Editing Caenorhabditis elegans (section)

=== Genome ===
{{Infobox genome <!-- a.k.a GenomeInfo for short -->
| image = Karyotype of Caenorhabditis elegans.png
| caption = [[Karyotype]] of ''C. elegans''<br />{{hidden|explanation of colors|Mitotic chromosomes of ''C. elegans''. DNA (red)/ [[Kinetochore]]s (green). [[holocentric chromosome|Holocentric]] organisms, including ''C. elegans'', assemble diffuse kinetochores along the entire poleward face of each sister chromatid.}}
| taxId = 41 
| ploidy = diploid 
| chromosomes = 5 pairs of autosomes (I, II, III, IV and V) + 1 or 2 sex chromosomes (X<ref>{{cite journal | vauthors = Strome S, Kelly WG, Ercan S, Lieb JD | title = Regulation of the X chromosomes in ''Caenorhabditis elegans'' | journal = Cold Spring Harbor Perspectives in Biology | volume = 6 | issue = 3 | pages = a018366 | date = March 2014 | pmid = 24591522 | pmc = 3942922 | doi = 10.1101/cshperspect.a018366 }}</ref>)
| size = 101.169 Mb (haploid)
| year = 1998
| organelle = mitochondrion 
| organelle-size = 0,01 Mb
| organelle-year = <!-- year of sequencing of organelle -->
}}
[[File:CelegansGoldsteinLabUNC.jpg|thumb|right|''C. elegans'' hermaphrodite]]
''C. elegans'' was the first multicellular organism to have its [[whole genome sequencing|whole genome sequenced]]. The sequence was published in 1998,<ref>
{{cite journal |author=The ''C. elegans'' Sequencing Consortium | title = Genome sequence of the nematode ''C. elegans'': a platform for investigating biology | journal = Science | volume = 282 | issue = 5396 | pages = 2012–8 | date = December 1998 | pmid = 9851916 | doi = 10.1126/science.282.5396.2012 | bibcode = 1998Sci...282.2012. }}</ref> although some small gaps were present; the last gap was finished by October 2002.{{citation needed|date=January 2022}} In the run up to the whole genome the ''C. elegans'' Sequencing Consortium/''C. elegans'' Genome Project released several partial scans including Wilson et al. 1994.<ref name="Sadler-1998">{{cite journal | last=Sadler | first=J. Evan | title=Biochemistry and genetics of von Willebrand factor | journal=[[Annual Review of Biochemistry]] | publisher=[[Annual Reviews (publisher)|Annual Reviews]] | volume=67 | issue=1 | year=1998 | issn=0066-4154 | doi=10.1146/annurev.biochem.67.1.395 | pages=395–424| pmid=9759493 | doi-access=free }}</ref><ref name="Hahn-2002">{{cite journal | last=Hahn | first=Mark E. | title=Aryl hydrocarbon receptors: diversity and evolution | journal=[[Chemico-Biological Interactions]] | publisher=[[Elsevier]] | volume=141 | issue=1–2 | year=2002 | issn=0009-2797 | doi=10.1016/s0009-2797(02)00070-4 | pages=131–160| pmid=12213389 | bibcode=2002CBI...141..131H }}</ref><ref name="Bustelo-2000">{{cite journal | last=Bustelo | first=Xosé R. | title=Regulatory and Signaling Properties of the Vav Family | journal=[[Molecular and Cellular Biology]] | publisher=[[American Society for Microbiology]] | volume=20 | issue=5 | year=2000 | issn=0270-7306 | doi=10.1128/mcb.20.5.1461-1477.2000 | pages=1461–1477| pmid=10669724 | pmc=85310 }}</ref>

====Size and gene content====
The ''C. elegans'' genome is about 100 million [[base pair]]s long and consists of six pairs of chromosomes in hermaphrodites or five pairs of autosomes with XO chromosome in male ''C. elegans'' and a [[mitochondrial genome]]. Its [[gene density]] is about one gene per five [[kilo-base pair]]s. [[Intron]]s make up 26% and [[intergenic region]]s 47% of the genome. Many genes are arranged in clusters and how many of these are [[operon]]s is unclear.<ref>{{cite journal | vauthors = Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK | title = A global analysis of ''Caenorhabditis elegans'' operons | journal = Nature | volume = 417 | issue = 6891 | pages = 851–4 | date = June 2002 | pmid = 12075352 | doi = 10.1038/nature00831 | bibcode = 2002Natur.417..851B | s2cid = 4351788 }}</ref> ''C. elegans'' and other nematodes are among the few eukaryotes currently known to have operons; these include [[trypanosomes]], [[flatworm]]s (notably the [[trematode]] ''[[Schistosoma mansoni]]''), and a primitive [[chordate]] [[tunicate]] ''[[Oikopleura dioica]]''. Many more organisms are likely to be shown to have these operons.<ref>{{cite journal | vauthors = Blumenthal T | title = Operons in eukaryotes | journal = Briefings in Functional Genomics & Proteomics | volume = 3 | issue = 3 | pages = 199–211 | date = November 2004 | pmid = 15642184 | doi = 10.1093/bfgp/3.3.199 | doi-access = free }}</ref>

The genome contains an estimated 20,470 [[protein]]-coding [[gene]]s.<ref>{{cite web
 |date=10 August 2011
 |title=WS227 Release Letter
 |url=http://www.wormbase.org/wiki/index.php/WS227
 |publisher=[[WormBase]]
 |access-date=2013-11-19
 |archive-url=https://archive.today/20131128221823/http://www.wormbase.org/wiki/index.php/WS227
 |archive-date=28 November 2013
 |url-status=dead
 }}</ref> About 35% of ''C. elegans'' genes have human [[Homology (biology)|homologs]]. Remarkably, human genes have been shown repeatedly to replace their ''C. elegans'' homologs when introduced into ''C. elegans''. Conversely, many ''C. elegans'' genes can function similarly to mammalian genes.<ref name="Introduction to C. Elegans" />

