Abstract
Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses.
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Reference
Leplae R, Hebrant A, Wodak SJ, Toussaint A (2004) ACLAME: a CLAssification of Mobile genetic Elements. Nucleic Acids Res 32:D45–D49
McNair K, Bailey BA, Edwards RA (2012) PHACTS, a computational approach to classifying the lifestyle of phages. Bioinformatics 28:614–618
Abedon ST, Ackermann H-W (2001) Bacteriophage names 2000. The Bacteriophage Ecology Group (BEG). http://www.phage.org/names.htm
Kropinski AM, Prangishvili D, Lavigne R (2009) Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea. Environ Microbiol 11:2775–2777
Roberts RJ, Vincze T, Posfai J, Macelis D (2003) REBASE: restriction enzymes and methyltransferases. Nucleic Acids Res 31:418–420
Ackermann HW, Prangishvili D (2012) Prokaryote viruses studied by electron microscopy. Arch Virol 157:1843–1849
Ackermann H-W (2014) Sad state of phage electron microscopy. Please shoot the messenger. Microorganisms 2:1–10
Ackermann HW, Tiekotter KL (2012) Murphy's law-if anything can go wrong, it will: Problems in phage electron microscopy. Bacteriophage 2:122–129
Casjens SR, Gilcrease EB (2009) Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol 502:91–111
Li SS, Fan H, An XP, Fan HH, Jiang HH, Mi ZQ, Tong YG (2013) Utility of high throughput sequencing technology in analyzing the terminal sequence of caudovirales bacteriophage genome. Bing Du Xue Bao 29:39–43
Lingohr E, Frost S, Johnson RP (2009) Determination of bacteriophage genome size by pulsed-field gel electrophoresis. Methods Mol Biol 502:19–25
Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T, Izumi T, Akiba T, Mitsuoka K, Toh H, Yamashita A, Arisaka F, Hattori M, Oshima T, Yamagishi A (2011) Genomic and proteomic characterization of the large Myoviridae bacteriophage ϕTMA of the extreme thermophile Thermus thermophilus. Bacteriophage 1:152–164
Sharp R, Jansons IS, Gertman E, Kropinski AM (1996) Genetic and sequence analysis of the cos region of the temperate Pseudomonas aeruginosa bacteriophage, D3. Gene 177:47–53
Juhala RJ, Ford ME, Duda RL, Youlton A, Hatfull GF, Hendrix RW (2000) Genetic sequences of bacteriophages HK97 and HK022: Pervasive genetic mosaicism in the lambdoid bacteriophages. J Mol Biol 299:27–51
Ceyssens PJ, Lavigne R, Mattheus W, Chibeu A, Hertveldt K, Mast J, Robben J, Volckaert G (2006) Genomic analysis of Pseudomonas aeruginosa phages LKD16 and LKA1: establishment of the ϕKMV subgroup within the T7 supergroup. J Bacteriol 188:6924–6931
Glukhov AS, Krutilina AI, Shlyapnikov MG, Severinov K, Lavysh D, Kochetkov VV, McGrath JW, de LC SOV, Krylov VN, Akulenko NV, Kulakov LA (2012) Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions. PLoS One 7:e51163
Darling AE, Mau B (2010) Perna NT: progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 5:e11147
Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J (2005) ACT: the Artemis comparison tool. Bioinformatics 21:3422–3423
Becker EA, Burns CM, Leon EJ, Rajabojan S, Friedman R, Friedrich TC, O'Connor SL, Hughes AL (2012) Experimental analysis of sources of error in evolutionary studies based on Roche/454 pyrosequencing of viral genomes. Genome Biol Evol 4:457–465
Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010
Basrai MA, Hieter P, Boeke JD (1997) Small open reading frames: beautiful needles in the haystack. Genome Res 7:768–771
Kropinski AM, Waddell T, Meng J, Franklin K, Ackermann HW, Ahmed R, Mazzocco A, Yates J, Lingohr EJ, Johnson RP (2013) The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5. Virol J 10:76
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16
Carver T, Berriman M, Tivey A, Patel C, Bohme U, Barrell BG, Parkhill J, Rajandream MA (2008) Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 24:2672–2676
Kropinski AM, Borodovsky M, Carver TJ, Cerdeno-Tarraga AM, Darling A, Lomsadze A, Mahadevan P, Stothard P, Seto D, Van DG, Wishart DS (2009) In silico identification of genes in bacteriophage DNA. Methods Mol Biol 502:57–89
Okonechnikov K, Golosova O, Fursov M (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9:75
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Shukla M, Thomason JA III, Stevens R, Vonstein V, Wattam AR, Xia F (2015) RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 5:8365
Aziz RK, Devoid S, Disz T, Edwards RA, Henry CS, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Stevens RL, Vonstein V, Xia F (2012) SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models. PLoS One 7:e48053
Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069
Van Domselaar GH, Stothard P, Shrivastava S, Cruz JA, Guo A, Dong X, Lu P, Szafron D, Greiner R, Wishart DS (2005) BASys: a web server for automated bacterial genome annotation. Nucleic Acids Res 33:W455–W459
Galens K, Orvis J, Daugherty S, Creasy HH, Angiuoli S, White O, Wortman J, Mahurkar A, Giglio MG (2011) The IGS standard operating procedure for automated prokaryotic annotation. Stand Genomic Sci 4:244–251
Campbell MS, Holt C, Moore B, Yandell M (2014) Genome annotation and curation using MAKER and MAKER-P. Curr Protoc Bioinformatics 48:4.11.1–4.11.39. doi:10.1002/0471250953.bi0411s48.:4
Pearson WR (2013) An introduction to sequence similarity (“homology”) searching. Curr Protoc Bioinformatics, Chapter 3:Unit3.1.:Unit3
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211–D222
Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH (2011) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res 39:D225–D229
Soding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244–W248
Holbrook R, Anderson JM, Baird-Parker AC (1969) The performance of a stable version of Baird-Parker’s medium for isolating Staphylococcus aureus. J Appl Bacteriol 32:187–192
Calderon IL, Arenas FA, Perez JM, Fuentes DE, Araya MA, Saavedra CP, Tantalean JC, Pichuantes SE, Youderian PA, Vasquez CC (2006) Catalases are NAD(P)H-dependent tellurite reductases. PLoS One 1:e70
Walter EG, Thomas CM, Ibbotson JP, Taylor DE (1991) Transcriptional analysis, translational analysis, and sequence of the kilA-tellurite resistance region of plasmid RK2Ter. J Bacteriol 173:1111–1119
Whelan KF, Colleran E, Taylor DE (1995) Phage inhibition, colicin resistance, and tellurite resistance are encoded by a single cluster of genes on the IncHI2 plasmid R478. J Bacteriol 177:5016–5027
O'Gara JP, Gomelsky M, Kaplan S (1997) Identification and molecular genetic analysis of multiple loci contributing to high-level tellurite resistance in Rhodobacter sphaeroides 2.4.1. Appl Environ Microbiol 63:4713–4720
Fischer D, Eisenberg D (1999) Finding families for genomic ORFans. Bioinformatics 15:759–762
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. AAAI Press, Menlo Park, CA, pp 28–36
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 37:W202–W208
Lavigne R, Sun WD, Volckaert G (2004) PHIRE, a deterministic approach to reveal regulatory elements in bacteriophage genomes. Bioinformatics 20:629–6135
Lavigne R, Villegas A, Kropinski AM (2009) In silico characterization of DNA motifs with particular reference to promoters and terminators. Methods Mol Biol 502:113–129. doi:10.1007/978-1-60327-565-1_8
Jeng ST, Lay SH, Lai HM (1997) Transcription termination by bacteriophage T3 and SP6 RNA polymerases at Rho-independent terminators. Can J Microbiol 43:1147–1156
Mitra A, Kesarwani AK, Pal D, Nagaraja V (2011) WebGeSTer DB--a transcription terminator database. Nucleic Acids Res 39:D129–D135
Naville M, Ghuillot-Gaudeffroy A, Marchais A, Gautheret D (2011) ARNold: a web tool for the prediction of Rho-independent transcription terminators. RNA Biol 8:11–13
Solovyev V, Salamov A (2011) Automatic annotation of microbial genomes and metagenomic sequences. In: Li RW (ed) Metagenomics and its applications in agriculture, biomedicine and environmental studies. Nova Science Publishers, Hauppauge, NY, pp 61–78
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
Rice P, Longden I, Bleasby A, Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276–277
Figueras MJ, Beaz-Hidalgo R, Hossain MJ, Liles MR (2014) Taxonomic affiliation of new genomes should be verified using average nucleotide identity and multilocus phylogenetic analysis. Genome Announc 2:e00927–e00914
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91
Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351
Konstantinidis KT, Ramette A, Tiedje JM (2006) Toward a more robust assessment of intraspecies diversity, using fewer genetic markers. Appl Environ Microbiol 72:7286–7293
Konstantinidis KT, Tiedje JM (2005) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci U S A 102:2567–2572
Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E, Thompson FL (2013) Microbial genomic taxonomy. BMC Genomics 14:913. doi:10.1186/1471-2164-14-913.:913-914
Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 106:19126–19131
Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 12:402. doi:10.1186/1471-2164-12-402.:402-412
Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539
Abbott JC, Aanensen DM, Rutherford K, Butcher S, Spratt BG (2005) WebACT--an online companion for the Artemis Comparison Tool. Bioinformatics 21:3665–3666
Lavigne R, Seto D, Mahadevan P, Ackermann H-W, Kropinski AM (2008) Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools. Res Microbiol 159:406–414
Lavigne R, Darius P, Summer EJ, Seto D, Mahadevan P, Nilsson AS, Ackermann H-W, Kropinski AM (2009) Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol 9:224
Kovalyova IV, Kropinski AM (2003) The complete genomic sequence of lytic bacteriophage gh-1 infecting Pseudomonas putida-evidence for close relationship to the T7 group. Virology 311:305–315
Kropinski AM, Lingohr EJ, Moyles DM, Ojha S, Mazzocco A, She YM, Bach SJ, Rozema EA, Stanford K, McAllister TA, Johnson RP (2012) Endemic bacteriophages: a cautionary tale for evaluation of bacteriophage therapy and other interventions for infection control in animals. J Virol 9:207
Zhao Y, Wang K, Jiao N, Chen F (2009) Genome sequences of two novel phages infecting marine roseobacters. Environ Microbiol 11:2055–2064
Hatfull GF (2012) The secret lives of mycobacteriophages. Adv Virus Res 82:179–288
Hatfull GF (2012) Complete genome sequences of 138 mycobacteriophages. J Virol 86:2382–2384
Hatfull GF (2014) Molecular genetics of Mycobacteriophages. Microbiol Spect 2:1–36
Grose JH, Casjens SR (2014) Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae. Virology 468-470:421–443
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Aziz, R.K., Ackermann, HW., Petty, N.K., Kropinski, A.M. (2018). Essential Steps in Characterizing Bacteriophages: Biology, Taxonomy, and Genome Analysis. In: Clokie, M., Kropinski, A., Lavigne, R. (eds) Bacteriophages. Methods in Molecular Biology, vol 1681. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7343-9_15
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