October 14, 2012

Why are genomes so large?

  • The C-value is the total amount of DNA in the genome (per haploid set of chromosomes).
  • The C-value paradox describes the lack of relationship between the DNA content (C-value) of an organism and its coding potential.
  • There is no good correlation between genome size and genetic complexity.
  • There is an increase in the minimum genome size required to make organisms of increasing complexity.
  • There are wide variations in the genome sizes of organisms within many phyla. 

The total amount of DNA in the (haploid) genome is a characteristic of each living species known as its C-value. There is enormous variation in the range of C-values, from <106 bp for a mycoplasma to >1011 bp for some plants and amphibians

Figure 3.5 summarizes the range of C-values found in different evolutionary phyla. There is an increase in the minimum genome size found in each group as the complexity increases. But as absolute amounts of DNA increase in the higher eukaryotes, we see some wide variations in the genome sizes within some phyla.

Plotting the minimum amount of DNA required for a member of each group suggests in Figure 3.6 that an increase in genome size is required to make more complex prokaryotes and lower eukaryotes.
Mycoplasma are the smallest prokaryotes, and have genomes only ~3× the size of a large bacteriophage. Bacteria start at ~2 × 106 bp. Unicellular eukaryotes (whose life-styles may resemble the prokaryotic) get by with genomes that are also small, although larger than those of the bacteria. Being eukaryotic per se does not imply a vast increase in genome size; a yeast may have a genome size of ~1.3 × 107 bp, only about twice the size of the largest bacterial genomes.
A further twofold increase in genome size is adequate to support the slime mold D. discoideum, able to live in either unicellular or multicellular modes. Another increase in complexity is necessary to produce the first fully multicellular organisms; the nematode worm C. elegans has a DNA content of 8 × 107 bp.

We can also see the steady increase in genome size with complexity in the listing in Figure 3.7 of some of the most commonly analyzed organisms. It is necessary to increase the genome size in order to make insects, birds or amphibians, and mammals. However, after this point there is no good relationship between genome size and morphological complexity of the organism.
We know that genes are much larger than the sequences needed to code for proteins, because exons (coding regions) may comprise only a small part of the total length of a gene). This explains why there is much more DNA than is needed to provide reading frames for all the proteins of the organism. Large parts of an interrupted gene may not be concerned with coding for protein. And there may also be significant lengths of DNA between genes. So it is not possible to deduce from the overall size of the genome anything about the number of genes.
The C-value paradox refers to the lack of correlation between genome size and genetic complexity (Gall, 1981; Gregory, 2001). There are some extremely curious variations in relative genome size. The toad Xenopus and man have genomes of essentially the same size. But we assume that man is more complex in terms of genetic development! And in some phyla there are extremely large variations in DNA content between organisms that do not vary much in complexity (see Figure 3.5). (This is especially marked in insects, amphibians, and plants, but does not occur in birds, reptiles, and mammals, which all show little variation within the group, with an ~2× range of genome sizes.) A cricket has a genome 11× the size of a fruit fly. In amphibians, the smallest genomes are <109 bp, while the largest are ~1011 bp. There is unlikely to be a large difference in the number of genes needed to specify these amphibians. We do not understand why natural selection allows this variation and whether it has evolutionary consequences.

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