CPT Canonical Phage Genomes List

Overview

Questions

Objectives

Time estimation:

Canonical Phage List

A general reference on virus groups is available by searching at ViralZone. Additional information on currently accepted phage taxonomy is put forth by the ICTV International Committee on the Taxonomy of Viruses and also searchable in the NCBI Taxonomy Browser. While the taxonimical classification system used by these groups is not completely accurate, it can provide a useful way to find the closest related type phage for comparison purposes.

Lambda

Most trusted record: RefSeq NC_001416

Basic Stats

• Host: E. coli
• 48,502 base pairs in genome
• Siphophage
• Lambda ViralZone page

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU.

Phage T1

Most trusted record: RefSeq NC_005833

Basic Stats

• Host: E. coli
• 48,836 base pairs in genome
• Siphophage
• T1 ViralZone page

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU. Additionally, since the T1 genome is deposited backwards, we refer to T1-like phage TLS for re-opening and orientation RefSeq NC_009540.1.

Phage T3

Most trusted record: RefSeq NC_003298

Basic Stats

• Host: E. coli
• 38,208 base pairs in genome
• Podophage

Phage T4

Most trusted record: RefSeq NC_000866

Basic Stats

• Host: E. coli
• 168,903 base pairs in genome
• Myophage
• T4 ViralZone page

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU.

Phage T5

Most trusted record: RefSeq NC_005859

Basic Stats

• Host: E. coli
• 121,750 base pairs in genome (the RefSeq sequence comes from the Russian version NCBI AY543070.1
• Siphophage
• T5 ViralZone page

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU. Two other annotated T5 genomes that have some good calls in other parts of the genome are the Hangzhou, China version (NCBI AY587007.1) and the Paris-Orsay version (NCBI AY692264.1).

References:

• Y. Zvanoic, F. Confalonieri, L. Ponchon, R. Lurz, M. Chami, A. Flayhan, M. Renouard, A. Huet, P. Decottignies, A. R. Davidson, C. Breyton, P. Boulanger Insights into Bacteriophage T5 Structure from Analysis of Its Morphogenesis Genes and Protein Components J Virol, 88 (2014), pp. 1162-1174

• J. Wang, Y. Jiang, M. Vincent, Y. Sun, H. Yu, J. Wang, Q. Bao, H. Kong, S. Hu Complete genome sequnece of bacteriophage T5. Virology, 5 (2005), pp. 45-65

Phage T7

Most trusted record: RefSeq NC_001604

Basic Stats

• Host: E. coli
• 39,937 base pairs in genome
• Podophage
• T7 ViralZone page

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU.

Phage N4

Most trusted record: RefSeq NC_008720

Basic Stats

• Host: E. coli
• 70,153 base pairs in genome
• Podophage
• N4 ViralZone page

Useful readings:

• Work published by the Rothman-Denes lab at the University of Chicago

Phage P1

Most trusted record: RefSeq NC_005856

Basic Stats

• Host: E. coli
• 94,800 base pairs in genome
• Podophage
• P1 ViralZone page

References:

• M.B. Łobocka, D.J. Rose, G. Plunkett, M. Rusin, A. Samojedny, H. Lehnherr, M.B. Yarmolinsky, F.R. Blattner Genome of bacteriophage P1 J Bacteriol, 186 (2004), pp. 7032‐7068

Phage P2

Most trusted record: RefSeq NC_001895

Basic Stats

• Host: E. coli
• 33,593 base pairs in genome
• Myophage
• P2 ViralZone page

Phage P4

Most trusted record: RefSeq NC_001609

Basic Stats

• Host: E. coli
• 11,624 base pairs in genome
• Myophage

Useful readings:

• G. Truss, R. N. Goldstein, R. Calendar In Vitro Packaging of Satellite Phage P4 DNA Proc Natl Acad Sci USA, 71 (1984), pp. 2367-2371

Phage P22

Most trusted record: RefSeq NC_002371

Basic Stats

• Host: Salmonella
• 41,724 base pairs in genome
• Podophage
• P22 ViralZone page

References:

• Corrected sequence of the bacteriophage p22 genome. (2003). Corrected sequence of the bacteriophage p22 genome., 185(4), 1475–1477.
• A. S. Olia, P. E. Prevelige, J. E. Johnson, G. Cingolani Three-dimensional structure of a viral genome-delivery portal vertex. Nat Struct Mol Biol, 18 (2011), pp. 597-603

Phage Chi

Most trusted record: RefSeq NC_025442

Basic Stats

• Host: Salmonella
• 59,578 base pairs in genome
• Siphophage
• Chi ViralZone page

Phage K

Most trusted record: RefSeq NC_005880

Basic Stats

• Host: Staphylococcus aureus
• 148,317 base pairs in genome
• Myophage

Phage Epsilon15

Most trusted record: RefSeq NC_004775

Basic Stats

• Host: Salmonella
• 148,317 base pairs in genome
• Myophage
• Epsilon15 ViralZone page

Phage Felix01

Most trusted record: RefSeq NC_005282

Basic Stats

• Host: Salmonella
• 86,155 base pairs in genome
• Myophage

Phage Mu

Most trusted record: RefSeq NC_000929

Basic Stats

• Host: E. coli
• 36,717 base pairs in genome
• Myophage
• Mu ViralZone page

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU.

