Genome size

Genome size refers to the total amount of DNA contained within one copy of a genome. It is typically measured in terms of mass (in picograms, or trillionths [10^-12] of a gram [abbreviated pg], or less frequently in Daltons) or as the total number of nucleotide base pairs (typically in millions of base pairs, or megabases [abbreviated Mb or Mbp]). One picogram (pg) equals 978 megabases (Mb) (Dolezel et al. 2003). In diploid organisms, genome size is used interchangeably with the term C-value. Interestingly, an organism's complexity is not directly proportional to its genome size; some single cell organisms have much more DNA than humans (see Junk DNA and C-value enigma).

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Origin of the term

The term "genome size" is often erroneously attributed to Hinegardner (1976), even in discussions dealing specifically with terminology in this area of research (e.g., Greilhuber et al. 2005). Notably, Hinegardner (1976) used the term only once: in the title. The term actually seems to have first appeared in 1968 when Hinegardner wondered, in the last paragraph of his article, whether "cellular DNA content does, in fact, reflect genome size". In this context, "genome size" was being used in the sense of genotype to mean the number of genes. In a paper submitted only two months later (in February of 1969), Wolf et al. (1969) used the term "genome size" throughout and in its present usage; therefore these authors should probably be credited with originating the term in its modern sense. By the early 1970s, "genome size" was in common usage with its present definition, probably as a result of its inclusion in Susumu Ohno’s influential book Evolution by Gene Duplication, published in 1970.

Variation in genome size

The genome sizes of thousands of eukaryotes have been analyzed over the past 50 years, and these data are available in online databases for animals, plants, and fungi (see external links). Nuclear genome size is typically measured in eukaryotes using either densitometric measurements of Feulgen-stained nuclei (previously using specialized densitometers, now more commonly using computerized image analysis; Hardie et al. 2002) or flow cytometry. In prokaryotes, pulsed-field gel electrophoresis and complete genome sequencing are the predominant methods of genome size determination. Nuclear genome sizes are well known to vary enormously among eukaryotic species. In animals they range more than 3,300-fold, and in land plants they differ by a factor of about 1,000 (Bennett and Leitch 2005; Gregory 2005). 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. In eukaryotes (but not prokaryotes), variation in genome size bears no relationship to the number of genes, 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 genome size 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 by one author to more accurately comprise a puzzle or an enigma (the C-value enigma). Genome size correlates 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; Gregory 2005).

Genome reduction

Genome reduction, also known as Genome degradation, is the process by which a genome shrinks relative to its ancestor. Genomes fluctuate in size regularly, especially in Bacteria, but in some situations a genome has drastically lost content during some period.

The most evolutionary significant cases of genome reduction may be the eukaryotic organelles that are derived from bacteria: the mitochondrion and plastid. These organelles are descended from endosymbionts, which could only survive within the host cell and which the host cell likewise needs for survival. Many mitochondria have less than 20 genes in their entire genome, whereas a free-living bacteria generally has at least 1000 genes. Many genes have been transferred to the host nucleus, while others have simply been lost and their function replaced by host processes.

Other bacteria have become endosymbionts or obligate intracellular pathogens and experienced extensive genome reduction as a result. This process seems to be dominated by genetic drift resulting from small population size, low recombination rates, and high mutation rates, as opposed to selection for smaller genomes.

A cyanobacterium also shows signs of genome reduction, but with continued selection.

Genome reduction in obligate endosymbiotic species

Obligate endosymbiotic species are characterized by a complete inability to survive external to their host environment. These species have become a considerable threat to human health, as they are often highly capable of evading human immune systems and manipulating the host environment to acquire nutrients. A common explanation for these keen manipulative abilities is the compact and efficient genomic structure consistently found in obligate endosymbionts. This compact genome structure is the result of massive losses of extraneous DNA - an occurrence that is exclusively associated with the loss of a free-living stage. In fact, as much as 90% of the genetic material can be lost when a species makes the evolutionary transition from a free-living to obligate intracellular lifestyle. Common examples of species with reduced genomes include: Buchnera aphidicola, Rickettsia prowazekii and Mycobacterium leprae. It is important to note, however, that some obligate intracellular species have positive fitness effects on their hosts. (See also mutualists and parasites).

The reductive evolution model has been proposed as an effort to define the genomic commonalities seen in all obligate endosymbionts [Wernegreen]. This model illustrates four general features of reduced genomes and obligate intracellular species:

1. ‘genome streamlining’ resulting from relaxed selection on genes that are superfluous in the intracellular environment;
2. a bias towards Single nucleotide polymorphism (SNP) deletions (rather than additions), which heavily affects genes that have been disrupted by accumulation of mutations (pseudogenes);
3. very little or no capability for acquiring new DNA; and
4. considerable reduction of effective population size in endosymbiotic populations, particularly in species that rely on vertical transmission.

Based on this model, it is clear that endosymbionts face different adaptive challenges than free-living species.

References

• Bennett, M.D. and I.J. Leitch. 2005. Genome size evolution in plants. In The Evolution of the Genome (ed. T.R. Gregory), pp. 89-162. Elsevier, San Diego.
• Doležel, J., J. Bartoš, H. Voglmayr, and J. Greilhuber. 2003. Nuclear DNA content and genome size of trout and human. Cytometry 51A: 127-128.
• Gregory, T.R. 2005. Genome size evolution in animals. In The Evolution of the Genome (ed. T.R. Gregory), pp. 3-87. Elsevier, San Diego.
• Greilhuber, J., J. Doležel, M. Lysák, and M.D. Bennett. 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.
• Hardie, D.C., T.R. Gregory, and P.D.N. Hebert. 2002. From pixels to picograms: a beginners' guide to genome quantification by Feulgen image analysis densitometry. Journal of Histochemistry and Cytochemistry 50: 735-749.
• Hinegardner, R. 1968. Evolution of cellular DNA content in teleost fishes. American Naturalist 102: 517-523.
• Hinegardner, R. 1976. Evolution of genome size. In Molecular Evolution (ed. F.J. Ayala), pp. 179-199. Sinauer Associates, Inc., Sunderland.
• Ohno, S. 1970. Evolution by Gene Duplication. Springer-Verlag, New York.
• Wernegreen, J. (2005). For better or worse: Genomic consequences of genomic mutualism and parasitism. Current Opinion in Genetics and Development. 15: 1-12.
• Wolf, U., H. Ritter, N.B. Atkin, and S. Ohno. 1969. Polyploidization in the fish family Cyprinidae, Order Cypriniformes. I. DNA-content and chromosome sets in various species of Cyprinidae. Humangenetik 7: 240-244.
• Evolution of Chlamydiaceae
• JO Andersson and SG Andersson. Genome degradation is an ongoing process in Rickettsia. Molecular Biology and Evolution, Vol 16, 1178-1191.

See also

• Animal Genome Size Database
• Cell nucleus
• Comparative genomics
• C-value
• C-value enigma
• Genome
• Human genome
• Junk DNA
• Noncoding DNA
• Plant DNA C-values Database
• Selfish DNA
• Transposable elements