Table 1.
Contents of DEG 15
| Domain of life | Organism | No. of essential genomic elements | Method | Saturated | Reference | Notea | |
|---|---|---|---|---|---|---|---|
| Coding | Noncoding | ||||||
| Acinetobacter baumannii ATCC 17978 | 453 | 59 | INSeq | Yes | (24) | ||
| Acinetobacter baumannii ATCC 17978 | 157 | 1 | INSeq | Yes | (24) | In the mouse lung | |
| Acinetobacter baylyi | 499 | Single-gene knockout | Yes | (57) | Minimal medium | ||
| Aggregatibacter actinomycetemcomitans | 59 | Tn-seqb | Yes | (58) | For coinfection with sympatric and allopatric microbes | ||
| Agrobacterium fabrum str. C58 | 361 | 11 | Tn-seq | Yes | (25) | ||
| Bacillus subtilis | 261 | 2 | Single-gene knockout | Yes | (59) | ||
| Bacteria | Bacillus thuringiensis BMB171 | 516 | Tn-seq | Yes | (60) | ||
| Bacteroides fragilis | 550 | Tn-seq | Yes | (61) | |||
| Bacteroides thetaiotaomicron | 325 | INSeq | Yes | (21) | |||
| Bifidobacterium breve | 453 | TraDIS | Yes | (62) | |||
| Brevundimonas subvibrioides | 448 | Tn-seq | Yes | (25) | |||
| Brevundimonas subvibrioides ATCC 15264 | 412 | 35 | Tn-seq | Yes | (25) | ||
| Burkholderia cenocepacia J2315 | 383 | TraDIS | Yes | (63) | |||
| Burkholderia cenocepacia K56–2 | 508 | Tn-seq | Yes | (64) | |||
| Burkholderia pseudomallei K96243 | 505 | TraDIS | Yes | (65) | |||
| Burkholderia thailandensis | 406 | Tn-seq | Yes | (66) | |||
| Campylobacter jejuni | 233 | Tn-seq | Yes | (67) | |||
| Campylobacter jejuni subsp. jejuni 81–176 | 384 | Tn-seq | Yes | (68) | |||
| Campylobacter jejuni subsp. jejuni NCTC 11168 | 166 | Tn-seq | Yes | (68) | |||
| Caulobacter crescentus | 480 | 532 | Tn-seq | Yes | (69) | ||
| Escherichia coli | 620 | Genetic footprinting | Yes | (70) | |||
| Escherichia coli | 303 | Single-gene knockout | Yes | (71) | |||
| Escherichia coli | 379 | CRISPR | Yes | (72) | |||
| Escherichia coli O157:H7 | 1265 | 37 | Tn-seq | Yes | (26) | ||
| Escherichia coli ST131 strain EC958 | 315 | TraDIS | Yes | (73) | |||
| Francisella novicida | 396 | Tn-seq | Yes | (74) | |||
| Francisella tularensis Schu S4 | 453 | TraDIS | Yes | (75) | |||
| Haemophilus influenzae | 667 | Genetic footprinting | Yes | (76) | |||
| Helicobacter pylori | 344 | MATT | Yes | (77) | |||
| Mycobacterium avium subsp. hominissuis strain MAC109 | 230 | Tn-seq | Yes | (78) | |||
| Mycobacterium tuberculosis | 614 | TraSH | Yes | (79) | |||
| Mycobacterium tuberculosis | 774 | Tn-seq | Yes | (80) | |||
| Mycobacterium tuberculosis | 742 | 35 | Tn-seq | Yes | (27) | ||
| Mycobacterium tuberculosis | 461 | Tn-seq | Yes | (81) | |||
| Mycobacterium tuberculosis | 601 | Tn-seq | Yes | (82) | |||
| Mycoplasma genitalium | 382 | Tn-seq | Yes | (19,83) | |||
| Mycoplasma pneumoniae | 342 | 34 | Tn-seq | Yes | (28) | ||
| Mycoplasma pulmonis | 321 | Tn-seq | Yes | (84) | |||
| Neisseria gonorrhoeae MS11 | 751 | Tn-seq | Yes | (85) | |||
| Porphyromonas gingivalis | 463 | Tn-seq | Yes | (86) | |||