Phage N15

Most trusted record: RefSeq NC_001901

Basic Stats

• Host: E. coli
• 46,375 base pairs in genome
• Siphophage
• N15 ViralZone page

Phage Phi29

Most trusted record: RefSeq_011048

Basic Stats

• Host: Bacillus subtilis
• 19,282 base pairs in genome
• Podophage
• Phi29 ViralZone page

Phage PhiKMV

Most trusted record: RefSeq NC_005045

Basic Stats

• Host: Pseudomonas aeruginosa
• 42,519 base pairs in genome
• Podophage
• PhiKMV ViralZone page

Phage SP6

Most trusted record: RefSeq NC_004831

Basic Stats

• Host: Salmonella
• 43,769 base pairs in genome
• Podophage
• SP6 ViralZone page

Phage SPO1

Most trusted record: RefSeq NC_011421

Basic Stats

• Host: Bacillus subtilis
• 132,562 base pairs in genome
• Myophage
• SPO1 ViralZone page

Phage SPP1

Most trusted record: RefSeq NC_004166

Basic Stats

• Host: Bacillus subtilis
• 44,010 base pairs in genome
• Siphophage

References: The Revisited Genome of Bacillus subtilis Bacteriophage SPP1. (2018). The Revisited Genome of Bacillus subtilis Bacteriophage SPP1., 10(12). http://doi.org/10.3390/v10120705

Phage PRD1

Most trusted record: RefSeq NC_001421

Basic Stats

• Host: E. coli
• 14,927 base pairs in genome
• Tectiphage

References: International Committee on Taxonomy of Viruses Virus Taxonomy - Family - Tectiviridae ICTV, 9 (2012), pp. 317-321

Phage PhiP68

Most trusted record: RefSeq NC_004679

Basic Stats

• Host: Staphylococcus aureus
• 18,227 base pairs in genome
• Podophage

Phage 9NA

Most trusted record: RefSeq NC_025443

Basic Stats

• Host: Salmonella
• 52,869 base pairs in genome
• Podophage

Phage Vi01

Most trusted record: RefSeq NC_015296

Basic Stats

• Host: Salmonella
• 157,061 base pairs in genome
• “Viunalikevirus”

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU.

References: E. M. Adriaenssens, H. Ackermann, H. Anna, B. Blasdel, I. F. Connerton, D. Goulding, M. W/ Griffiths, S. P. Hooton, E. M. Kutter, A. M. Kropinski, J. Lee, M. Maes, D. Pickard, S. Ryu, Z. Sepehrizadeh, S. S. Shahrbabak, A. L. Toribio, R. Lavigne A suggested new bacteriophage genus: “Viunalikevirus” Arch Virol, 157 (2012), pp. 2035-2046

Phage Phi92

Most trusted record: RefSeq NC_023693

Basic Stats

• Host: E. coli
• 148,612 base pairs in genome
• Myophage

Note that…

Genome present in the CPT Apollo instance. Access to the record can be requested after making an account on CPT Public Galaxy or CPT Galaxy for TAMU.

Phage PhiETA

Most trusted record: RefSeq NC_003288

Basic Stats

• Host: Staphylococcus aureus
• 43,081 base pairs in genome
• Siphophage
• PhiETA ViralZone page

Phage HK97

Most trusted record: RefSeq NC_002167

Basic Stats

• Host: E. coli
• 39,732 base pairs in genome
• Siphophage

Phage HK022

Most trusted record: RefSeq NC_002166

Basic Stats

• Host: E. coli
• 40,751 base pairs in genome
• Siphophage

Phage 186

Most trusted record: RefSeq NC_001317

Basic Stats

• Host: E. coli
• 30,624 base pairs in genome
• Myophage

Phage Tuc2009

Most trusted record: RefSeq NC_002703

Basic Stats

• Host: Lactococcus
• 38,347 base pairs in genome
• Siphophage

Phage P335

Most trusted record: RefSeq NC_004746

Basic Stats

• Host: Lactococcus
• 36,596 base pairs in genome
• Siphophage

Phage TP901-1

Most trusted record: RefSeq NC_002747

Basic Stats

• Host: Lactococcus
• 37,667 base pairs in genome
• Siphophage

Phage A118

Most trusted record: RefSeq NC_003216

Basic Stats

• Host: Listeria monocytogenes
• 40,834 base pairs in genome
• Siphophage

Phage L5

Most trusted record: RefSeq NC_001335

Basic Stats

• Host: Mycobacterium smegmatis
• 52,297 base pairs in genome
• Siphophage
• L5 ViralZone page

Phage Bxb1

Most trusted recored: RefSeq NC_2656

Basic Stats

• Host: Mycobacterium smegmatis
• 50,550 base pairs in genome
• Siphophage

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