C-value: Difference between revisions

Revision as of 08:30, 15 November 2018

Revision as of 22:21, 21 February 2019

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== Origin of the term ==

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}}</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}}</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}}</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}}</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 TR |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-coding 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 '''C-value enigma''' or '''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]].

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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|display-authors=8 }}</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 |accessdate=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’sMotulsky'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}}</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}}</ref> human haploid GC contents are 40.97460% for X gametes, and 41.01724% for Y gametes.

Summarizing these numbers: