Editing Escherichia coli (section)

==Genomics==
[[File:E.coli image.jpg|thumb|An image of ''E. coli'' using early [[electron microscopy]]]]
The first complete [[DNA sequence]] of an ''E. coli'' [[genome]] (laboratory strain K-12 derivative MG1655) was published in 1997. It is a circular [[DNA]] molecule 4.6&nbsp;million [[base pair]]s in length, containing 4288 annotated protein-coding genes (organized into 2584 [[operons]]), seven [[ribosomal RNA]] (rRNA) operons, and 86 [[transfer RNA]] (tRNA) genes. Despite having been the subject of intensive genetic analysis for about 40 years, many of these genes were previously unknown. The coding density was found to be very high, with a mean distance between genes of only 118 base pairs. The genome was observed to contain a significant number of [[transposon|transposable genetic elements]], repeat elements, cryptic [[prophages]], and [[bacteriophage]] remnants.<ref name="Blattner_1997">{{cite journal | vauthors = Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y | display-authors = 6 | title = The complete genome sequence of ''Escherichia coli'' K-12 | journal = Science | volume = 277 | issue = 5331 | pages = 1453–62 | date = September 1997 | pmid = 9278503 | doi = 10.1126/science.277.5331.1453 | doi-access = free }}</ref> Most genes have only a single copy.<ref>{{Cite web |last=Philips |first=Ron Milo & Ron |title=» How many ribosomal RNA gene copies are in the genome? |url=https://book.bionumbers.org/how-many-ribosomal-rna-gene-copies-are-in-the-genome/ |access-date=2024-06-20 |website=book.bionumbers.org |language=en}}</ref>

More than three hundred complete genomic sequences of ''Escherichia'' and ''Shigella'' species are known. The genome sequence of the type strain of ''E. coli'' was added to this collection before 2014.<ref name="Meier-Kolthoff14" /> Comparison of these sequences shows a remarkable amount of diversity; only about 20% of each genome represents sequences present in every one of the isolates, while around 80% of each genome can vary among isolates.<ref name="comparison" /> Each individual genome contains between 4,000 and 5,500 genes, but the total number of different genes among all of the sequenced ''E. coli'' strains (the pangenome) exceeds 16,000. This very large variety of component genes has been interpreted to mean that two-thirds of the ''E. coli'' [[pangenome]] originated in other species and arrived through the process of horizontal gene transfer.<ref name="pmid21481756">{{cite journal | vauthors = Zhaxybayeva O, Doolittle WF | s2cid = 14499247 | title = Lateral gene transfer | journal = Current Biology | volume = 21 | issue = 7 | pages = R242–46 | date = April 2011 | pmid = 21481756 | doi = 10.1016/j.cub.2011.01.045 | doi-access = free | bibcode = 2011CBio...21.R242Z }}</ref>