Читать книгу Algorithms in Bioinformatics - Paul A. Gagniuc - Страница 71

Some viruses contain a RNA-based genome and others contain a DNA-based genome. Among the DNA-based viral genomes, some species contain dsDNA and other species show a ssDNA. The same is true for RNA-based viruses; some species contain double-stranded RNA (dsRNA) and other species show a single-stranded RNA (ssRNA) [215]. Prokaryotic and eukaryotic viruses, taken together, show an average genome size of ∼ 0.04 Mb (40 kb) (Tables 2.1 and 2.5). Eukaryotes contain both the smallest and largest viral dimensions, and the smallest and largest viral genome sizes. Viruses with RNA genomes dominate the eukaryotic world [215]. RNA viruses without DNA replication intermediates are called riboviruses. Some famous riboviruses are influenza, SARS, COVID-19, hepatitis C, hepatitis E, Ebola, rabies, polio, and so on. RNA viruses that include DNA intermediates are called retroviruses. The most famous retroviruses are the human immuno-deficiency viruses (HIV-1 and HIV-2) that cause the acquired immuno-deficiency syndrome (AIDS). But what are DNA replication intermediates? Retroviruses use their own reverse transcriptase enzymes to produce a DNA copy of their RNA genome. The new DNA fragment is then incorporated into the genome of the host cell by an integrase enzyme. Post incorporation, the cell transcribes and translates its own genes and the viral genes needed to assemble new copies of the virus. It is worth mentioning here that mutation rates in RNA viruses are up to a million times higher than their hosts [216].

Table 2.5 The average genome size of different eukaryotic and prokaryotic viruses.

Viruses	Average genome size (Mb)	GC%
AV	0.0339	45.3970
SD	±0.0652	±9.2474
Samples	37962	37962

Note that smaller standard deviation (SD) values indicate that more of the data are clustered about the mean while a larger SD value indicates the data are more spread out (larger variation in the data). The unit of length for DNA is shown in mega bases (Mb). DNA fragments equal to 1 million nucleotides (1 000 000 b) are 1 mega base in length (1 Mb) or 1000 kilo bases (1000 kb) in length. For instance, an average genome size of 0.0339 Mb is 33.9 kb. The last row (samples) indicates how many sequenced genomes were used for this calculation.

The physical size of organisms and the size of their genomes lack any proportionality or correlation. But the relationship between DNA quantity and physical size is partially different in the case of viruses. Interestingly, the largest viruses also contain the largest genomes and the smallest viruses contain the smallest genomes [91]. However, these extremes are occupied by virus species with a DNA-based genome. For instance, Pandoravirus salinus is among the largest virus species (1 μm long) and contains 2.5 Mb of dsDNA packed in particles of bacterium-like shapes [217]. Their large size is explained by DNA transposons that have colonized the genome of the giant virus P. salinus over long periods of time [218]. On the other hand, Porcine circovirus is the smallest virus, with a capsid diameter of 17 nm and a ssDNA-based genome size of ∼1.7 kb [219, 220]. RNA-based viral genomes are also among the smallest. For instance, hepatitis delta virus (HDV) contains a 36-nm virion (virus particle) and an ssRNA molecule around ∼1.7 kb [221–223]. As previously stated, plasmids, and viruses show a close GC% average of ∼ 45% (Tables 2.1 and 2.5). Evidence suggests that prokaryotic and eukaryotic ssDNA viruses have their origin in bacterial and archaeal plasmids [183]. Furthermore, as mentioned earlier, giant viruses overlap the cellular world. For instance, DNA methylation contributes to various regulations in all domains of life. Genes of giant dsDNA viruses encode DNA methyltransferases, which make use of this mechanism [224].