| Porphyromonas gingivalis ATCC 33277 | 281 | Tn-seq | Yes | (87) | |||
| Providencia stuartii strain BE2467 | 496 | 25 | Tn-seq | Yes | (88) | ||
| Pseudomonas aeruginosa | 335 | TraSH | Yes | (89) | |||
| Pseudomonas aeruginosa | 117 | Tn-seq | Yes | (23) | |||
| Pseudomonas aeruginosa | 321 | Tn-seq | Yes | (90) | |||
| Pseudomonas aeruginosa PAO1 | 336 | Tn-seq | Yes | (91) | |||
| Pseudomonas aeruginosa PAO1 | 551 | Tn-seq | Yes | (92) | |||
| Ralstonia solanacearum GMI1000 | 465 | Tn-seq | Yes | (93) | |||
| Rhodobacter sphaeroides | 493 | Tn-seq | Yes | (94) | |||
| Rhodopseudomonas palustris CGA009 | 522 | Tn-seq | Yes | (95) | |||
| Salmonella enterica Typhimurium | 306 | 15 | TraDIS | Yes | (29) | ||
| Salmonella entericaserovar Typhi | 356 | TraDIS | Yes | (20) | |||
| Salmonella entericaserovar Typhi Ty2 | 358 | 24 | TraDIS | Yes | (29) | ||
| Salmonella entericaserovar Typhimurium | 105 | Tn-seq | Yes | (96) | |||
| Salmonella entericaserovar Typhimurium SL1344 | 353 | 23 | TraDIS | Yes | (29) | ||
| Salmonella typhimurium | 490 | Insertion-duplication | Yes | (97) | |||
| Shewanella oneidensis | 403 | Transposon mutagenesis | Yes | (98) | |||
| Sphingomonas wittichii | 579 | 32 | Tn-seq | Yes | (30) | ||
| Staphylococcus aureus | 302 | Antisense RNA | No | (99,100) | |||
| Staphylococcus aureus | 351 | TMDH | Yes | (101) | |||
| Staphylococcus aureus subsp. aureus MRSA252 | 295 | Tn-seq | Yes | (102) | |||
| Staphylococcus aureus subsp. aureus MSSA476 | 305 | Tn-seq | Yes | (102) | |||
| Staphylococcus aureus subsp. aureus MW2 | 256 | Tn-seq | Yes | (102) | |||
| Staphylococcus aureus subsp. aureus NCTC 8325 | 288 | Tn-seq | Yes | (102) | |||
| Staphylococcus aureus subsp. aureus USA300 TCH1516 | 295 | Tn-seq | Yes | (102) | |||
| Streptococcus agalactiae A909 | 317 | Tn-seq | Yes | (103) | |||
| Streptococcus mutans UA159 | 197 | 6 | Tn-seq | Yes | (104) | ||
| Streptococcus pneumoniae | 113 | Insertion-duplication | No | (105) | |||
| Streptococcus pneumoniae | 133 | allelic replacement mutagenesis | No | (106) | |||
| Streptococcus pneumoniae | 72 | Tn-seq | Yes | (31) | |||
| Streptococcus pyogenes MGAS5448 | 227 | Tn-seq | Yes | (107) | |||
| Streptococcus pyogenes NZ131 | 241 | Tn-seq | Yes | (107) | |||
| Streptococcus sanguinis | 218 | Single-gene knockout | Yes | (108) | |||
| Streptococcus suis | 361 | Tn-seq | Yes | (109) | |||
| Synechococcus elongatus PCC 7942 | 682 | 34 | Tn-seq | Yes | (110) | ||
| Vibrio cholerae | 789 | Tn-seq | Yes | (111) | |||
| Vibrio cholerae C6706 | 343 | Tn-seq | Yes | (112) | |||
| Vibrio vulnificus | 316 | Tn-seq | Yes | (113) | |||
| Archaea | Methanococcus maripaludis | 519 | Tn-seq | Yes | (32) | ||
| Sulfolobus islandicus M.16.4 | 441 | Tn-seq | Yes | (33) | |||
| Eukaryotes | Arabidopsis thaliana | 358 | Single-gene knockout | No | (54) | ||
| Aspergillus fumigatus | 35 | Conditional promoter replacement | No | (114) | |||
| Bombyx mori | 1006 | CRISPR | Yes | (115) | |||
