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| ''[[Streptococcus pneumoniae]]'' Rx-1||Targeted||Clones||Colony formation||2,043||234||113||n/a||c||<ref name="Thanassi2002">{{cite journal | vauthors = Thanassi JA, Hartman-Neumann SL, Dougherty TJ, Dougherty BA, Pucci MJ | title = Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae | journal = Nucleic Acids Research | volume = 30 | issue = 14 | pages = 3152–62 | date = July 2002 | pmid = 12136097 | pmc = 135739 | doi = 10.1093/nar/gkf418 }}</ref>
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| ''[[Streptococcus pneumoniae]]'' D39||Targeted||Clones||Colony formation||2,043||560||133||n/a||c||<ref name="Song2005">{{cite journal | vauthors = Song JH, Ko KS, Lee JY, Baek JY, Oh WS, Yoon HS, Jeong JY, Chun J | title = Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis | journal = Molecules and Cells | volume = 19 | issue = 3 | pages = 365–74 | date = June 2005 | doi = 10.1016/S1016-8478(23)13181-5 | pmid = 15995353 | doi-access = free }}</ref>
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| ''[[Streptococcus pyogenes]]'' 5448 || Random || Transposon || Tn-seq || 1,865 ||?|| 227 ||12%||---||<ref name="LeBreton">{{cite journal | vauthors = Le Breton Y, Belew AT, Valdes KM, Islam E, Curry P, Tettelin H, Shirtliff ME, El-Sayed NM, McIver KS | title = Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes | journal = Scientific Reports | volume = 5 | pages = 9838 | date = May 2015 | pmid = 25996237 | pmc = 4440532 | doi = 10.1038/srep09838 | bibcode = 2015NatSR...5E9838L }}</ref>
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| ''[[Mycobacterium tuberculosis]]'' H37Rv ||Targeted||CRISPRi||NG-Sequencing|| 4,052 ||33,15||737||18%||---||<ref name="Bosch2021">{{cite journal | vauthors = Bosch, B, DeJesus, MA, Poulton, NC, Zhang, W, Engelhart, CA, Zaveri, A, Lavalette, S, Ruecker, N, Trujillo, C, Wallach, JB, Li, S, Ehrt, S, Chait, BT, Schnappinger, S, Rock, JM | title = Genome-wide gene expression tuning reveals diverse vulnerabilities of M. tuberculosis | journal = Cell | volume = 184 | issue = 17 | pages = 4579–4592.e24 | date = July 2021 | pmid = 34297925 | pmc = 8382161 | doi = 10.1016/j.cell.2021.06.033 }}</ref>
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| ''[[Bacillus subtilis]]'' 168||Targeted||Clones||Colony formation||4,105||3,830||261||7%||a,d,g||<ref name="Kobayashi2003">{{cite journal | vauthors = Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauël C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Séror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N | display-authors = 6 | title = Essential Bacillus subtilis genes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 100 | issue = 8 | pages = 4678–83 | date = April 2003 | pmid = 12682299 | pmc = 153615 | doi = 10.1073/pnas.0730515100 | bibcode = 2003PNAS..100.4678K | doi-access = free }}</ref><ref name="Commichau2013">{{cite journal | vauthors = Commichau FM, Pietack N, Stülke J | s2cid = 23769853 | title = Essential genes in Bacillus subtilis: a re-evaluation after ten years | journal = Molecular BioSystems | volume = 9 | issue = 6 | pages = 1068–75 | date = June 2013 | pmid = 23420519 | doi = 10.1039/c3mb25595f | url =
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| ''[[Escherichia coli]]'' K-12 MG1655||Random||Population||Footprint-PCR||4,308||3,126||620||14%||---||<ref name="Gerdes2003">{{cite journal | vauthors = Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási AL, Oltvai ZN, Osterman AL | display-authors = 6 | title = Experimental determination and system level analysis of essential genes in Escherichia coli MG1655 | journal = Journal of Bacteriology | volume = 185 | issue = 19 | pages = 5673–84 | date = October 2003 | pmid = 13129938 | pmc = 193955 | doi = 10.1128/JB.185.19.5673-5684.2003 }}</ref>
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'''Minimal genomes'''. It was also thought that essential genes could be inferred from [[minimal genome]]s which supposedly contain only essential genes. The problem here is that the smallest genomes belong to parasitic (or symbiontic) species which can survive with a reduced gene set as they obtain many nutrients from their hosts. For instance, one of the smallest genomes is that of ''[[Hodgkinia cicadicola]]'', a [[symbiont]] of cicadas, containing only 144 Kb of DNA encoding only 188 genes.<ref name="Hodgkinia">{{cite journal | vauthors = McCutcheon JP, McDonald BR, Moran NA | title = Origin of an alternative genetic code in the extremely small and GC-rich genome of a bacterial symbiont | journal = PLOS Genetics | volume = 5 | issue = 7 | pages = e1000565 | date = July 2009 | pmid = 19609354 | pmc = 2704378 | doi = 10.1371/journal.pgen.1000565 | veditors = Matic I | doi-access = free }}</ref> Like other symbionts, ''Hodgkinia'' receives many of its nutrients from its host, so its genes do not need to be essential.
'''Metabolic modelling'''. Essential genes may be also predicted in completely sequenced genomes by '''[[Metabolic network modelling|metabolic reconstruction]]''', that is, by reconstructing the complete metabolism from the gene content and then identifying those genes and pathways that have been found to be essential in other species. However, this method can be compromised by proteins of unknown function. In addition, many organisms have backup or alternative pathways which have to be taken into account (see figure 1). Metabolic modeling was also used by Basler (2015) to develop a method to predict essential metabolic genes.<ref name="Basler">{{cite book | vauthors = Basler G | chapter = Computational Prediction of Essential Metabolic Genes Using Constraint-Based Approaches | volume = 1279 | pages = 183–204 | year = 2015 | pmid = 25636620 | doi = 10.1007/978-1-4939-2398-4_12 | isbn = 978-1-4939-2397-7 | series = Methods in Molecular Biology | title = Gene Essentiality }}</ref> '''[[Flux balance analysis]]''', a method of metabolic modeling, has recently been used to predict essential genes in clear cell renal cell carcinoma metabolism.<ref name="Gatto">{{cite journal | vauthors = Gatto F, Miess H, Schulze A, Nielsen J | title = Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism | journal = Scientific Reports | volume = 5 | pages = 10738 | date = June 2015 | pmid = 26040780 | pmc = 4603759 | doi = 10.1038/srep10738 | bibcode = 2015NatSR...
'''Genes of unknown function'''. Surprisingly, a significant number of essential genes has no known function. For instance, among the 385 essential candidates in ''M. genitalium'', no function could be ascribed to 95 genes<ref name="Glass2006"/> even though this number had been reduced to 75 by 2011.<ref name="Juhas"/> Most of unknown functionally essential genes have potential biological functions related to one of the three fundamental functions.<ref name=":1" />
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