Genome size

Since the 1950s, with the emergence of various molecular techniques, the genome sizes of thousands of eukaryotes have been analyzed, 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. Genome size in eukaryotes was thought to be proportional to the complexity of an organism but by the mid-20th century it became apparent that closely related species could differ substantially in the size of their genomes. This counter-intuitive observation gave rise to what became known as the "C-value paradox." By the end of 1960s this "paradox" was resolved by the discovery of repetitive DNA and the realization that much of the differences in genomes sizes was due to the presence or absence of large amounts of repetitive DNA. Further advances at that time indicated that most of the DNA in large genomes was non-functional junk DNA and only a small fraction corresponded to functional DNA, including the functional parts of genes. Genome size correlates with a range of measurable characteristics 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. Although the latter contrasts with the previous view that no correlation exists for the eukaryotes, the observed nonlinear correlation for eukaryotes may reflect disproportionately fast-increasing junk 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 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 possible correlation. Human genome size of a human. It shows 22 homologous chromosomes, both the female (XX) and male (XY) versions of the sex chromosome (bottom right), as well as the mitochondrial genome (to scale at bottom left). The blue scale to the left of each chromosome pair (and the mitochondrial genome) shows its length in terms of millions of DNA base pairs. In humans, the total female diploid nuclear genome per cell extends for 6.37 Gigabase pairs (Gbp), is 208.23 cm long and weighs 6.51 picograms (pg). Male values are 6.27 Gbp, 205.00 cm, 6.41 pg. In eukaryotes, in addition to nuclear DNA, there is also mitochondrial DNA (mtDNA) which encodes certain proteins used by the mitochondria. The mtDNA is usually relatively small in comparison to the nuclear DNA. For example, the human mitochondrial DNA forms closed circular molecules, each of which contains 16,569 DNA base pairs, with each such molecule normally containing a full set of the mitochondrial genes. Each human mitochondrion contains, on average, approximately 5 such mtDNA molecules. ==Genome reduction==

Genome reduction, also known as genome degradation, is the process by which an organism's genome shrinks relative to that of its ancestors. Genomes fluctuate in size regularly, and genome size reduction is most significant in bacteria. The most evolutionarily significant cases of genome reduction may be observed in the eukaryotic organelles known to be derived from bacteria: mitochondria and plastids. These organelles are descended from primordial endosymbionts, which were capable of surviving within the host cell and which the host cell likewise needed for survival. Many present-day mitochondria have less than 20 genes in their entire genome, whereas a modern free-living bacterium generally has at least 1,000 genes. Many genes have apparently 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. Some free-living marine bacterioplanktons also shows signs of genome reduction, which are hypothesized to be driven by natural selection. In contrast, terrestrial prokaryotes appear to have larger genome sizes than both aquatic and host-associated prokaryotes (average of 3.7 Mbp for terrestrial, 3.1 Mbp for aquatic and 3.0 Mbp for host-associated). 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 capable of evading human immune systems and manipulating the host environment to acquire nutrients. A common explanation for these manipulative abilities is their consistently compact and efficient genomic structure. These small genomes are the result of massive losses of extraneous DNA, an occurrence that is exclusively associated with the loss of a free-living stage. As much as 90% of the genetic material can be lost when a species makes the evolutionary transition from a free-living to an obligate intracellular lifestyle. During this process the future parasite subjected to an environment rich of metabolite where somehow needs to hide within the host cell, those factors reduce the retention and increase the genetic drift leading to an acceleration of the loss of non-essential genes. Common examples of species with reduced genomes include Buchnera aphidicola, Rickettsia prowazekii, and Mycobacterium leprae. One obligate endosymbiont of leafhoppers, Nasuia deltocephalinicola, has the smallest genome currently known among cellular organisms at 112 kb. Despite the pathogenicity of most endosymbionts, some obligate intracellular species have positive fitness effects on their hosts. The reductive evolution model has been proposed as an effort to define the genomic commonalities seen in all obligate endosymbionts. This model illustrates four general features of reduced genomes and obligate intracellular species: • "genome streamlining" resulting from relaxed selection on genes that are superfluous in the intracellular environment; • a bias towards deletions (rather than insertions), which heavily affects genes that have been disrupted by accumulation of mutations (pseudogenes); • very little or no capability for acquiring new DNA; and • considerable reduction of effective population size in endosymbiotic populations, particularly in species that rely on vertical transmission of genetic material. Based on this model, it is clear that endosymbionts face different adaptive challenges than free-living species and, as emerged from the analysis between different parasites, their genes inventories are extremely different, leading us to the conclusion that the genome miniaturization follows a different pattern for the different symbionts. ==Conversion from picograms (pg) to base pairs (bp)==