The number of known [[RNA gene]]s in the genome has increased greatly due to the 2006 discovery of a new class called ''[[21U-RNA]]'' genes,<ref>{{cite journal | vauthors = Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP | title = Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in ''C. elegans'' | journal = Cell | volume = 127 | issue = 6 | pages = 1193–207 | date = December 2006 | pmid = 17174894 | doi = 10.1016/j.cell.2006.10.040 | doi-access = free }}</ref> and the genome is now believed to contain more than 16,000 RNA genes, up from as few as 1,300 in 2005.<ref>{{cite journal | vauthors = Stricklin SL, Griffiths-Jones S, Eddy SR | title = ''C. elegans'' noncoding RNA genes | journal = WormBook | pages = 1–7 | date = June 2005 | pmid = 18023116 | pmc = 4781554 | doi = 10.1895/wormbook.1.1.1 }}</ref>

Scientific curators continue to appraise the set of known genes; new gene models continue to be added and incorrect ones modified or removed.

The reference ''C. elegans'' genome sequence continues to change as new evidence reveals errors in the original sequencing. Most changes are minor, adding or removing only a few base pairs of DNA. For example, the WS202 release of WormBase (April 2009) added two base pairs to the genome sequence.<ref name="WS202">{{cite web
 |date=29 May 2009
 |title=WS202 Release Letter
 |url=http://www.wormbase.org/wiki/index.php/WS202
 |archive-url=https://archive.today/20131201022934/http://www.wormbase.org/wiki/index.php/WS202
 |url-status=dead
 |archive-date=December 1, 2013
 |publisher=[[WormBase]]
 |access-date=2013-11-19
 }}</ref> Sometimes, more extensive changes are made as noted in the WS197 release of December 2008, which added a region of over 4,300 bp to the sequence.<ref name="WS197">{{cite web
 |date=27 November 2008
 |title=WS197 Release Letter
 |url=http://www.wormbase.org/wiki/index.php/WS197
 |publisher=[[WormBase]]
 |access-date=2013-11-19
 |archive-url=https://web.archive.org/web/20191017232138/https://wiki.wormbase.org/index.php/WS197
 |archive-date=17 October 2019
 |url-status=dead
 }}</ref><ref name="GenomeChanges">{{cite web
 |date=15 June 2011
 |title=Genome sequence changes
 |url=http://www.wormbase.org/wiki/index.php/Genome_sequence_changes
 |access-date=2011-08-13
 |publisher=[[WormBase]]
 |archive-url=https://web.archive.org/web/20191017232140/https://wiki.wormbase.org/index.php/Genome_sequence_changes
 |archive-date=17 October 2019
 |url-status=dead
 }}</ref>

The ''C. elegans'' Genome Project's Wilson et al. 1994 found [[CelVav]]<ref name="Bustelo-2000" /> and a [[von Willebrand factor A]] domain<ref name="Sadler-1998" /> and with Wilson et al. 1998 provides the first credible evidence for an [[aryl hydrocarbon receptor]] (AHR) [[homologous gene|homolog]] outside of vertebrates.<ref name="Hahn-2002" /> 2

====Related genomes====
In 2003, the genome sequence of the related nematode ''[[Caenorhabditis briggsae|C. briggsae]]'' was also determined, allowing researchers to study the [[comparative genomics]] of these two organisms.<ref>{{cite journal | vauthors = Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH | title = The genome sequence of ''Caenorhabditis briggsae'': a platform for comparative genomics | journal = PLOS Biology | volume = 1 | issue = 2 | pages = E45 | date = November 2003 | pmid = 14624247 | pmc = 261899 | doi = 10.1371/journal.pbio.0000045 | doi-access = free }}</ref> The genome sequences of more nematodes from the same [[genus]] e.g., ''[[Caenorhabditis remanei|C. remanei]]'',<ref>{{cite web |url=http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis%20remanei |author=Genome Sequencing Center |title=''Caenorhabditis remanei'': Background |access-date=2008-07-11 |publisher=[[Washington University School of Medicine]] |archive-url=https://web.archive.org/web/20080616091639/http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+remanei  |archive-date=2008-06-16}}</ref> ''[[Caenorhabditis japonica|C. japonica]]''<ref>{{cite web |url=http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis%20japonica |author=Genome Sequencing Center |title=''Caenorhabditis japonica'': Background |access-date=2008-07-11 |publisher=[[Washington University School of Medicine]] |archive-url=https://web.archive.org/web/20080626053444/http://genome.wustl.edu/genome.cgi?GENOME=Caenorhabditis+japonica  |archive-date=2008-06-26}}</ref> and ''[[Caenorhabditis brenneri|C. brenneri]]'' (named after Brenner), have also been studied using the [[shotgun sequencing]] technique.<ref>{{cite journal | vauthors = Staden R | title = A strategy of DNA sequencing employing computer programs | journal = Nucleic Acids Research | volume = 6 | issue = 7 | pages = 2601–10 | date = June 1979 | pmid = 461197 | pmc = 327874 | doi = 10.1093/nar/6.7.2601 }}</ref> These sequences have now been completed.<ref>{{cite web|url=http://genome.ucsc.edu |title=UCSC genome browser |access-date=8 July 2014}}</ref><ref>{{cite journal | vauthors = Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ | title = The UCSC Genome Browser Database: update 2009 | journal = Nucleic Acids Research | volume = 37 | issue = Database issue | pages = D755–61 | date = January 2009 | pmid = 18996895 | pmc = 2686463 | doi = 10.1093/nar/gkn875 }}</ref>