plastids (>1.5 billion years ago) [192]. Paulinella lineage gained the chromatophores independently. Thus, chromatophores are considered a valuable model for recent endosymbiosis and a perfect example of organellogenesis. The chromatophore genome is 1 Mb in length and encompasses ∼800 protein-coding genes [193]. A uniformity exists between the genome size of different organelles, except for chromatophores (Table 2.2). Synechococcus (WH5701) is a unicellular cyanobacterium found in the marine environment and the closest relative of the chromatophore. Bioinformatic evidence shows that chromatophores experienced a genome reduction compared to Synechococcus, from which about 74% of the genes were lost. Consequently, these reductions led to the loss of essential functions and made the chromatophore totally dependent on the host for growth and survival [193].
2.4.4 Cyanelles
Cyanelles (or muroplasts) are photosynthetic organelles found in glaucocystophyte algae [194]. The Cyanophora paradoxa is a representative member of the glaucocystophyceae and is used as a biological model for the study of these plastids [195]. Cyanelles are surrounded by a peptidoglycan-like envelope (a peptidoglycan wall) [196, 197]. These organelles show close morphological and biochemical resemblance to endosymbiotic cyanobacteria. The cyanelle genome is 0.136 Mb (136 kb; Table 2.3) in length [198].
2.4.5 Kinetoplasts
Kinetoplasts are networks of circular DNA molecules (kDNA), found in the mitochondria of kinetoplastids (unicellular eukaryotic organisms capable of self-propulsion) [199]. The mitochondrial genome (kinetoplast) of these flagellated protozoans is considered of the highest complexity encountered among all known organelles. The kinetoplast is physically connected to the flagellar basal bodies of these organisms [200]. The kDNA isolated for electron microscopy may span on a 2D grid of 10 by 15 μm [201]. Depending on the species, the kDNA network can exist in many configurations. kDNA is composed of two types of linked DNA rings. Variations include 5000 up to 10 000 minicircles and 25–50 maxicircles. The minicircles are approximately 0.5–10 kb in size and the maxicircles range from 20 to 40 kb [201]. kDNA represents approximately 30% of the total DNA of these protists. It is worth mentioning here that studies done on kinetoplastids have helped our understanding of the RNA-editing mechanisms [202, 203].
2.4.6 Mitochondria
Mitochondria are the most investigated organelle (Figure 1.2a–c). Mitochondria arose about 2.3–1.6 billion years ago from an α-proteobacterial endosymbiont [204, 205]. Energy production is the main function of this organelle. Potential energy is created by oxidation of glucose and the release of adenosine triphosphate (ATP). ATP is generated by the mitochondrial ATP synthase from adenosine diphosphate (ADP) and phosphate ions (Pi). In turn, ATP hydrolysis leads to ADP and energy release (ATP + H2O ⇄ ADP + Pi), which drives all the fundamental cell functions in most eukaryotes. To put things in perspective, the human body uses an average of 50 kg of ATP per day [206]. Depending on the species and type of tissue, mitochondria ranges from hundreds to thousands of copies per cell [207]. Mitochondria contain their own genome [208]. The average length of the mitochondrial genome is 31 kb (Table 2.3).
2.5 Plasmids
Plasmids are circular or linear dsDNA molecules found in all kingdoms of life [209]. Each plasmid carries only a few genes and is capable of replicating autonomously in the host environment. Their importance is crucial, as these are among the main vectors of horizontal gene transfer [210]. Plasmids naturally exist in prokaryotes, where they were first described [211]. In eukaryotes, plasmids are most common among fungi and higher plants [212]. The average length of plasmid DNA is 0.11 Mb (±0.23; that is 110 kb) (Table 2.1). Note that bacterial plasmids contain the largest number of samples and weigh the most on the main average shown in Table 2.1. Nevertheless, plasmids vary in size and some of the largest can reach the size of a bacterial chromosome (e.g. megaplasmids). For instance, Ralstonia solanacearum is a plant pathogen that contains one of the largest megaplasmids (2.1 Mb) [213]. Another example is Streptomyces clavuligerus, a bacterium that contains a linear megaplasmid of 1.8 Mb [214]. Of course, these observations can quickly lead to hypotheses regarding speciation and the origin of chromosomes (not discussed here). Eukaryotic plasmids show an average DNA size of about 0.01 Mb (10 kb) and an average GC% close to that of organelles (37%) (Table 2.4).
Table 2.4 The average DNA length of different plasmids.
| Archaea | Bacteria | Euryarchaeota | ||||
|---|---|---|---|---|---|---|
| Plasmids | Size (Mb) | GC% | Size (Mb) | GC% | Size (Mb) | GC% |
| AV | 0.15 | 53.07 | 0.11 | 45.87 | 0.01 | 37.14 |
| SD | ±0.17 | ±9.77 | ±0.23 | ±11.31 | ±0.04 | ±5.71 |
| Samples | 256 | 256 | 21426 | 21426 | 118 | 118 |
Note that 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, 0.15 Mb is 150 kb. The last row (samples) indicates how many sequenced plasmids have been used for these computations.
It was previously mentioned that archaeal genomes showed an average size and a GC% much lower than what it was observed in bacterial genomes (Table 2.2). However, the situation seems to be reversed in the case of plasmids. The bacterial plasmids show an average size and a GC% much lower than what it was observed in archaeal plasmids (Table 2.4).
2.6 Virus Genomes
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