Table 1.
Genomes used in this study
| GPID | Strain | Size (bp) | No of genes | Gene density (genes/Kbp) | No of contigs | Accession number | Quality score | Pathotype, serotype, other characteristics | Reference |
|---|---|---|---|---|---|---|---|---|---|
| 225 | E. coli K12 MG1655 | 4,639,675 | 4,149 | 0.894 | 1 | U00096 | 1 | Commensal, K12 | [2] |
| 226 | E. coli 0157:H7 Sakai | 5,594,477 | 5,230 | 0.934 | 3 | BA000007 | 1 | EHEC, O157:H7 | [15] |
| 259 | E. coli 0157:H7 EDL933 | 5,620,522 | 5,312 | 0.945 | 2 | AE005174 | 2 | EHEC, O157:H7 | [33] |
| 313 | E. coli CFT073 | 5,231,428 | 5,339 | 1.020 | 1 | AE014075 | 1 | UPEC, O6:K2:H1 | [45] |
| 13959 | E. coli HS | 4,643,538 | 4,378 | 0.942 | 1 | CP000802 | 1 | Commensal, O9 | [37] |
| 13960 | E. coli E24377A | 5,249,288 | 4,749 | 0.904 | 7 | CP000800 | 1 | ETEC, O139:H28 | [37] |
| 15572 | E. coli B7A | 5,300,242 | 4,648 | 0.876 | 289 | AAJT00000000 | 4 | ETEC, O148:H28 | [37] |
| 15576 | E. coli F11 | 5,215,961 | 4,704 | 0.901 | 119 | AAJU00000000 | 3 | ExPEC, O6:H31 | [37] |
| 15577 | E. coli E22 | 5,528,238 | 5,105 | 0.923 | 127 | AAJV00000000 | 3 | EPEC, O103:H2 | [37] |
| 15578 | E. coli E110019 | 5,376,211 | 4,934 | 0.917 | 137 | AAJW00000000 | 3 | EPEC, O111:H9 | [37] |
| 15639 | E. coli 53638 | 5,371,790 | 4,803 | 0.894 | 4 | AAKB00000000 | 2 | EIEC, O144 | TIGR |
| 16193 | E. coli 101-1 | 4,979,767 | 4,607 | 0.925 | 91 | AAMK00000000 | 3 | EAEC, O-:H10 | [18, 37] |
| 16235 | E. coli 536 | 4,938,920 | 4,620 | 0.935 | 1 | CP000247 | 1 | UPEC, O6:K15:H31 | [7] |
| 16259 | E. coli UTI89 | 5,179,971 | 5,021 | 0.969 | 2 | CP000243 | 1 | UPEC | [5] |
| 16351 | E. coli K12 W3110 | 4,646,332 | 4,226 | 0.909 | 1 | AP009048 | 1 | Commensal, K12 | [16] |
| 16718 | E. coli APECO1 | 5,497,653 | 4,428 | 0.801 | 3 | CP000468 | 1 | APEC, O1:K1:H7 | [21] |
| 18083 | E. coli ATCC8739 | 4,746,218 | 4,200 | 0.884 | 1 | CP000946 | 1 | K12 derivative | DOE JGI-PGF |
| 18057 | E. coli SE11 | 5,155,626 | 4,679 | 0.907 | 7 | AP009240 | 1 | Commensal, O152:H28 | [32] |
| 18281 | E. coli B str. REL606 | 4,629,812 | 4,205 | 0.908 | 1 | CP000819 | 1 | Commensal, strain B | [19] |
| 19053 | E. coli SE15 | 4,839,683 | 4,488 | 0.927 | 2 | AP009378 | 1 | Commensal, O150:H5 | [42] |
| 19469 | E. coli SMS-3-5 | 5,215,377 | 4,743 | 0.909 | 5 | CP000970 | 1 | Environmental isolate | [11] |
| 20079 | E. coli K12 DH10B | 4,686,137 | 4,126 | 0.880 | 1 | CP000948 | 1 | K12 derivative | [8] |
| 20713 | E. coli BL21(DE3) | 4,557,508 | 4,157 | 0.912 | 1 | CP001509 | 1 | Commensal, strain B phylogroup | Korea Research Institure of Bioscience and Biotechnology |
| 27737 | E. coli 0157:H7 EC4042 | 5,617,728 | 5,232 | 0.931 | 4 | ABHM00000000 | 2 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27733 | E. coli 0157:H7 EC4045 | 5,660,958 | 5,343 | 0.943 | 8 | ABHL00000000 | 2 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27745 | E. coli 0157:H7 EC4076 | 5,705,645 | 5,342 | 0.936 | 135 | ABHQ00000000 | 2 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27743 | E. coli 0157:H7 EC4113 | 5,655,847 | 5,005 | 0.884 | 231 | ABHP00000000 | 3 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27739 | E. coli 0157:H7 EC4115 | 5,704,171 | 5,315 | 0.931 | 1 | CP001164 | 1 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27741 | E. coli 0157:H7 EC4196 | 5,620,606 | 5,072 | 0.902 | 186 | ABHO00000000 | 3 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27735 | E. coli 0157:H7 EC4206 | 5,629,932 | 5,202 | 0.923 | 7 | ABHK00000000 | 2 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27749 | E. coli 0157:H7 EC4401 | 5,733,133 | 5,185 | 0.904 | 186 | ABHR00000000 | 3 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27751 | E. coli 0157:H7 EC4486 | 5,933,166 | 5,429 | 0.915 | 165 | ABHS00000000 | 3 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27753 | E. coli 0157:H7 EC4501 | 5,677,181 | 5,124 | 0.902 | 250 | ABHT00000000 | 4 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27755 | E. coli 0157:H7 EC508 | 5,656,666 | 5,019 | 0.887 | 272 | ABHW00000000 | 4 | EHEC, O157:H7 | J. Craig Venter Institute |
