C-value
The term C-value refers to the amount of DNA contained within a haploid 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 polyploids the C-value may represent two genomes contained within the same nucleus. Greilhuber et al.[1] have suggested some new layers of terminology and associated abbreviations to clarify this issue, but these somewhat complex additions have yet to be used by other authors. C-values are reported in picograms.
Contents
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.[2] 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[3], 2002[4]); 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[5]). 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).[6] 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.[5][7] Protist genomes have been reported to vary more than 300,000-fold in size, but the high end of this range (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, an observation that was deemed wholly counterintuitive before the discovery of non-coding DNA and which became known as the C-value paradox as a result. However, although there is no longer any paradoxical 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 and organism levels, including cell size, cell division rate, and, depending on the taxon, body size, metabolic rate, developmental rate, organ complexity, geographical distribution, and/or extinction risk (for recent reviews, see Bennett and Leitch 2005[5]; Gregory 2005[7].)
Calculating C-values
| Nucleotide | Chemical formula | Relative molecular weight |
|---|---|---|
| 2′-deoxyadenosine 5′-monophosphate | C10H14N5O6P | 331.2213 |
| 2′-deoxythymidine 5′-monophosphate | C10H15N2O8P | 322.2079 |
| 2′-deoxyguanosine 5′-monophosphate | C10H14N5O7P | 347.2207 |
| 2′-deoxycytidine 5′-monophosphate | C9H14N3O7P | 307.1966 |
†Source of table: Doležel et al., 2003[8]
By using the data in Table 1, relative weights of nucleotide pairs can be calculated as follows: AT = 615.3830 and GC = 616.3711. Provided the ratio of AT to GC pairs is 1:1, the mean relative weight of one nucleotide pair is 615.8771 (±1%).[8]
The relative molecular weight may be converted to an absolute value by multiplying it by the atomic mass unit (1 u), which equals one-twelfth of a mass of 12C, i.e., 1.660539 × 10-27 kg. Consequently, the mean weight of one nucleotide pair would be 1.023 × 10-9 pg, and 1 pg of DNA would represent 0.978 × 109 base pairs.[8]
The formulas for converting the number of nucleotide pairs (or base pairs) to picograms of DNA and vice-versa are:[8]
genome size (bp) = (0.978 x 10<sup><font size="2">9</font></sup>) x DNA content (pg) DNA content (pg) = genome size (bp) / (0.978 x 10<sup><font size="2">9</font></sup>) 1 pg = 978 Mb
The current estimates for human female and male diploid genome sizes are 6.406 × 109 bp and 6.294 × 109 bp, respectively.[9] By using the conversion formulas given above, diploid human female and male nuclei in G1 phase of the cell cycle should contain 6.550 and 6.436 pg of DNA, respectively.
References
- ^ Greilhuber J, Doležel J, Lysák M, Bennett MD (2005). "The origin, evolution and proposed stabilization of the terms 'genome size' and 'C-value' to describe nuclear DNA contents". Annals of Botany 95: 255–260.
- ^ Swift H (1950). "The constancy of deoxyribose nucleic acid in plant nuclei". Proceedings of the National Academy of Sciences of the USA 36: 643–654.
- ^ Gregory TR (2001). "Coincidence, coevolution, or causation? DNA content, cell size, and the C-value enigma". Biological Reviews 76: 65–101.
- ^ Gregory TR (2002). "A bird's-eye view of the C-value enigma: genome size, cell size, and metabolic rate in the class Aves". Evolution 56: 121–130.
- ^ a b c Bennett MD, Leitch IJ (2005). "Genome size evolution in plants". In T.R. Gregory. The Evolution of the Genome. San Diego: Elsevier. p. 89–162.
- ^ Vendrely R, Vendrely C (1948). "La teneur du noyau cellulaire en acide désoxyribonucléique à travers les organes, les individus et les espèces animales : Techniques et premiers résultats" (in French). Experientia 4: 434–436.
- ^ a b Gregory TR (2005). "Genome size evolution in animals". In T.R. Gregory. The Evolution of the Genome. San Diego: Elsevier. p. 3–87.
- ^ a b c d Doležel J, Bartoš J,Voglmayr H, Greilhuber J (2003). "Letter to the editor: Nuclear DNA Content and Genome Size of Trout and Human". Cytometry 51A (2): 127–128. doi:10.1002/cyto.a.10013. PMID 12541287.
- ^ Lander, ES; Linton, LM; Birren, B; Nusbaum, C; Zody, MC; Baldwin, J; Devon, K; Dewar, K et al. (2001). "International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome". Nature 409 (6822): 860–921. doi:10.1038/35057062. PMID 11237011.