr Opin Virol 3(5):546–557

    Article  PubMed  PubMed Central  Google Scholar 

  • Koonin EV, Senkevich TG, Dolja VV (2006) The ancient virus world and evolution of cells. Biol Direct 1(1):29

    Article  PubMed  PubMed Central  Google Scholar 

  • Kostyuchenko VA, Leiman PG, Chipman PR, Kanamaru S, van Raaij MJ, Arisaka F, Mesyanzhinov VV, Rossmann MG (2003) Three-dimensional structure of bacteriophage T4 baseplate. Nat Struct Mol Biol 10(9):688–693

    Article  CAS  Google Scholar 

  • Kristensen DM, Waller AS, Yamada T, Bork P, Mushegian AR, Koonin EV (2013) Orthologous gene clusters and taxon signature genes for viruses of prokaryotes. J Bacteriol 195(5):941–950

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krupovic M, Prangishvili D, Hendrix RW, Bamford DH (2011) Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere. Microbiol Mol Biol Rev 75(4):610–635

    Article  PubMed  PubMed Central  Google Scholar 

  • Kuznetsov YG, Chang S-C, Credaroli A, McPherson A (2013) Unique tail appendages of marine bacteriophages. Adv Microbiol 3:55

    Article  CAS  Google Scholar 

  • La Scola B, Audic S, Robert C, Jungang L, de Lamballerie X, Drancourt M, Birtles R, Claverie J-M, Raoult D (2003) A giant virus in amoebae. Science 299(5615):2033–2033

    Article  PubMed  Google Scholar 

  • Labonté JM, Suttle CA (2013) Metagenomic and whole-genome analysis reveals new lineages of gokushoviruses and biogeographic separation in the sea. Front Microbiol 4(404):1–11

    Google Scholar 

  • Lang AS, Zhaxybayeva O, Beatty JT (2012) Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 10(7):472–482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lavigne R, Lecoutere E, Wagemans J, Cenens W, Aertsen A, Schoofs L, Landuyt B, Paeshuyse J, Scheer M, Schobert M (2013) A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19. MBio 4(2):e00061-00013

    Article  Google Scholar 

  • Le S, He X, Tan Y, Huang G, Zhang L, Lux R, Shi W, Hu F (2013) Mapping the tail fiber as the receptor binding protein responsible for differential host specificity of Pseudomonas aeruginosa bacteriophages PaP1 and JG004. PLoS One 8(7):e68562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Leiman P, Kanamaru S, Mesyanzhinov V, Arisaka F, Rossmann M (2003) Structure and morphogenesis of bacteriophage T4. Cell Mol Life Sci 60(11):2356–2370

    Article  CAS  PubMed  Google Scholar 

  • Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Res 41(D1):D499–D507

    Article  CAS  PubMed  Google Scholar 

  • Li J, Halgamuge SK, Tang S-L (2008) Genome classification by gene distribution: an overlapping subspace clustering approach. BMC Evol Biol 8(1):116

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu B, Shadrin A, Sheppard C, Mekler V, Xu Y, Severinov K, Matthews S, Wigneshweraraj S (2014a) The sabotage of the bacterial transcription machinery by a small bacteriophage protein. Bacteriophage 4(e28520):1–4

    Google Scholar 

  • Liu X, Basu U, Miller P, McMullen LM (2014b) Stress and adaptation of Listeria monocytogenes 08-5923 exposed to a sublethal dose of carnocyclin A. Appl Environ Microbiol 80:3835–3841. 00350-00314

    Article  PubMed  PubMed Central  Google Scholar 

  • Marinelli LJ, Hatfull GF, Piuri M (2012) Recombineering: a powerful tool for modification of bacteriophage genomes. Bacteriophage 2(1):5–14

    Article  PubMed  PubMed Central  Google Scholar 

  • Martinsohn JT, Radman M, Petit M-A (2008) The λ red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. PLoS Genet 4(5):e1000065

    Article  PubMed  PubMed Central  Google Scholar 

  • Marvin DA, Symmons MF, Straus SK (2014) Structure and assembly of filamentous bacteriophages. Prog Biophys Mol Biol 114(2):80–122

