How to name and classify your phage: An informal guide

Viruses

Volumn 9, Issue 4, 2017, Pages

  Adriaenssens, Evelien M ^a,b   Rodney Brister, J ^b,c  

^a UNIVERSITY OF LIVERPOOL   (United Kingdom)

^b Bacterial and Archaeal Viruses Subcommittee   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Bacteriophages; Classification guide; Naming guide; Phage classification; Phage taxonomy

Indexed keywords

ARCHAEAL VIRUS; HUMAN; NONHUMAN; SCIENTIST; TAXONOMY; BACTERIOPHAGE; CLASSIFICATION; NOMENCLATURE;

BACTERIOPHAGES; TERMINOLOGY AS TOPIC;

EID: 85017428187     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v9040070     Document Type: Article

References (47)

1. International Committee on Taxonomy of Viruses (ICTV). Available online: http://www.ictvonline.org/ (accessed on 23 February 2017).
2. Bacterial and Archaeal Viruses Subcommittee. Available online: https://talk.ictvonline.org/information/w/ members/441/bacterial-and-archaeal-viruses-subcommittee (accessed on 23 February 2017).
3. Bradley, D.E. Ultrastructure of bacteriophage and bacteriocins. Bacteriol. Rev. 1967, 31, 230-314.
4. Ackermann, H.-W. Classification of bacteriophages. In The Bacteriophages, 2nd ed.; Calendar, R., Ed.; Oxford University Press: New York, NY, USA, 2006; pp. 8-17.
5. Francki, R.; Fauquet, C.; Knudson, D.; Brown, F. Classification and Nomenclature of Viruses: Fifth Report of the International Committee on the Taxonomy of Viruses; Springer: Wien, NY, USA, 1991.
6. Fauquet, M.C.; Mayo, A.M. The 7th ICTV Report. Arch. Virol. 2001, 146, 189-194.
7. Fauquet, C.; Mayo, M.; Maniloff, J.; Desselberger, U.; Ball, L. Virus Taxonomy: Eighth Report of the International Committee on Taxonomy of Viruses; Elsevier Academic Press: San Diego, CA, USA, 2005.
8. Nelson, D. Phage taxonomy: We agree to disagree. J. Bacteriol. 2004, 186, 7029-7031.
9. Brister, J.R.; Ako-Adjei, D.; Bao, Y.; Blinkova, O. NCBI viral genomes resource. Nucleic Acids Res. 2015, 43, D571-D577.
10. Rohwer, F.; Edwards, R. The Phage Proteomic Tree: A genome-based taxonomy for phage. J. Bacteriol. 2002, 184, 4529-4535.
11. Lima-Mendez, G.; Van Helden, J.; Toussaint, A.; Leplae, R. Reticulate representation of evolutionary and functional relationships between phage genomes. Mol. Biol. Evol. 2008, 25, 762-777.
12. Pride, D.T.; Wassenaar, T.M.; Ghose, C.; Blaser, M.J. Evidence of host-virus co-evolution in tetranucleotide usage patterns of bacteriophages and eukaryotic viruses. BMC Genom. 2006, 7, 8.
13. Asare, P.T.; Jeong, T.; Ryu, S.; Klumpp, J.; Loessner, M.J.; Merrill, B.D.; Kim, K. Putative type 1 thymidylate synthase and dihydrofolate reductase as signature genes of a novel bastille-like group of phages in the subfamily Spounavirinae. BMC Genom. 2015, 16, 582.
14. Grose, J.H.; Casjens, S.R. Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae. Virology 2014, 468-470, 421-443.
15. Adriaenssens, E.M.; Edwards, R.; Nash, J.H.E.; Mahadevan, P.; Seto, D.; Ackermann, H.-W.; Lavigne, R.; Kropinski, A.M. Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology 2015, 477, 144-154.
16. Lavigne, R.; Seto, D.; Mahadevan, P.; Ackermann, H.-W.; Kropinski, A.M. Unifying classical and molecular taxonomic classification: Analysis of the Podoviridae using BLASTP-based tools. Res. Microbiol. 2008, 159, 406-414.
17. Lavigne, R.; Darius, P.; Summer, E.J.; Seto, D.; Mahadevan, P.; Nilsson, A.S.; Ackermann, H.-W.; Kropinski, A.M. Classification of Myoviridae bacteriophages using protein sequence similarity. BMC Microbiol. 2009, 9, 224.
18. Krupovic, M.; Dutilh, B.E.; Adriaenssens, E.M.; Wittmann, J.; Vogensen, F.K.; Sullivan, M.B.; Rumnieks, J.; Prangishvili, D.; Lavigne, R.; Kropinski, A.M.; et al. Taxonomy of prokaryotic viruses: update from the ICTV bacterial and archaeal viruses subcommittee. Arch. Virol. 2016, 4, 1095-1099.
19. Adriaenssens, E.M.; Krupovic, M.; Knezevic, P.; Ackermann, H.-W.; Barylski, J.; Brister, J.R.; Clokie, M.R.C.; Duffy, S.; Dutilh, B.E.; Edwards, R.A.; et al. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Arch. Virol. 2017, doi:10.1007/s00705-016-3173-4.
20. Virus Taxonomy: 2015 Release. Available online: http://talk.ictvonline.org/taxonomy/ (accessed 23 February 2017).
