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Table 3 The abundances of 22 REP classes in genomes of 63 sequenced fluorescent pseudomonads

From: Evolution of REP diversity: a comparative study

Bacterial strain Clade REP copy number
Ortho group I* Ortho group II* Ortho group III* Ortho group IV* NO* NO* NO* NO* NO* NO*
PF 1 PF 2 PF 3 PF 4 PF 5 PF 6 PF 7 PF 8 PF 9 PF 10 PF 11 PF 12 PF 13 PF 14 PF 15 PF 16 PF 17 PF 18 PF 19 PF 20 PF 21 PF 22
P. agarici NCPPB 2289 A 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
P. fuscovaginae CB98818 0 0 0 7 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 2 0
P. fuscovaginae UPB0736 0 0 0 6 0 0 1 0 2 1 0 0 0 0 0 0 0 0 0 0 2 0
P. fluorescens NZI7 B 0 0 319 0 0 0 0 1 0 13 4 3 1 0 0 0 40 46 0 0 0 0
P. fluorescens Wayne1 0 0 420 0 0 0 0 0 0 0 0 0 0 0 0 0 4 35 0 0 0 0
P . protegens Pf-5 0 0 457 0 0 0 0 0 0 0 0 0 0 0 0 0 1 37 0 0 0 0
P. chlororaphis GP72 C 0 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 0 282 0 0 258 0
P. chlororaphis O6 0 0 1 0 0 0 0 2 0 0 0 0 0 0 0 0 0 269 0 0 255 0
P. chlororaphis 30-84 0 0 0 0 0 0 0 3 0 0 0 0 0 0 0 0 0 297 1 0 17 0
P. sp. GM17 0 0 1 0 0 0 0 4 0 3 0 0 0 0 0 0 0 198 3 0 194 0
P. fluorescens BBc6R8 D 0 0 3 0 0 3 1 0 739 3 0 110 5 0 0 0 155 67 0 0 0 0
P. sp. Ag1 0 0 4 0 0 13 0 0 787 0 0 96 4 0 0 0 154 66 0 0 0 0
P. sp. PAMC 26793 0 0 0 0 0 1 0 0 684 2 0 106 4 0 0 0 155 76 0 0 0 0
P. sp. PAMC 25886 0 0 8 1 0 72 0 0 32 0 0 425 14 3 0 0 117 20 0 0 0 39
P . fluorescens A506 15 0 0 0 0 0 0 0 103 0 0 681 63 2 0 0 6 62 0 0 0 0
P. fluorescens SS101 12 1 0 0 0 0 0 0 101 0 0 627 47 1 0 0 3 434 0 0 0 0
P. synxantha BG33R 73 225 0 0 0 0 0 0 15 0 0 326 18 0 0 0 5 64 0 0 0 0
P. fluorescens NZ007 0 0 0 0 0 0 0 1 22 0 0 606 70 0 0 0 54 0 0 0 0 0
P . fluorescens SBW25 387 123 0 0 0 0 0 0 6 0 0 43 6 2 0 0 104 0 0 0 0 202
P. sp. R81 45 2 3 0 0 0 0 0 304 0 0 140 9 2 0 0 0 27 0 0 0 0
P. fluorescens NZ052 24 2 11 0 0 1 0 0 199 0 2 226 21 1 0 0 28 281 0 0 0 3
P. tolaasii 6264 2 0 0 0 0 0 0 0 10 1 0 797 151 0 0 0 20 0 0 0 0 0
P. tolaasii PMS117 4 0 0 0 0 0 0 0 10 8 0 824 143 1 0 0 33 0 0 0 0 0
P. fluorescens BRIP34879 12 62 0 0 0 0 0 0 21 0 0 144 21 0 0 0 0 4 0 0 0 0
P. extremaustralis 14-3 20 168 4 1 0 0 0 0 4 0 0 0 2 0 0 0 3 201 0 0 0 0
P. fluorescens BS2 55 181 0 0 0 0 0 0 10 0 0 1 0 0 0 0 1 0 0 0 0 0
P. fluorescens WH6 9 41 0 0 0 0 1 2 4 0 0 2 0 0 0 0 27 0 0 0 0 17
P. sp. UK4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0
P. psychrophila HA-4 E 0 0 0 0 0 0 0 1 2 0 0 0 4 1 0 0 0 21 0 9 0 0
P. fragi A22 0 0 0 0 0 0 0 0 0 0 0 1 17 116 0 0 0 155 0 0 0 0
P. fragi B25 0 0 0 0 0 0 0 2 17 4 0 67 163 2 0 0 0 0 0 0 0 0
P . fluorescens Pf0-1 F 0 0 0 0 0 0 0 3 10 10 0 0 14 31 7 0 0 0 0 0 0 0
