C-value: Difference between revisions

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'''C-value''' is the amount, in [[picogram]]s, of [[DNA]] contained within a [[haploid]] [[Cell nucleus|nucleus]] (e.g. a [[gamete]]) or one half the amount in a [[diploid]] [[somatic cell]] of a [[eukaryotic]] organism. In some cases (notably among diploid organisms), the terms C-value and [[genome size]] are used interchangeably; however, in [[Polyploidy|polyploids]] the C-value may represent two or more [[genome]]s contained within the same nucleus. Greilhuber ''et al.''<ref name="Greilhuber2005">{{cite journal |vauthors=Greilhuber J, Doležel J, Lysák M, Bennett MD |year=2005 |title=The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents |journal=Annals of Botany |volume=95 |doi=10.1093/aob/mci019 |pmid=15596473 |issue=1 |pages=255–60|pmc=4246724 }}</ref> have suggested some new layers of terminology and associated abbreviations to clarify this issue, but these somewhat complex additions are yet to be used by other authors.

== Origin of the termTerm - C-value==

Many authors have incorrectly assumed that the 'C' in "C-value" refers to "characteristic", "content", or "complement". Even among authors who have attempted to trace the origin of the term, there had been some confusion because Hewson Swift did not define it explicitly when he coined it in 1950.<ref name="Swift1950">{{cite journal |author=Swift H |year=1950 |title=The constancy of deoxyribose nucleic acid in plant nuclei |journal=Proceedings of the National Academy of Sciences of the USA |volume=36 |issue=11 |pages=643–654|pmid=14808154 |pmc=1063260 |doi=10.1073/pnas.36.11.643|bibcode=1950PNAS...36..643S |doi-access=free }}</ref> In his original paper, Swift appeared to use the designation "1C value", "2C value", etc., in reference to "classes" of DNA content (e.g., Gregory 2001,<ref name="Gregory2001">{{cite journal |author=Gregory TR |year=2001 |title=Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma |journal=Biological Reviews |volume=76 | doi = 10.1017/S1464793100005595 | pmid=11325054 |issue=1 |pages=65–101 |article-number=S1464793100005595 }}</ref> 2002<ref name="Gregory2002">{{cite journal |author=Gregory TR |year=2002 |title=A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class Aves |journal=Evolution |volume=56 |pmid=11913657 |issue=1 |pages=121–30 |doi=10.1111/j.0014-3820.2002.tb00854.x|doi-access=free }}</ref>); however, Swift explained in personal correspondence to Prof. Michael D. Bennett in 1975 that "I am afraid the letter C stood for nothing more glamorous than 'constant', i.e., the amount of DNA that was characteristic of a particular [[genotype]]" (quoted in Bennett and Leitch 2005<ref name="Bennett2005">{{cite book |vauthors=Bennett MD, Leitch IJ |year=2005 |chapter=Genome size evolution in plants |title=The Evolution of the Genome |editor=T.R. Gregory |pages=89–162 |publisher=Elsevier |___location=San Diego|title-link=The Evolution of the Genome }}</ref>). This is in reference to the report in 1948 by Vendrely and Vendrely of a "remarkable constancy in the nuclear DNA content of all the cells in all the individuals within a given animal species" (translated from the original [[French language|French]]).<ref name="Vendrely1948">{{cite journal |author=Vendrely R, Vendrely C |year=1948 |title=La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales&nbsp;: Techniques et premiers résultats |journal=Experientia |volume=4 |issue=11 |pages=434–436 |language=French|pmid=18098821 |last2=Vendrely |doi=10.1007/bf02144998|s2cid=22272730 }}</ref> Swift's study of this topic related specifically to variation (or lack thereof) among [[chromosome]] sets in different cell types within individuals, but his notation evolved into "C-value" in reference to the haploid DNA content of individual species and retains this usage today.

