5.9: Genome Sizes

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The genome of an organism is the complete set of genes specifying how its phenotype will develop (under a certain set of environmental conditions). In this sense, then, diploid organisms (like ourselves) contain two genomes, one inherited from our mother, the other from our father. The table below presents a selection of representative genome sizes from the rapidly-growing list of organisms whose genomes have been sequenced.

Table of Genome Sizes (haploid)
	Base pairs	Genes	Notes
φX174	5,386	11	virus of E. coli
Human mitochondrion	16,569	37
Nasuia deltocephalinicola	112,091	137	smallest genome yet found in a bacterium. This β-proteobacterium lives in a mutualistic relationship within a special organ of an insect (a leaf hopper) which it supplies with essential amino acids.
Epstein-Barr virus (EBV)	172,282	80	causes mononucleosis
nucleomorph of Guillardia theta	551,264	511	all that remains of the nuclear genome of a red alga (a eukaryote) engulfed long ago by another eukaryote
Mycoplasma genitalium	580,073	525	two of the smallest true organisms
Mycoplasma pneumoniae	816,394	679	two of the smallest true organisms
Rickettsia prowazekii	1,111,523	834	bacterium that causes epidemic typhus
Treponema pallidum	1,138,011	1,039	bacterium that causes syphilis
Pelagibacter ubique	1,308,759	1,354	smallest genome yet found in a free-living organism (marine α-proteobacterium)
Helicobacter pylori	1,667,867	1,589	chief cause of stomach ulcers (not stress and diet)
Methanocaldococcus jannaschii	1,664,970	1,783	These unicellular microbes look like typical bacteria but their genes are so different from those of either bacteria or eukaryotes that they are classified in a third kingdom: Archaea.
Aeropyrum pernix	1,669,695	1,885
Methanothermobacter thermoautotrophicus	1,751,377	2,008
Streptococcus pneumoniae	2,160,837	2,236	the pneumococcus
Pandoravirus	2,473,870	2556	A virus (of an amoeba) with a genome larger than that of the bacteria and archaea above and about the same as that of some parasitic eukaryotes.
Listeria monocytogenes	2,944,528	2,926	2,853 of these encode proteins; the rest RNAs
Synechocystis	3,573,470	4,003	a marine cyanobacterium ("blue-green alga")
E. coli K-12	4,639,221	4,377	4,290 of these genes encode proteins; the rest RNAs
E. coli O157:H7	5.44 x 10⁶	5,416	strain that is pathogenic for humans; has 1,346 genes not found in E. coli K-12
Schizosaccharomyces pombe	12,462,637	4,929	Fission yeast. A eukaryote with fewer genes than the three bacteria below.
Agrobacterium tumefaciens	4,674,062	5,419	Useful vector for making transgenic plants; shares many genes with Sinorhizobium meliloti
Pseudomonas aeruginosa	6.3 x 10⁶	5,570	Increasingly common cause of opportunistic infections in humans.
Sinorhizobium meliloti	6,691,694	6,204	The rhizobial symbiont of alfalfa. Genome consists of one chromosome and 2 large plasmids.
Saccharomyces cerevisiae	12,495,682	5,770	Budding yeast. A eukaryote.
Neurospora crassa	38,639,769	10,082	Plus 498 RNA genes.
Thalassiosira pseudonana	34.5 x 10⁶	11,242	A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteins
Naegleria gruberi	41 x 10⁶	15,727	This free-living unicellular organism lives as both an amoeboid and a flagellated form. 4,133 of its genes are also found in other eukaryotes suggesting that they were present in the common ancestor of all eukaryotes. The great variety of functions encoded by these genes also suggests that the common ancestor of all eukaryotes was itself as complex as many of the present-day unicellular members.
Drosophila melanogaster	122,653,977	~17,000	the "fruit fly"
Caenorhabditis elegans	100,258,171	21,733
Humans	3.3 x 10⁹	~21,000
Tetraodon nigroviridis (a pufferfish)	3.42 x 10⁸	27,918	Although Tetraodon seems to have more protein-encoding genes than we do, it has much less non-coding DNA so its total genome is about a tenth the size of ours.
Mouse	2.8 x 10⁹	~23,000
Amphibians	10⁹–10¹¹	?
Arabidopsis thaliana	0.135 x 10⁹	27,407	a flowering plant (angiosperm) with one of the smallest genomes known in the plant kingdom.
Picea abies	19.6 x 10⁹	28,354	the Norway spruce, a conifer (gymnosperm). Even though it has only ~900 more genes than Arabidopsis, it has 145 times as much DNA. Most of this appears to be derived from transposons.
Psilotum nudum	2.5 x 10¹¹	?

Even though Psilotum nudum (sometimes called the "whisk fern") is a far simpler plant than Arabidopsis (it has no true leaves, flowers, or fruit), it has 3000 times as much DNA. No one knows why, but 80% or more of it is repetitive DNA containing no genetic information. This is also the case for some amphibians, which contain 30 times as much DNA as we do, but certainly are not 30 times as complex. The total amount of DNA in the haploid genome is called its C value. The lack of a consistent relationship between the C value and the complexity of an organism (e.g., amphibians vs. mammals) is called the C value paradox.

Not all genes are Indispensable

The scientists at The Institute for Genomic Research (now known as the J. Craig Venter Institute) who determined the Mycoplasma genitalium sequence have followed this work by systematically destroying its genes (by mutating them with insertions) to see which ones are essential to life and which are dispensable. Of the 485 protein-encoding genes, they have concluded that only 381 of them are essential to life. In other words, the loss of any one of the 381 is lethal; the loss of any one of the others is not. (This is not to say that all the organism needs are those 381 — see "A Minimal Genome?" below.)

Using similar techniques, three groups have recently found that only about 10% of the genes in the human genome (~2000 of them) must be present for human cells to grow successfully in culture. These genes encode proteins for such essential functions as controlling the cell cycle, DNA replication, DNA transcription and RNA translation. The cells can tolerate the loss of any one of the other ~18,000 genes. Thus the human genome appears to have redundant pathways that can often compensate for the loss of a single gene at least for cells growing in culture. Probably others will turn out to be essential for the development and functioning of the various types of differentiated cells in the intact body.

A Minimal Genome?

In March of 2016, workers at the J. Craig Venter Institute reported that they had created a strain of mycoplasma containing only 473 genes. This synthetic organism, which grows vigorously in culture, now holds the record for the smallest genome of a free-living organism.