P. sp. GM25 0 0 0 0 0 0 0 29 27 66 0 0 4 9 24 8 0 0 0 0 0 0
P. sp. R62 0 0 0 0 150 0 0 0 5 832 7 0 43 145 0 2 0 6 0 99 0 0
P. sp. GM30 0 0 0 0 139 0 0 3 51 582 249 0 19 178 7 0 380 13 0 97 0 0
P. fluorescens R124 0 0 0 0 37 0 0 1 1009 265 217 0 1 30 5 2 261 12 0 59 0 0
P. fluorescens NZ011 0 0 0 0 0 0 0 2 2 1035 240 0 0 6 4 2 2 12 0 111 0 0
P. sp. GM16 0 0 0 0 0 0 0 0 0 159 272 1 14 357 2 8 2 9 0 323 0 0
P. sp. GM24 0 0 0 0 0 0 0 0 0 153 261 1 14 325 2 8 2 9 0 304 0 0
P. sp. GM80 0 0 0 0 306 0 0 0 1 9 182 0 88 535 2 0 4 11 2 0 0 0
P . sp . UW4 G 0 0 0 0 0 0 84 427 363 435 0 14 60 48 0 0 2 398 0 25 0 0
P. sp. GM33 0 0 0 1 0 0 92 438 540 156 0 7 34 21 0 0 58 272 0 145 0 0
P. sp. GM48 0 0 1 1 0 0 64 48 1283 8 0 1 5 0 0 0 212 233 0 1 0 0
P. sp. GM49 0 0 1 0 0 0 108 550 151 47 1 4 79 3 0 0 3 502 0 2 0 0
P. sp. GM55 0 0 391 90 0 0 1 33 15 45 0 4 203 35 0 0 1 435 0 0 1 0
P. sp. GM74 0 0 1 0 0 0 0 232 428 11 0 2 120 55 0 0 19 50 0 19 0 0
P. sp. GM78 0 0 17 0 0 0 0 9 12 101 92 1 188 114 117 7 0 150 12 70 53 0
P. fluorescens NCIMB 11764 H 0 0 2 2 51 0 1 2 13 11 0 1 11 5 59 31 186 2 0 12 2 0
P. mandelii JR-1 0 0 0 1 2 0 2 6 5 166 84 0 5 2 3 8 164 68 0 0 355 0
P. fluorescens HK44 0 0 0 0 0 0 56 10 5 29 0 1 0 0 0 0 304 1 100 1 1 0
P. sp. GM50 0 0 0 0 3 0 392 1 198 32 0 4 20 0 15 11 13 4 0 67 667 0
P. sp. GM102 0 0 0 0 0 0 140 2 77 6 0 16 116 1 11 14 245 0 0 57 679 0
P. sp. GM79 0 0 1 400 0 0 16 2 1417 8 0 9 62 0 0 0 127 0 0 168 75 0
P. sp. GM60 0 0 31 398 0 0 0 1 175 30 50 0 5 3 17 6 0 297 0 1 379 0
P. sp. GM67 0 0 20 301 0 0 0 2 33 41 23 0 4 1 37 26 0 101 1 0 656 0
P. sp. GM21 0 0 3 0 1 0 0 12 48 147 20 4 35 4 38 9 0 11 0 0 0 0
P. sp. GM18 0 0 0 0 0 0 27 1 2 3 0 1 7 0 0 0 28 1 1 65 35 0
P. sp. GM41(2012) 0 0 0 1 55 0 73 7 72 91 13 2 13 0 19 5 0 5 174 89 24 0
P. fluorescens Q2-87 I 0 0 0 0 47 0 0 75 576 130 0 0 2 0 0 0 586 2 1 0 0 0
P . fluorescens F113 0 0 0 0 331 0 0 749 60 91 0 0 0 0 0 0 54 3 198 9 0 0
P. fluorescens Q8r1-96 0 0 0 0 30 0 0 661 61 109 0 0 0 0 0 0 44 5 295 17 0 0
P. fluorescens Wood1R 0 0 0 0 21 0 0 290 26 62 0 0 1 0 0 0 37 6 181 15 0 0
P . brassicacearum NFM421 0 0 0 0 23 0 0 632 60 116 0 0 1 0 0 0 46 6 303 14 0 0
  1. The values represent total numbers of REP sequences from Table 1 in different strains´ genomes. The values are denoted in bold and underlined in cases where RAYT gene associated with a particular REP class is present in the genome. Presence of pseudogenized RAYT genes, containing nonsense or frameshift mutations or deletions, is denoted by italics. The phylogenetic groups are marked with letters A to G as in Figure 1. The names of strains whose complete genomic sequences were determined are in bold.
  2. * - as in Table 1.
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