Table 1 Putative horizontally transferred genes and pseudogenes
Species | Gene | Pseudogene | Failed transfer index | ||
|---|---|---|---|---|---|
| Â | All | HT | All | HT | Â |
Archaea | Â | Â | Â | Â | Â |
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 | Â | Â | Â | Â | Â |
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 | Â | Â | Â | Â | Â |
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 |