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Table 2 T4-related phages with sequenced genomes

From: Genomes of the T4-related bacteriophages as windows on microbial genome evolution

Phage or genome type

Phage

Genome size (bp)

Database reference(1)

ORFs (T4-like/Total)

tRNA genes

Shared or unique properties of the genomes(2)

T-even

E. coli phage T4

168,903

NC_000866

278

8

The T-even type genomes share 85-95% ORF homology with one another and >90% nucleotide sequence identity between most of their shared alleles. Also, these genomes encode glucosyl transferases and dCMP hydroxymethylases, but their DNA modification patterns vary (see text and Table 3). Some members of this cluster are known to be partially compatible with each other in genetic crosses (see text). Phage RB70 (Table 1) might be identical to phage RB51.

 

E. coli phage T4T

168920

HM137666

280

8

 
 

E. coli phage T2

163,793

Tulane

232/269

9

 
 

E. coli phage T6

168,974

Tulane

228/270

7

 
 

E. coli phage RB3

~168,000

Tulane

~240/~270

10

 
 

E. coli phage RB14

165,429

NC_012638

235/274

10

 
 

E. coli phage RB15

~167,000

Tulane

~236/~269

7

 
 

E. coli phage RB18

166,677

Tulane

237/268

10

 
 

E. coli phage RB26

163,036

Tulane

232/~269

10

 
 

E. coli phage RB32

165,890

NC_008515

237/270

8

 
 

E. coli phage RB51

168,394

NC_012635

242/273

9

 
 

E. coli phage LZ2

>159,664

Tulane

~240/>260

10

 

RB69

E. coli phage RB69

167,560

NC_004928

212/273

2

~20% of the ORFs in this genome are unique to RB69; this phage excludes T4 in RB69 × T4 crosses [25].

RB49

E. coli phage RB49

164,018

NC_005066

120/279

0

The 3 genomes of this type share 96-99% ORF homology with one another

 

E. coli phage phi1

164,270

NC_009821

115/276

0

 
 

E. coli phage JSE

166,418

NC_012740

122/277

0

 

JS98

E. coli phage JS98

170,523

NC_010105

202/266

3

JS98 and JS10 share ~98% ORF homology with each other.

 

E. coli phage JS10

171,451

NC_012741

197/265

3

 

CC31

E. coli phage CC31

165,540

GU323318

156/279

8

~43% of the CC31 ORFs are unique to this phage. Also, CC31 is the only known nonT-even type phage predicted to encode glucosyl transferase genes (see Table 3)

RB43

E. coli phage RB16

176,789

HM134276

115/260

2

The genomes of RB16 and RB43are similarly organized and share >85% ORF homology with each other [14]

 

E. coli phage RB43

180,500

NC_007023

118/292

1

 

133

Acinetobacter phage133

159,897

HM114315

110/257

14

Each of these Acinetobacter phages has a unique set of ORFs that occupy ~35% of the genome. That is, each represents a different type of T4-related phage genome.

Acj9

Acinetobacter phage Acj9

169,953

HM004124

97/253

16

 

Acj61

Acinetobacter phage Acj61

164,093

GU911519

101/241

13

 

Ac42

Acinetobacter phage Ac42

167,718

HM032710

117/257

3

 

44RR

Aeromonas phage 44RR

173,591

NC_005135

118/252

17

Phages 44RR and 31 share ~98% ORF homology (and ~97% sequence identity) with each other. Also, they exhibit ~80% ORF homology with phage 25

 

Aeromonas phage 31

172,963

NC_007022

117/247

15

 

25

Aeromonas phage 25

161,475

NC_008208

116/242

13

The phage 25 genome is 11-12 kb shorter than the genome of 44RR (or 31). Also, ~14% of the phage 25 ORFs are unique to this phage.

Aeh1

Aeromonas phage Aeh1

233,234

NC_005260

106/352

23

Phages Aeh1 and PX29 share ~95% ORF homology with each other and partially overlap in host-range properties

 

Aeromonas phage PX29

222,006

GU396103

109/342

25

 

65

Aeromonas phage 65

235,289

GU459069

102/439

17

~55% of the ORFs in this genome are unique to phage 65

KVP40

Vibrio phage KVP40

244,834

NC_005083

99/381

29

Phages KVP40 and nt-1 share ~85% ORF homology with each other and partially overlap in host range properties

 

Vibrio phage nt-1

247,144

Tulane

95/400

26

 

S-PM2

Marine Synechococcus phage S-PM2

196,280

NC_006820

40/236

1

See [31] for comparisons between the marine cyano phages. Based on their diversity, each represents a different type of T4-related phage genome.

S-RSM4

Marine Synechococcus phage S-RSM4

194,454

NC_013085

41/237

12

 

Syn9

Marine Synechococcus phage Syn9

177,300

NC_008296

43/226

6

 

P-SSM2

Marine Prochlorococcus phage P-SSM2

252,401

NC_006883

47/329

1

 

P-SSM4

Marine Prochlorococcus phage P-SSM4

178,249

NC_006884

46/198

0

 

KP15

Klebsiella pneumoniae phage KP15

174,436

GU295964

116/239

1

~80% of KP15 ORFs are homologous and similarly organized to ORFs in RB43

W14

Delftia acidovorance phage phiW-14

157,486

NC_013697

60/236

0

 

AG3

Shigella boydii phage phiSboM-AG3

158,006

NC_013693

64/260

4

 
  1. (1) In this column, numbers with the prefixes NC, GU and HM refer to GenBank accession numbers and the designation "Tulane" refers to the database at http://phage.bioc.tulane.edu (soon to be transferred to http://phage.ggc.edu). The NC_000866 accession is for the T4 genome sequence that was compiled from data contributed by many laboratories [2, 7]. The HM137666 accession is for the T4 genome sequence determined on DNA from a single source, termed T4T, which is the wild-type T4D strain maintained by the Karam laboratory at Tulane University, New Orleans.
  2. (2)In this column, "% ORF homology" refers to the percentage of ORFs that are alleles between the compared genomes.