Table 3.
The abundances of 22 REP classes in genomes of 63 sequenced fluorescent pseudomonads
| 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 | |
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.
* - as in Table 1.