== Variation among species ==

C-values vary enormously among species. In animals they range more than 3,300-fold, and in land plants they differ by a factor of about 1,000.<ref name="Bennett2005"/><ref name="Gregory2005">{{cite book |author=Gregory T.R. |year=2005 |chapter=Genome size evolution in animals |title=The Evolution of the Genome |editor=T.R. Gregory |pages=3–87 |publisher=Elsevier |___location=San Diego|title-link=The Evolution of the Genome }}</ref> [[Protist]] genomes have been reported to vary more than 300,000-fold in size, but the high end of this range ([[Amoeba (genus)|''Amoeba'']]) has been called into question. Variation in C-values bears no relationship to the complexity of the organism or the number of [[genes]] contained in its genome; for example, some single-celled [[protozoa|protists]] have genomes much larger than that of [[humans]]. This observation was deemed counterintuitive before the discovery of [[non-codingRepeated sequence (DNA)|repetitive DNA]]. It became known as the C-value paradox as a result. However, although there is no longer any [[paradox]]ical aspect to the discrepancy between C-value and gene number, this term remains in common usage. For reasons of conceptual clarification, the various puzzles that remain with regard to genome size variation instead have been suggested to more accurately comprise a complex but clearly defined puzzle known as the C-value enigma. C-values correlate with a range of features at the [[Cell (biology)|cell]] and organism levels, including [[cell size]], [[cell division]] rate, and, depending on the [[taxon]], body size, [[metabolic rate]], developmental rate, [[Organ (anatomy)|organ]] complexity, geographical distribution, or [[extinction]] risk (for recent reviews, see Bennett and Leitch 2005;<ref name="Bennett2005"/> Gregory 2005<ref name="Gregory2005"/>).

The '''{{visible anchor|C-value enigma}}''' or '''{{visible anchor|C-value paradox}}''' is the complex puzzle surrounding the extensive variation in nuclear [[genome size]] among [[eukaryotic]] species. At the center of the C-value enigma is the observation that genome size does not correlate with organismal complexity; for example, some single-celled [[Protozoa|protists]] have genomes much larger than that of [[humans]].

Some prefer the term C-value enigma because it explicitly includes all of the questions that will need to be answered if a complete understanding of [[genome size]] [[evolution]] is to be achieved (Gregory 2005). Moreover, the term [[paradox]] implies a lack of understanding of one of the most basic features of eukaryotic genomes: namely that they are composed primarily of [[non-coding DNA]]. Some have claimed that the term paradox also has the unfortunate tendency to lead authors to seek simple one-dimensional solutions to what is, in actuality, a multi-faceted puzzle.<ref name="kew" /> For these reasons, in 2003 the term "C-value enigma" was endorsed in preference to "C-value paradox" at the Second Plant Genome Size Discussion Meeting and Workshop at the [[Royal Botanic Gardens, Kew]], [[United Kingdom|UK]],<ref name=kew>{{Cite web |url=http://www.rbgkew.org.uk/cval/pgsm/index.html# |title=Second Plant Genome Size Discussion Meeting and Workshop |access-date=2015-04-19 |archive-url=https://web.archive.org/web/20081201130244/http://www.rbgkew.org.uk/cval/pgsm/index.html# |archive-date=2008-12-01 |url-status=dead }}</ref>

and an increasing number of authors have begun adopting this term.