| 27757 | E. coli 0157:H7 EC869 | 5,731,065 | 5,220 | 0.910 | 147 | ABHU00000000 | 3 | EHEC, O157:H7 | J. Craig Venter Institute |
| 28847 | E. coli 0157:H7 TW14588 | 5,670,297 | 5,803 | 1.023 | 10 | ABKY00000000 | 2 | EHEC, O157:H7 | J. Craig Venter Institute |
| 28965 | E. coli BL21 (DE3) | 4,557,041 | 4,087 | 0.896 | 1 | AM946981 | 1 | Commensal, strain B | Australian Center for Biopharmaceutical Technology |
| 30031 | E. coli DH1 | 4,630,707 | 4,160 | 1 | CP001637 | 1 | K12 derivative | DOE JGI-PGF | |
| 30681 | E. coli BL21(DE3) | 4,570,938 | 4,228 | 0.949 | 1 | CP001665 | 1 | Commensal, strain B | DOE JGI-PGF |
| 32571 | E. coli 0127:H6 E2348/69 | 5,069,678 | 4,554 | 0.898 | 3 | FM180568 | 1 | EPEC, O127:H6 | [17] |
| 33413 | E. coli 55989 | 5,154,862 | 4,763 | 0.923 | 1 | CU928145 | 1 | EAEC | [43] |
| 33373 | E. coli IAI1 | 4,700,560 | 4,353 | 0.926 | 1 | CU928160 | 1 | Commensal, O8 | [43] |
| 33375 | E. coli S88 | 5,032,268 | 4,696 | 0.933 | 2 | CU928161 | 1 | ExPEC, O45:K1:H7 | [43] |
| 33409 | E. coli ED1a | 5,209,548 | 4,915 | 0.943 | 1 | CU928162 | 1 | Commensal, O81 | [43] |
| 33411 | E. coli IAI39 | 5,132,068 | 4,732 | 0.922 | 1 | CU928164 | 1 | UPEC, O7:K1 | [43] |
| 33415 | E. coli UMN026 | 5,324,391 | 4,826 | 0.906 | 3 | CU928163 | 1 | UPEC, O7:K1 | [43] |
| 33775 | E. coli BW2952 | 4,578,159 | 4,084 | 0.892 | 1 | CP001396 | 1 | K12 derivative | [10] |
| 41013 | E. coli 0103:H2 12009 | 5,524,860 | 5,121 | 0.926 | 2 | AP010958 | 1 | EHEC, O103:H2 | [31] |
| 41021 | E. coli O26:H11 11368 | 5,851,458 | 5,516 | 0.942 | 4 | AP010958 | 1 | EHEC, O26:H11 | [31] |
| 41023 | E. coli 0111:H- 11128 | 5,766,081 | 5,407 | 0.937 | 6 | AP010960 | 1 | EHEC, O111:H- | [31] |
| E. coli 0103 Oslo | 4,960,076 | 4,571 | 0.921 | 153 | Unpublished | 4 | EHEC, O103 | Norwegian Vet Institute | |
| E. coli LANL ECA | 5,489,845 | 4,750 | 0.865 | 64 | Unpublished | 3 | EHEC, O157:H7 | Los Alamos National Lab | |
| E. coli LANL ECF | 5,556,393 | 4,813 | 0.866 | 63 | Unpublished | 3 | EHEC, O157:H7 | Los Alamos National Lab | |
| 310 | S. flexneri 2a 301 | 4,828,821 | 4,177 | 0.865 | 1 | AE005674 | 1 | Dysentery, Serogroup 2a | [20] |
| 408 | S. flexneri 2a 2457T | 4,599,354 | 4,061 | 0.882 | 1 | AE014073 | 1 | Dysentery, Serogroup 2a | [44] |
| 16375 | S. flexneri 5 8401 | 4,574,284 | 4,115 | 0.899 | 1 | CP000266 | 1 | Dysentery, Serogroup 5 | [29] |
| 15637 | S. boydii CDC 3083-94 | 4,874,659 | 4,246 | 0.871 | 1 | CP001063 | 1 | Dysentery, Serogroup 1 | [35] |
| 13146 | S. boydii Sb227 | 4,646,520 | 4,134 | 0.889 | 1 | CP000036 | 1 | Dysentery, Serogroup 4 | [41] |
| 13145 | S. dysenteriae Sd197 | 4,560,911 | 4,271 | 0.936 | 1 | CP000034 | 1 | Dysentery, Serogroup 1 | [41] |
| 16194 | S. dysenteriae 1012 | 5,235,535 | 4,419 | 0.846 | 189 | AAMJ00000000 | 3 | Dysentery, Serotype 4 | TIGR, [34] |
| 13151 | S. sonnei Ss046 | 5,055,316 | 4,219 | 0.834 | 1 | CP000038 | 1 | Dysentery | [47] |
| 28851 | E. albertii TW07627 | 4,698,533 | 4,386 | 0.933 | 64 | ABKX01000000 | 3 | Enteropathogenic | J. Craig Venter Institute |
| 33369 | E. fergusonii ATCC 35469 | 4,643,861 | 4,319 | 0.930 | 2 | CU928158 | 1 | Commensal | [43] |
| 241 | S. enterica serovar Typhimurium LT2 | 4,951,371 | 4,525 | 0.913 | 2 | AE006468 | 1 | Enteropathogenic | [27] |
GPID genome project identifier at NCBI (http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi).
EPEC enteropathogenic, UPEC uropathogenic, ExPEC extra-intestinal pathogenic, ETEC enterotoxigenic, EIEC enteroinvasive, EAEC enteroaggregative, APEC avian pathogenic E. coli