:\text{number of base pairs} = \text{mass in pg}\times9.78\times10^8 or simply: :1\text{pg} = 978 \text{ Mbp} ==Drake's rule==

In 1991, John W. Drake proposed a general rule: that the mutation rate within a genome and its size are inversely correlated. This rule has been found to be approximately correct for simple genomes such as those in DNA viruses and unicellular organisms. Its basis is unknown. It has been proposed that the small size of RNA viruses is locked into a three-part relation between replication fidelity, genome size, and genetic complexity. The majority of RNA viruses lack an RNA proofreading facility, which limits their replication fidelity and hence their genome size. This has also been described as the Eigen paradox. An exception to the rule of small genome sizes in RNA viruses is found in the Nidoviruses. These viruses appear to have acquired a 3′-to-5′ exoribonuclease (ExoN) which has allowed for an increase in genome size. == Genome miniaturization and optimal size ==

In 1972 Michael David Bennett hypothesized that there was a correlation with the DNA content and the nuclear volume while Commoner and van't Hoff and Sparrow before him postulated that even cell size and cell-cycle length were controlled by the amount of DNA. More recent theories have brought us to discuss about the possibility of the presence of a mechanism that constrains physically the development of the genome to an optimal size. Those explanations have been disputed by Cavalier-Smith's article where the author pointed that the way to understand the relation between genome size and cell volume was related to the skeletal theory. The nucleus of this theory is related to the cell volume, determined by an adaptation balance between advantages and disadvantages of bigger cell size, the optimization of the ratio nucleus:cytoplasm (karyoplasmatic ratio) and the concept that larger genomes provides are more prone to the accumulation of duplicative transposons as consequences of higher content of non-coding skeletal DNA. Cavalier-Smith also proposed that, as consequent reaction of a cell reduction, the nucleus will be more prone to a selection in favor for the deletion compared to the duplication. From the economic way of thinking, since phosphorus and energy are scarce, a reduction in the DNA should be always the focus of the evolution, unless a benefit is acquired. The random deletion will be then mainly deleterious and not selected due to the reduction of the gained fitness but occasionally the elimination will be advantageous as well. This trade-off between economy and accumulation of non-coding DNA is the key to the maintenance of the karyoplasmatic ratio. == Mechanisms of genome miniaturization ==

The base question behind the process of genome miniaturization is whether it occurs through large steps or due to a constant erosion of the gene content. In order to assess the evolution of this process is necessary to compare an ancestral genome with the one where the shrinkage is supposed to be occurred. Thanks to the similarity among the gene content of Buchnera aphidicola and the enteric bacteria Escherichia coli, 89% identity for the 16S rDNA and 62% for orthologous genes was possible to shed light on the mechanism of genome miniaturization. The genome of the endosymbiont B. aphidicola is characterized by a genome size that is seven times smaller than E. coli (643 kb compared to 4.6 Mb) and can be view as a subset of the enteric bacteria gene inventory. This hypothesis is confirmed by the analysis of the pseudogenes of Buchnera where the number of deletions was more than ten times higher compared to the insertion. content due to mutation and substitutions. especially in the early stages where a larger number of genes became superfluous. One of the consequences of the elimination of such amount of sequences affected even the regulation of the remaining genes. The loss of large section of genomes could in fact lead to a loss in promotor sequences. This could in fact pushed the selection for the evolution of polycistronic regions with a positive effect for both size reduction and transcription efficiency. == Evidence of genome miniaturization ==

One example of the miniaturization of the genome occurred in the microsporidia, an anaerobic intracellular parasite of animals evolved from aerobic fungi. During this process the mitosomes was formed consequent to the reduction of the mitochondria to a relic voided of genomes and metabolic activity except to the production of iron sulfur centers and the capacity to enter into the host cells. Except for the ribosomes, miniaturized as well, many other organelles have been almost lost during the process of the formation of the smallest genome found in the eukaryotes. This extreme process was possible thanks to the advantageous selection for a smaller cell size imposed by the parasitism. Another example of miniaturization is represented by the presence of nucleomorphs, enslaved nuclei, inside of the cell of two different algae, cryptophytes and chlorarachneans. Nucleomorphs are characterized by one of the smallest genomes known (551 and 380 kb) and as noticed for microsporidia, some genomes are noticeable reduced in length compared to other eukaryotes due to a virtual lack of non-coding DNA. The most interesting factor is represented by the coexistence of those small nuclei inside of a cell that contains another nucleus that never experienced such genome reduction. Moreover, even if the host cells have different volumes from species to species and a consequent variability in genome size, the nucleomorph remain invariant denoting a double effect of selection within the same cell. == See also ==