    Article  CAS  PubMed  Google Scholar 

  • Matos RC, Lapaque N, Rigottier-Gois L, Debarbieux L, Meylheuc T, Gonzalez-Zorn B, Repoila F, Lopes M d F, Serror P (2013) Enterococcus faecalis prophage dynamics and contributions to pathogenic traits. PLoS Genet 9(6):e1003539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maurice C, Bouvier C, Wit R, Bouvier T (2013) Linking the lytic and lysogenic bacteriophage cycles to environmental conditions, host physiology and their variability in coastal lagoons. Environ Microbiol 15(9):2463–2475

    Article  CAS  PubMed  Google Scholar 

  • Maxwell KL, Davidson AR (2013) A shifty chaperone for phage tail assembly. J Mol Biol 426(5):1001–1003

    Article  PubMed  Google Scholar 

  • McNair K, Bailey BA, Edwards RA (2012) PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28(5):614–618

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W (2003) Bacteriophage T4 genome. Microbiol Mol Biol Rev 67(1):86–156

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mizuno CM, Rodriguez-Valera F, Kimes NE, Ghai R (2013) Expanding the marine virosphere using metagenomics. PLoS Genet 9(12):e1003987

    Article  PubMed  PubMed Central  Google Scholar 

  • Modi SR, Lee HH, Spina CS, Collins JJ (2013) Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499(7457):219–222

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mokili JL, Rohwer F, Dutilh BE (2012) Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2(1):63–77

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muniesa M, Allué-Guardia A, Martínez-Castillo A (2013) Bacteriophage-driven emergence of novel pathogens. Futur Virol 8(4):323–325

    Article  CAS  Google Scholar 

  • Orlova EV, Gowen B, Dröge A, Stiege A, Weise F, Lurz R, van Heel M, Tavares P (2003) Structure of a viral DNA gatekeeper at 10 Å resolution by cryo-electron microscopy. EMBO J 22(6):1255–1262

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pedulla ML, Ford ME, Houtz JM, Karthikeyan T, Wadsworth C, Lewis JA, Jacobs-Sera D, Falbo J, Gross J, Pannunzio NR (2003) Origins of highly mosaic mycobacteriophage genomes. Cell 113(2):171–182

    Article  CAS  PubMed  Google Scholar 

  • Petrov VM, Ratnayaka S, Nolan JM, Miller ES, Karam JD (2010) Genomes of the T 4-related bacteriophages as windows on microbial genome evolution. Virol J 7:292

    Article  PubMed  PubMed Central  Google Scholar 

  • Piuri M, Rondón L, Urdániz E, Hatfull GF (2013) Generation of affinity-tagged fluoromycobacteriophages by mixed assembly of phage capsids. Appl Environ Microbiol 79(18):5608–5615

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Proux C, van Sinderen D, Suarez J, Garcia P, Ladero V, Fitzgerald GF, Desiere F, Brüssow H (2002) The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J Bacteriol 184(21):6026–6036

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quirós P, Colomer-Lluch M, Martínez-Castillo A, Miró E, Argente M, Jofre J, Navarro F, Muniesa M (2014) Antibiotic resistance genes in the bacteriophage DNA fraction of human fecal samples. Antimicrob Agents Chemother 58(1):606–609

    Article  PubMed  PubMed Central  Google Scholar 

  • Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie J-M (2004) The 1.2-megabase genome sequence of mimivirus. Science 306(5700):1344–1350

    Article  CAS  PubMed  Google Scholar 

  • Ray J, Dondrup M, Modha S, Steen IH, Sandaa R-A, Clokie M (2012) Finding a needle in the virus metagenome haystack-micro-metagenome analysis captures a snapshot of the diversity of a bacteriophage armoire. PLoS One 7(4):e34238

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rohwer F, Edwards R (2002) The phage proteomic tree: a genome-based taxonomy for phage. J Bacteriol 184(16):4529–4535

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sanger F, Air G, Barrell B, Brown N, Coulson A, Fiddes C, Hutchison C, Slocombe P, Smith M (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265(5596):687–695

    Article  CAS  PubMed  Google Scholar 

  • Sanger F, Coulson AR, Hong G, Hill D, Petersen G (1982) Nucleotide sequence of bacteriophage λ DNA. J Mol Biol 162(4):729–773

    Article  CAS  PubMed  Google Scholar 

  • Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D (2010) Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol 18(1):20–29

    Article  CAS  PubMed  Google Scholar 

  • Schofield DA, Sharp NJ, Vandamm J, Molineux IJ, Spreng KA, Rajanna C, Westwater C, Stewart GC (2013) Bacillus anthracis diagnostic detection and rapid antibiotic susceptibility determination using ‘bioluminescent’ reporter phage. J Microbiol Methods 95(2):156–161

