Table 1 |
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|
Putative horizontally transferred genes and pseudogenes |
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|
Species |
Gene |
Pseudogene |
Failed transfer index |
||
|
|
|
|
|||
|
All |
HT |
All |
HT |
||
|
|
|||||
|
Archaea |
|||||
|
A. pernix |
615 |
45 |
4 |
2 |
6.8 |
|
S. solfataricus |
2,235 |
231 |
48 |
6 |
1.2 |
|
S. tokodaii |
1,797 |
185 |
35 |
19 |
5.3 |
|
P. aerophilum |
1,855 |
171 |
10 |
3 |
3.3 |
|
Halobacterium sp. NRC-1 |
1,383 |
100 |
1 |
1 |
13.8 |
|
M. thermautotrophicus |
1,350 |
122 |
5 |
5 |
11.1 |
|
M. jannaschii |
1,280 |
106 |
15 |
8 |
6.4 |
|
P. abyssi |
891 |
75 |
6 |
2 |
4.0 |
|
P. horikoshii |
553 |
50 |
8 |
0 |
0.0 |
|
T. acidophilum |
1,169 |
106 |
5 |
4 |
8.8 |
|
T. volcanium |
1,061 |
100 |
16 |
6 |
4.0 |
|
Non-pathogenic bacteria |
|||||
|
A. aeolicus |
1,244 |
107 |
3 |
0 |
0.0 |
|
Synechocystis sp. PCC 6803 |
2,696 |
237 |
5 |
1 |
2.3 |
|
Nostoc sp. PCC 7120 |
3,672 |
332 |
10 |
2 |
2.2 |
|
S. coelicolor |
6,012 |
536 |
14 |
4 |
3.2 |
|
B. halodurans |
3,279 |
299 |
11 |
3 |
3.0 |
|
B. subtilis |
1223 |
102 |
44 |
3 |
0.8 |
|
L. innocua |
2,924 |
263 |
1 |
1 |
11.1 |
|
C. acetobutylicum |
3,129 |
295 |
5 |
1 |
2.1 |
|
L. lactis subsp. lactis |
1,870 |
156 |
13 |
2 |
1.8 |
|
C. vibrioides |
2,699 |
231 |
6 |
1 |
1.9 |
|
M. loti |
5,235 |
476 |
14 |
3 |
2.4 |
|
S. meliloti |
2,985 |
240 |
9 |
6 |
8.3 |
|
E. coli K12 |
2,897 |
230 |
63 |
23 |
4.6 |
|
T. maritima |
1,445 |
137 |
8 |
0 |
0.0 |
|
D. radiodurans |
1,964 |
134 |
9 |
1 |
1.6 |
|
Pathogenic bacteria |
|||||
|
Buchnera sp. APS |
477 |
42 |
5 |
2 |
4.5 |
|
U. urealyticum |
467 |
40 |
2 |
1 |
5.8 |
|
M. pneumoniae |
610 |
55 |
30 |
19 |
7.0 |
|
B. burgdorferi |
590 |
63 |
1 |
0 |
0.0 |
|
M. pulmonis |
595 |
53 |
2 |
1 |
5.6 |
|
C. trachomatis |
597 |
67 |
3 |
1 |
3.0 |
|
C. muridarum |
815 |
81 |
2 |
0 |
0.0 |
|
R. prowazekii |
504 |
49 |
7 |
1 |
1.5 |
|
T. pallidum |
727 |
64 |
12 |
5 |
4.7 |
|
C. pneumoniae J138 |
839 |
74 |
1 |
0 |
0.0 |
|
C. pneumoniae AR39 |
831 |
70 |
5 |
1 |
2.4 |
|
C. pneumoniae CWL029 |
845 |
71 |
7 |
0 |
0.0 |
|
R. conorii |
695 |
67 |
9 |
0 |
0.0 |
|
M. leprae |
1,440 |
119 |
271 |
53 |
2.4 |
|
C. jejuni |
1,291 |
108 |
2 |
0 |
0.0 |
|
H. pylori J99 |
856 |
70 |
5 |
1 |
2.4 |
|
H. pylori 26695 |
1,055 |
90 |
13 |
3 |
2.7 |
|
S. pyogenes M1 GAS |
1,348 |
108 |
14 |
1 |
0.9 |
|
S. pneumoniae |
1,632 |
114 |
54 |
2 |
0.5 |
|
N. meningitidis Z2491 |
1,432 |
112 |
26 |
4 |
2.0 |
|
P. multocida |
1,035 |
96 |
7 |
2 |
3.1 |
|
N. meningitidis MC58 |
1,466 |
121 |
44 |
14 |
3.9 |
|
X. fastidiosa |
1,550 |
152 |
15 |
1 |
0.7 |
|
S. aureus subsp. aureus N315 |
1,557 |
140 |
4 |
2 |
5.6 |
|
S. aureus subsp. aureus Mu50 |
1,563 |
138 |
4 |
2 |
5.7 |
|
L. monocytogenes |
2,799 |
231 |
2 |
0 |
0.0 |
|
C. perfringens |
1,943 |
165 |
2 |
0 |
0.0 |
|
B. melitensis |
2,948 |
216 |
5 |
0 |
0.0 |
|
R. solanacearum |
3,032 |
252 |
5 |
0 |
0.0 |
|
V. cholerae |
2,846 |
216 |
24 |
5 |
2.7 |
|
M. tuberculosis CDC1551 |
2,837 |
262 |
49 |
7 |
1.5 |
|
M. tuberculosis H37Rv |
1,446 |
130 |
38 |
4 |
1.2 |
|
Y. pestis |
3,533 |
282 |
51 |
4 |
1.0 |
|
S. typhi CT18 |
3,986 |
338 |
147 |
18 |
1.4 |
|
S. typhimurium LT2 |
4,308 |
349 |
22 |
5 |
2.8 |
|
E. coli O157:H7 |
3,424 |
266 |
120 |
16 |
1.7 |
|
E. coli O157:H7 EDL933 |
4,322 |
353 |
73 |
5 |
0.8 |
|
P. aeruginosa |
3,716 |
281 |
7 |
3 |
5.7 |
|
Total |
123,420 |
10,571 |
1,458 |
290 |
2.3 |
|
|
|||||
|
All genes and pseudogenes and the fraction having atypical codon-position-specific GC contents in the 64 genomes studied. The failed horizontal transfer index was computed as described in Materials and methods. |
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|
Liu et al. Genome Biology 2004 5:R64 doi:10.1186/gb-2004-5-9-r64 |
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