Impact of Noncoding DNA on Phenotype Evolution

Abstract

A major discovery in science was the central dogma: that the digital code of DNA was read and translated by RNA into proteins. The information carried by DNA is thus the genotype, which constitutes the phenotype. While the genotype–phenotype discussion primarily concerns the role of ‘real’ protein‐coding genes, the impact of non‐protein‐coding elements like transposons on the phenotype has been less recognised. Such noncoding elements constitute however a major share of most genomes, and genome size per se may display a tremendous variability even between closely related organisms. Whether noncoding elements are parasitic ‘junk DNA’ or are transcribed and thus affect the phenotype is a matter of heated debate. Whether seen as junk or not, noncoding DNA strongly boosts the share genome size, thereby affecting a range of fitness‐related phenotypic traits like mutation rate, genomic flexibility, cell size, body size, morphology, growth rate, behaviour, life cycle and potentially also speciation.

Key Concepts

  • The central dogma postulates that the blueprint of life is coded in the genes, which is read by RNA to produce protein. Thus the genotype constitutes the phenotype.
  • The genotype (the sum of all DNA) is in most organisms made up by non‐protein‐coding DNA, often dominated by virus‐like transposable elements, and whether this is ‘junk’ or ‘parasitic’ DNA of which has a clear function is a heated debate.
  • The C‐value paradox points to the striking variability in genome size even between related organisms, which do not reflect organism complexity.
  • Even if the noncoding DNA is seen as ‘junk’, it has however wide implications for a range of phenotypic traits such as cell size, growth rate, metabolism and life history and is an important yet often neglected part of the genotype–phenotype link.
  • The genome is far more flexible and dynamic than often recognised and is still full of surprises.

Keywords: genome size; genotype; phenotype; selfish DNA; transposable elements

Figure 1. Variation in genome size in some animal groups where the mean is given in red and the horizontal line represents the full range for species where genome size has been estimated.
Figure 2. Conceptual illustration of potential phenotypic impacts of genome size. Small genomes (left) are typically characterised by modest fractions of transposons (bold line) and other nonprotein‐coding elements, while a high degree of transposon proliferation causes large genomes. There may be several proximate and ultimate drivers for evolution of genome size, and large genomes may also simply reflect a genetic drift or weak counter‐selective forces. Some major potential phenotypic consequences are indicated below. Note that these are examples, and upward arrow indicates that the causal direction could work both ways. It should also be noted that assessment of phenotypic genome size effects is most relevant within clades or taxa. (Note that eukaryotes do not have circular genomes; hence the circle is just for illustrative purpose.) Reproduced with permission from Hessen 2015 © Springer.
Figure 3. Approximate composition of the human genome. 1 (red) is the protein‐coding genes, 2 are regulatory elements, 3 are repetitive elements and 4–7 are different classes of transposable elements.
Figure 4. Three common species of northern marine copepods where body size scales with genome size. Reproduced with permission from Hessen et al. 2012 © John Wiley and Sons Ltd.
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Hessen, Dag O(May 2017) Impact of Noncoding DNA on Phenotype Evolution. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0027507]