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In 1948, Roger and Colette Vendrely reported a "remarkable constancy in the nuclear DNA content of all the cells in all the individuals within a given animal species",<ref>{{cite journal |vauthors=Vendrely R, Vendrely C|year=1948 |title=La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales: Techniques et premiers résultats |journal=Experientia |volume=4 |pages=434–436 |doi=10.1007/bf02144998 |pmid=18098821 |issue=11|s2cid=22272730 }}</ref> which they took as evidence that [[DNA]], rather than [[protein]], was the substance of which [[genes]] are composed. The term C-value reflects this observed constancy. However, it was soon found that C-values ([[genome size]]s) vary enormously among species and that this bears no relationship to the ''presumed'' number of genes (''as reflected by'' the [[complexity]] of the [[organism]]).<ref name="Ancestor">{{cite book |title=The Ancestor's Tale |isbn=978-0544859937 |last1=Dawkins |first1=Richard |last2=Wong |first2=Yan |year=2016 |title-link=The Ancestor's Tale |author1-link=Richard Dawkins }}</ref> For example, the [[Somatic cells|cells]] of some [[salamanders]] may contain 40 times more DNA than those of humans.<ref name="Gregory, T.R. (2013). Animal Genome Size Database">{{cite web|title=Animal Genome Size Database|url=http://www.genomesize.com/statistics.php?stats=amphibs|accessdate=14 May 2013}}</ref> Given that C-values were assumed to be constant because genetic information is encoded by DNA, and yet bore no relationship to presumed gene number, this was understandably considered [[paradox]]ical; the term "C-value paradox" was used to describe this situation by C.A. Thomas Jr. in 1971.

The discovery of [[non-codingrepetitive DNA]] in the earlylate 1970s1960s resolved the main question of the C-value paradox: [[genome size]] does not reflect [[gene]] number in [[eukaryotes]] since most of theirthe excess DNA isin non-codingmany andspecies thereforeappears doesto notbe consist of[[junk genesDNA]]. The [[human genome]], for example, comprisescontains lessabout than 210% protein-codingfunctional regions,elements withand the remainderremaining being90% variousis typesthought ofto non-codingbe DNAjunk. (especiallySpecies [[transposablewith elements]]).<ref>{{Citelarger journalgenomes are thought to contain a higher proportion of junk DNA.

| last1 = Elgar | first1 = G.

| last2 = Vavouri | first2 = T.

| doi = 10.1016/j.tig.2008.04.005

| title = Tuning in to the signals: Noncoding sequence conservation in vertebrate genomes

| journal = Trends in Genetics

| volume = 24

| issue = 7

| pages = 344–352

| year = 2008

| pmid = 18514361

| pmc =

}}</ref>

=== C-value enigma ===

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|2′-deoxycytidine 5′-monophosphate || C₉H₁₄N₃O₇P ||align="right"|307.1966

|}

†Source of table: Doležel ''et al.'', 2003<ref name="Dolezel2003">{{cite journal |vauthors=Doležel J, Bartoš J, Voglmayr H, Greilhuber J |title=Letter to the editor: Nuclear DNA Content and Genome Size of Trout and Human |journal=Cytometry |volume=51A |issue=2 |pages=127–128 |year=2003 |doi=10.1002/cyto.a.10013 |pmid=12541287|doi-access=free }}</ref>

</div>

The formulas for converting the number of nucleotide pairs (or base pairs) to picograms of DNA and vice versa are:<ref name="Dolezel2003"/>

genome size (bp) = (0.978 x 10⁹) x DNA content (pg)
DNA content (pg) = genome size (bp) / (0.978 x 10⁹)