| Caenorhabditis elegans | 44 | Genetic mapping | No | (116) | |||
| Caenorhabditis elegans | 294 | RNA interference | No | (56) | |||
| Danio rerio | 315 | Insertional mutagenesis | No | (117) | |||
| Drosophila melanogaster | 376 | P-element insertion | No | (118) | |||
| Homo sapiens | 2452 | OMIM annotationc | No | (119) | |||
| Homo sapiens | 1562 | CRISPR | Yes | (14) | Stem cells | ||
| Homo sapiens | 1593 | CRISPR | Yes | (14) | HAP1 cells | ||
| Homo sapiens | 1690 | CRISPR | Yes | (120) | Core essential genes among 17 cell lines | ||
| Homo sapiens | 3230 | Exome sequencing | Yes | (18) | |||
| Homo sapiens | 2054 | CRISPR | Yes | (12) | KBM7 cells | ||
| Homo sapiens | 2181 | CRISPR | Yes | (12) | HAP1 cells | ||
| Homo sapiens | 1878 | CRISPR | Yes | (11) | KBM7 cells | ||
| Homo sapiens | 1660 | CRISPR | Yes | (11) | K562 cells | ||
| Homo sapiens | 1630 | CRISPR | Yes | (11) | Jiyoye cells | ||
| Homo sapiens | 1461 | CRISPR | Yes | (11) | Raji cells | ||
| Homo sapiens | 1196 | CRISPR | Yes | (13) | A375 cells | ||
| Homo sapiens | 1892 | CRISPR | Yes | (13) | DLD1 cells | ||
| Homo sapiens | 2196 | CRISPR | Yes | (13) | GBM cells | ||
| Homo sapiens | 2073 | CRISPR | Yes | (13) | HCT116 cells | ||
| Homo sapiens | 386 | shRNA | Yes | (13) | HCT116 cells | ||
| Homo sapiens | 1696 | CRISPR | Yes | (13) | HeLa cells | ||
| Homo sapiens | 2038 | CRISPR | Yes | (13) | RPE1 cells | ||
| Homo sapiens | 92 | Functional genomics | No | (15) | Podocytes | ||
| Homo sapiens | 79 | CRISPR | Yes | (16) | Hepatocellular carcinoma | ||
| Homo sapiens | 191 | CRISPR | Yes | (17) | K562 cells | ||
| Komagataella phaffii GS115 | 753 | Tn-seq | Yes | (121) | |||
| Mus musculus | 435 | Single-gene knockout | No | (53) | Embryonic lethality | ||
| Mus musculus | 1933 | Single-gene knockout | No | (52) | Preweaning lethality | ||
| Mus musculus | 2136 | MGI annotationd | No | (122) | |||
| Plasmodium falciparum | 2680 | transposon mutagenesis | Yes | (34) | |||
| Saccharomyces cerevisiae | 1110 | Single-gene knockout | Yes | (123) | Six conditions including minimal medium | ||
| Schizosaccharomyces pombe | 1260 | Single-gene knockout | Yes | (124) | Rich medium | ||
aBacteria were cultured in rich media, unless otherwise indicated.
bTn-seq is a method that performs saturated transposon mutagenesis followed by parallel sequencing to determine the transposon integration sites. Tn-seq has many variants under different names, such as insertion sequencing (INSeq), Transposon Directed Insertion Sequencing (TraDIS), high-throughput insertion tracking by deep sequencing (HITS), transposon sequencing, Microarray tracking of transposon mutants (MATT), Transposon site hybridization (TraSH), transposon mutagenesis followed by Sanger sequencing, transposon mutagenesis followed by genetic footprinting, transposon-site hybridization, Transposon-Mediated Differential Hybridisation (TMDH).
cOMIM: Online Mendelian Inheritance in Man (125).
dMGI: Mouse Genome Informatics (126).