21. Karsch-Mizrachi, I.; Nakamura, Y.; Cochrane, G. The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2012, 40, D33-D37.
22. Ackermann, H.-W.; Abedon, S.T. Bacteriophage Names 2000. Available online: http://www. phage.org/names/2000/ (accessed 23 February 2017).
23. Abedon, S.T. Phage Name Check. Available online: http://www.phage.org/phage_name_check.html (accessed 28 March 2017).
24. NCBI Nucleotide Database. Available online: http://www.ncbi.nlm.nih.gov/nuccore (accessed 24 February 2017).
25. Kropinski, A.M.; Prangishvili, D.; Lavigne, R. Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea. Environ. Microbiol. 2009, 11, 2775-2777.
26. ICTV Code. Available online: http://talk.ictvonline.org/information/w/ictv-information/383/ictv-code (accessed 23 February 2017).
27. National Center for Biotechnology Information (US), The GenBank submissions handbook. Available online: https://www.ncbi.nlm.nih.gov/books/NBK51157/ (accessed 23 February 2017).
28. O’Leary, N.A.; Wright, M.W.; Brister, J.R.; Ciufo, S.; Haddad, D.; McVeigh, R.; Rajput, B.; Robbertse, B.; Smith-White, B.; Ako-Adjei, D.; et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016, 44, D733-D745.
29. Johnson, M.; Zaretskaya, I.; Raytselis, Y.; Merezhuk, Y.; McGinnis, S.; Madden, T.L. NCBI BLAST: A better web interface. Nucleic Acids Res. 2008, 36, 5-9.
30. Bao, Y.; Chetvernin, V.; Tatusova, T. Improvements to pairwise sequence comparison (PASC): A genomebased web tool for virus classification. Arch. Virol. 2014, 159, 3293-3304.
31. Ågren, J.; Sundström, A.; Håfström, T.; Segerman, B. Gegenees: Fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups. PLoS ONE 2012, 7, e39107.
32. ICTV Taxonomy Proposals Templates. Available online: https://talk.ictvonline.org/files/taxonomyproposal- templates/ (accessed 23 February 2017).
33. Petrov, V.M.; Ratnayaka, S.; Nolan, J.M.; Miller, E.S.; Karam, J.D. Genomes of the T4-related bacteriophages as windows on microbial genome evolution. Virol. J. 2010, 7, 292.
34. Roux, S.; Enault, F.; Ravet, V.; Pereira, O.; Sullivan, M.B. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages. Front. Microbiol. 2015, 6, 1-13.
35. Krumsiek, J.; Arnold, R.; Rattei, T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007, 23, 1026-1028.
36. Zafar, N.; Mazumder, R.; Seto, D. CoreGenes: A computational tool for identifying and cataloging "core" genes in a set of small genomes. BMC Bioinform. 2002, 3, 12.
37. Mahadevan, P.; King, J.F.; Seto, D. CGUG: In silico proteome and genome parsing tool for the determination of "core" and unique genes in the analysis of genomes up to ca. 1.9 Mb. BMC Res. Notes 2009, 2, 168.
38. Page, A.J.; Cummins, C.A.; Hunt, M.; Wong, V.K.; Reuter, S.; Holden, M.T.G.; Fookes, M.; Falush, D.; Keane, J.A.; Parkhill, J. Roary: Rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015, 31, 3691-3693.
39. Grazziotin, A.L.; Koonin, E.V.; Kristensen, D.M. Prokaryotic Virus Orthologous Groups (pVOGs): A resource for comparative genomics and protein family annotation. Nucleic Acids Res. 2016, 45, D491-D498.
40. Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T.J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J.; et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011, 7, 539.
41. Edgar, R.C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32, 1792-1797.
42. Dereeper, A.; Guignon, V.; Blanc, G.; Audic, S.; Buffet, S.; Chevenet, F.; Dufayard, J.-F.; Guindon, S.; Lefort, V.; Lescot, M.; et al. Phylogeny.fr: Robust phylogenetic analysis for the non-specialist. Nucleic Acids Res.2008, 36, W465-W469.
43. Tamura, K.; Stecher, G.; Peterson, D.; Filipski, A.; Kumar, S. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 2013, 30, 2725-2729.
44. Price, M.N.; Dehal, P.S.; Arkin, A.P. FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS ONE 2010, 5, e9490.
45. Darling, A.E.; Mau, B.; Perna, N.T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 2010, 5, e11147.
46. Sullivan, M.J.; Petty, N.K.; Beatson, S.A. Easyfig: A genome comparison visualizer. Bioinformatics 2011, 27, 1009-1010.
47. Alikhan, N.-F.; Petty, N.K.; Ben Zakour, N.L.; Beatson, S.A. BLAST Ring Image Generator (BRIG): Simple prokaryote genome comparisons. BMC Genom. 2011, 12, 402.