    Article  CAS  PubMed  Google Scholar 

  • Seco EM, Zinder JC, Manhart CM, Piano AL, McHenry CS, Ayora S (2013) Bacteriophage SPP1 DNA replication strategies promote viral and disable host replication in vitro. Nucleic Acids Res 41(3):1711–1721

    Article  CAS  PubMed  Google Scholar 

  • Seed KD, Lazinski DW, Calderwood SB, Camilli A (2013) A bacteriophage encodes its own CRISPR/Cas adaptive response to evade host innate immunity. Nature 494(7438):489–491

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sullivan MB, Coleman ML, Quinlivan V, Rosenkrantz JE, DeFrancesco AS, Tan G, Fu R, Lee JA, Waterbury JB, Bielawski JP (2008) Portal protein diversity and phage ecology. Environ Microbiol 10(10):2810–2823

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Summer EJ, Gonzalez CF, Bomer M, Carlile T, Embry A, Kucherka AM, Lee J, Mebane L, Morrison WC, Mark L, King MD, LiPuma JJ, Vidaver AK, Young R (2006) Divergence and mosaicism among virulent soil phages of the Burkholderia cepacia complex. J Bacteriol 188(1):255–268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Suttle CA (2007) Marine viruses – major players in the global ecosystem. Nat Rev Microbiol 5(10):801–812

    Article  CAS  PubMed  Google Scholar 

  • Swanson MM, Reavy B, Makarova KS, Cock PJ, Hopkins DW, Torrance L, Koonin EV, Taliansky M (2012) Novel bacteriophages containing a genome of another bacteriophage within their genomes. PLoS One 7(7):e40683

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Swenson KM, Guertin P, Deschênes H, Bergeron A (2013) Reconstructing the modular recombination history of Staphylococcus aureus phages. BMC Bioinf 14(Suppl 15):S17

    Article  Google Scholar 

  • Tagami S, Sekine S-i, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S (2014) Structural basis for promoter specificity switching of RNA polymerase by a phage factor. Genes Dev 28(5):521–531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4(4):470–483

    Article  CAS  PubMed  Google Scholar 

  • Turner D, Reynolds D, Seto D, Mahadevan P (2013) CoreGenes3. 5: a webserver for the determination of core genes from sets of viral and small bacterial genomes. BMC Res Notes 6(1):140

    Article  PubMed  PubMed Central  Google Scholar 

  • Twort FW (1915) An investigation on the nature of ultra-microscopic viruses. Lancet 186(4814):1241–1243

    Article  Google Scholar 

  • Vannucci FA, Kelley MR, Gebhart CJ (2013) Comparative genome sequencing identifies a prophage-associated genomic island linked to host adaptation of Lawsonia intracellularis infections. Vet Res 44(1):49

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Veesler D, Cambillau C (2011) A common evolutionary origin for tailed-bacteriophage functional modules and bacterial machineries. Microbiol Mol Biol Rev 75(3):423–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia H, Li T, Deng F, Hu Z (2013) Freshwater cyanophages. Virol Sin 28(5):253–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu J, Hendrix RW, Duda RL (2013) Chaperone–protein interactions that mediate assembly of the bacteriophage lambda tail to the correct length. J Mol Biol 426(5):1004–1018

    Article  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Food Biosciences, Teagasc Food Research Centre, Cork, Ireland

    Aidan Casey & Olivia McAuliffe

  2. Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland

    Aidan Coffey

Authors
  1. Aidan Casey
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  2. Aidan Coffey
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  3. Olivia McAuliffe
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Correspondence to Olivia McAuliffe .

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Editors and Affiliations

  1. Evolution Biotechnologies, Bedfordshire, UK

    David R. Harper

  2. Department of Microbiology, The Ohio State University, Mansfield, OH, USA

    Stephen T. Abedon

  3. Evolution Biotechnologies, Georgetown, TX, USA

    Benjamin H. Burrowes

  4. Evolution Biotechnologies, Bedfordshire, UK

    Malcolm L. McConville

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Casey, A., Coffey, A., McAuliffe, O. (2021). Genetics and Genomics of Bacteriophages. In: Harper, D.R., Abedon, S.T., Burrowes, B.H., McConville, M.L. (eds) Bacteriophages. Springer, Cham. https://doi.org/10.1007/978-3-319-41986-2_5

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