Table 1 Rates of the four types of genome dynamics events a
From: Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
ATGC | Genera | Gain | Loss | Expansion | Reduction | ||||
|---|---|---|---|---|---|---|---|---|---|
Site | Gene | Site | Gene | Site | Gene | Site | Gene | ||
ATGC001 | Enterobacteria | 18563 | 17.3 | 50517 | 47.1 | 1864 | 1.7 | 4405 | 4.1 |
ATGC002 | Enterobacter–Klebsiella | 25866 | 24.5 | 6448 | 6.1 | 1914 | 1.8 | 237 | 0.2 |
ATGC003 | Streptococcus | 11894 | 11.8 | 53500 | 53.0 | 1368 | 1.4 | 5092 | 5.0 |
ATGC004 | Streptococcus | 5633 | 5.5 | 29233 | 28.5 | 1601 | 1.6 | 2984 | 2.9 |
ATGC005 | Streptococcus | 11940 | 11.3 | 42215 | 40.0 | 3755 | 3.6 | 2380 | 2.3 |
ATGC014 | Bacillus | 25485 | 25.5 | 77488 | 77.7 | 3895 | 3.9 | 6908 | 6.9 |
ATGC015 | Bacillus | 6521 | 6.6 | 25293 | 25.5 | 804 | 0.8 | 1343 | 1.4 |
ATGC021 | Chlamydia | 16346 | 14.0 | 25968 | 22.3 | 419 | 0.4 | 240 | 0.2 |
ATGC022 | Chlamydia–Chlamydophila | 5434 | 5.2 | 11202 | 10.8 | 1213 | 1.2 | 524 | 0.5 |
ATGC025 | Mycobacterium | 50823 | 45.9 | 74868 | 67.6 | 5109 | 4.6 | 3708 | 3.3 |
ATGC033 | Mycoplasma | 5865 | 4.6 | 8335 | 6.6 | 2484 | 2.0 | 548 | 0.4 |
ATGC046 | Rickettsia | 6677 | 7.4 | 23674 | 26.4 | 325 | 0.4 | 750 | 0.8 |
ATGC052 | Helicobacter | 3733 | 3.6 | 8293 | 8.0 | 288 | 0.3 | 974 | 0.9 |
ATGC054 | Staphylococcus | 21512 | 19.9 | 146937 | 135.8 | 2924 | 2.7 | 21696 | 20.1 |
ATGC056 | Lactobacillus | 3417 | 3.3 | 17553 | 17.2 | 1094 | 1.1 | 314 | 0.3 |
ATGC067 | Corynebacterium | 10013 | 9.0 | 146236 | 131.5 | 1582 | 1.4 | 734 | 0.7 |
ATGC068 | Corynebacterium | 5338 | 4.9 | 82891 | 76.0 | 2335 | 2.1 | 4414 | 4.0 |
ATGC072 | Pseudomonas | 10467 | 9.2 | 25516 | 22.5 | 2162 | 1.9 | 1766 | 1.6 |
ATGC082 | Clostridium | 7223 | 6.6 | 82676 | 75.8 | 3745 | 3.4 | 1030 | 0.9 |
ATGC089 | Burkholderia | 39593 | 35.5 | 252406 | 226.3 | 4988 | 4.5 | 3417 | 3.1 |
ATGC090 | Burkholderia | 15276 | 13.6 | 54192 | 48.2 | 4582 | 4.1 | 1644 | 1.5 |
ATGC094 | Sulfolobus | 5956 | 6.1 | 42639 | 43.4 | 3931 | 4.0 | 1643 | 1.7 |
ATGC105 | Bifidobacterium | 10383 | 8.3 | 11148 | 9.0 | 655 | 0.5 | 817 | 0.7 |
ATGC106 | Bifidobacterium | 11039 | 8.9 | 16473 | 13.3 | 742 | 0.6 | 812 | 0.7 |
ATGC109 | Listeria | 7650 | 7.5 | 3411 | 3.4 | 551 | 0.5 | 207 | 0.2 |
ATGC121 | Shewanella | 8576 | 7.3 | 5340 | 4.5 | 973 | 0.8 | 348 | 0.3 |
ATGC128 | Yersinia | 20234 | 17.5 | 39460 | 34.2 | 2391 | 2.1 | 2369 | 2.1 |
ATGC135 | Xanthomonas | 13993 | 12.2 | 31495 | 27.4 | 3413 | 3.0 | 1518 | 1.3 |
ATGC137 | Brucella–Ochrobactrum | 16268 | 15.6 | 25177 | 24.1 | 1968 | 1.9 | 1033 | 1.0 |
ATGC138 | Neisseria | 7278 | 6.4 | 29817 | 26.4 | 990 | 0.9 | 2638 | 2.3 |
ATGC139 | Francisella | 2324 | 2.0 | 9075 | 7.7 | 546 | 0.5 | 401 | 0.3 |
ATGC144 | Campylobacter | 14997 | 14.6 | 6085 | 5.9 | 1365 | 1.3 | 109 | 0.1 |
ATGC153 | Acinetobacter | 5416 | 5.1 | 54454 | 51.7 | 3747 | 3.6 | 2029 | 1.9 |
ATGC163 | Propionibacterium | 2948 | 2.7 | 13223 | 12.0 | 446 | 0.4 | 145 | 0.1 |
ATGC186 | Legionella | 2082 | 1.9 | 99232 | 89.9 | 3546 | 3.2 | 1647 | 1.5 |
Median | Â | 10013 | 8.3 | 29233 | 26.4 | 1864 | 1.7 | 1343 | 1.3 |