Genome reduction

Genome size is the total amount of DNA contained within one copy of a single genome. It is typically measured in terms of mass in picograms (trillionths (10⁻¹²) of a gram, abbreviated pg) or less frequently in Daltons or as the total number of nucleotide base pairs typically in megabases (millions of base pairs, abbreviated Mb or Mbp). One picogram equals 978 megabases. In diploid organisms, genome size is used interchangeably with the term C-value. 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).

The term "genome size" is often erroneously attributed to Hinegardner, even in discussions dealing specifically with terminology in this area of research (e.g., Greilhuber, 2005). Notably, Hinegardner 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 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.

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) 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.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 is not proportional 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, or extinction risk (for recent reviews, see Bennett and Leitch 2005; Gregory 2005). Based on completely sequenced genome data currently (as of April 2009) available, log-transformed gene number forms a linear correlation with log-transformed genome size in bacteria, archea, viruses, and organelles combined whereas a nonlinear (semi-natural log) correlation in eukaryotes (Hou and Lin 2009 ). The nonlinear correlation for eukaryotes, although claim of its existence contrasts the previous view that no correlation exists for this group of organisms, reflects disproportionately fast increasing noncoding DNA in increasingly large eukaryotic genomes. Although sequenced genome data are practically biased toward small genomes, which may compromise the accuracy of the empirically derived correlation, and the ultimate proof of the correlation remains to be obtained by sequencing some of the largest eukaryotic genomes, current data do not seem to rule out a correlation.

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