1 pg = 978 Mbp

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===Human C-values===

The [[human genome]]<ref name="IHGSC2001">{{cite journal |title=International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome |journal=Nature |volume=409 |pages=860–921 |year=2001 |pmid=11237011 |last1=Lander |first1=ES |last2=Linton |first2=LM |last3=Birren |first3=B |last4=Nusbaum |first4=C |last5=Zody |first5=MC |last6=Baldwin |first6=J |last7=Devon |first7=K |last8=Dewar |first8=K |last9=Doyle |first9=M |last10=Fitzhugh |first10=William |last11=Funke |first11=Roel |last12=Gage |first12=Diane |last13=Harris |first13=Katrina |last14=Heaford |first14=Andrew |last15=Howland |first15=John |last16=Kann |first16=Lisa |last17=Lehoczky |first17=Jessica |last18=Levine |first18=Rosie |last19=McEwan |first19=Paul |last20=McKernan |first20=Kevin |last21=Meldrim |first21=James |last22=Mesirov |first22=Jill P. |last23=Miranda |first23=Cher |last24=Morris |first24=William |last25=Naylor |first25=Jerome |last26=Raymond |first26=Christina |last27=Rosetti |first27=Mark |last28=Santos |first28=Ralph |last29=Sheridan |first29=Andrew |last30=Sougnez |first30=Carrie |issue=6822 |doi=10.1038/35057062|bibcode=2001Natur.409..860L |display-authors=8 |url=https://deepblue.lib.umich.edu/bitstream/2027.42/62798/1/409860a0.pdf |doi-access=free }}</ref> varies in size; however, the current estimate of the nuclear haploid size of the reference human genome<ref name=GRCh38p2>{{cite web|title=Assembly Statistics for GRCh38.p2 |url=https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data |website=Genome Reference Consortium |accessdateaccess-date=8 February 2015 |date=8 December 2014}}</ref> is 3,031,042,417 bp for the X gamete and 2,932,228,937 bp for the Y gamete. The X gamete and Y gamete both contain 22 autosomes whose combined lengths comprise the majority of the genome in both gametes. The X gamete contains an [[X chromosome]], while the Y gamete contains a [[Y chromosome]]. The larger size of the X chromosome is responsible for the difference in the size of the two gametes. When the gametes are combined, the XX female zygote has a size of 6,062,084,834 bp while the XY male zygote has a size 5,963,271,354 bp. However, the base pairs of the XX female zygote are distributed among 2 homologous groups of 23 heterologous chromosomes each, while the base pairs of the XY male zygote are distributed among 2 homologous groups of 22 heterologous chromosomes each plus 2 heterologous chromosomes. Although each zygote has 46 chromosomes, 23 chromosomes of the XX female zygote are heterologous while 24 chromosomes of the XY male zygote are heterologous. As a result, the C-value for the XX female zygote is 3.099361 while the C-value for the XY male zygote is 3.157877.

The human genome's GC content is about 41%.<ref name=Antonarakis>{{cite book|author1=Stylianos E. Antonarakis|authorlink1=Human Genome Sequence and Variation|title=Vogel and Motulsky's Human Genetics: Problems and Approaches|date=2010|publisher=Springer-Verlag|___location=Berlin Heidelberg|isbn=978-3-540-37654-5|page=32|url=https://www.springer.com/cda/content/document/cda_downloaddocument/9783540376538-c1.pdf?SGWID=0-0-45-855435-p173877407|accessdate=8 February 2015|archive-date=24 September 2015|archive-url=https://web.archive.org/web/20150924123244/http://www.springer.com/cda/content/document/cda_downloaddocument/9783540376538-c1.pdf?SGWID=0-0-45-855435-p173877407|url-status=dead}}</ref> Accounting for the autosomal, X, and Y chromosomes,<ref>{{cite web|last1=Kokocinski|first1=Felix|title=Bioinformatics work notes|url=http://blog.kokocinski.net/index.php/gc-content-of-human-chromosomes?blog=2|website=GC content of human chromosomes|accessdate=8 February 2015|archive-date=10 February 2015|archive-url=https://web.archive.org/web/20150210115205/http://blog.kokocinski.net/index.php/gc-content-of-human-chromosomes?blog=2|url-status=dead}}</ref> human haploid GC contents are 40.97460% for X gametes, and 41.01724% for Y gametes.

Summarizing these numbers:

<div>

{| class="wikitable"

|+Table 2: Human Genome Size

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* [[Genome size]]

* [[Human genome]]

* [[JunkNoncoding DNA]], [[junk DNA]]

* [[NoncodingOnion DNAtest]]

* [[Plant DNA C-values Database]]

* [[Selfish DNA]]

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*[http://www.genomesize.com Animal Genome Size Database]

*[https://web.archive.org/web/20050901105257/http://www.rbgkew.org.uk/cval/homepage.html Plant DNA C-values Database]

*[http://www.zbi.ee/fungal-genomesize/index.php Fungal Genome Size Database] {{Webarchive|url=https://web.archive.org/web/20130207120355/http://www.zbi.ee/fungal-genomesize/index.php |date=2013-02-07 }}

[[Category:DNA]]