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Chargaff's rules say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T.

But what about the ratio $\frac{nA+nT}{nC+nG}$?

Is there variation along species of this ratio that is higher than expected by random processes? If yes, what causes this variation?

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3 Answers

up vote 4 down vote accepted

That ratio is essentially, as WYSIWYG pointed out, called GC-content. In actuality, GC-content is reported as $(G+C)/(A+C+G+T)$, converted to percent; i.e., what percent of the genome is G or C.

There is vast variation in GC-content, both amongst species and within a given species' own genome. For example, in humans the first intron and exon are generally more GC-rich than following introns/exons.1 Genes themselves are often found in higher GC areas,2,11 in particular CpG islands are found near a large number of (mammalian) promoters.3

Across species, there can be a big difference. Yeast and Arabidopsis are both around 35%4,5 whereas Plasmodium falciparum is around 24%;6 Carsonella are even lower, at around 16.5%.14 On the other hand, the plankton Emiliania huxleyi is around 65%7. We can use these differences to study genomic history. Bacteria often have genes from all over the place thanks to horizontal gene transfer, and GC-content can be used to differentiate between their own genes and those from horizontal gene transfer;8 a good example is the CRISPR-Cas system,9 even in a virus!10

Here's a list of a few things genomic GC-content is correlated with:15

  • genome size
  • whether the bacterium is free-living or not
  • the environment
  • aerobiosis
  • nitrogen utilization

In the lab, high GC-content often means a harder region to work with, as the presence of three instead of two bonds (between A and T) requires more energy to break;12 anything involving primers can be made more annoying, including (especially, to some) sequencing. There is a theory that high GC-content would be an adaptation to high temperatures, to avoid DNA damage, but that is controversial.13,16,17,18

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Yes that ratio varies and is generally referred to as GC-content which is expressed as percentage. Earlier, people used GC-content as one of the identifiers for a group of organisms.

Though there have been quite a few studies on the evolution and variation of GC-content, there is still no clear explanation for why certain organisms have a certain level of GC-content- it exerts no great bias on the protein composition though it is argued that it controls protein expression. Chemical mutability is higher for C->U and A->G because of deamination but this might not be the sole criterion. You may refer to this nice review for details.

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Well. i read that review fully, just now. Though it is nice, it doesnt summarize everything. But you may find a lot of analysis on this topic. Plus A doesn't get deaminated to G. It becomes Inosine which can base pair with C and thus can be read as G. –  WYSIWYG Aug 27 '13 at 18:13
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GC-content varies greatly among prokaryots, and it is used as a taxonomic characteristic. It is specially elevated in extremophyles, such as halophiles and thermophyles, and it's thought to be an adaptation to high temperature and other chemical and physical stresses. GC bonds are stronger than AT, so it's supossed to acts as a protection agains denaturalizing agents.

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