The archaeal genomes show an average size and a GC% much lower than what it was observed in bacterial genomes (Table 2.2). The same computations were made for DNA-containing organelles, plasmids, and viruses, and the results will be discussed further.
Table 2.2 The average genome size in prokaryotes.
| Archaea | Bacteria | |||
|---|---|---|---|---|
| Prokaryotes | Size (Mb) | GC% | Size (Mb) | GC% |
| AV | 2.56 | 47.18 | 4.03 | 49.58 |
| SD | ±0.98 | ±11.55 | ±1.79 | ±12.57 |
The table shows the average genome size and the average GC% content in bacteria and archaea. Note that the unit of length for DNA is shown in mega bases (Mb). For instance, 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.
2.4 Organellar Genomes
Chloroplasts were once free-living cyanobacteria, while mitochondria were once free-living proteobacteria. Both have preserved remnants of eubacterial genomes. The average genome size of eukaryotic organelles was calculated at 0.07 Mb (70 kb). With a few exceptions, the average values from each type of organelle show a uniformity regarding the genome size (Table 2.3). Assuming a somewhat constant reductive evolution, this observation may indicate the occurrence of primary and secondary endosymbiosis during the same period for most of the organelles.
Depending on the species, both chloroplasts and mitochondria have evolved slightly differently, however, sometimes even radically different by accelerated reductive evolution (e.g. hydrogenosomes). Many known membrane-bound organelles are derived from either cyanobacteria or proteobacteria lineages. Nonetheless, there are organelles that show a more recent history, different from that of chloroplasts or mitochondria. One such organelle is the chromatophore. About chromatophores and other plastid-like or mitochondria-like organelles, we will discuss further. However, discussions will include only the organelles currently considered by the NCBI database. Note that there are other variations of DNA-containing organelles that have been cataloged as “other plastids” and others who are just waiting to be discovered.
2.4.1 Chloroplasts
Chloroplasts are organelles found in plant cells. Chloroplasts sustain all life on earth by converting solar energy (photons of different frequencies) to carbohydrates through the process of photosynthesis and oxygen release. Like many other organelles, chloroplasts originated from endosymbiotic photosynthetic organisms and retain their own unique DNA [185]. The average length of the chloroplast genome (cpDNA) is 0.153 Mb (153 kb). The chloroplast genome encodes many key proteins that are involved in photosynthesis and other metabolic processes [186]. The chloroplast genome contains between 30 and 50 different RNA genes and a number of protein-coding genes, which range from about 100 in land plants and green algae to 150–200 in nongreen algae [187].
2.4.2 Apicoplasts
Apicoplasts are organelles discovered in parasites [188]. The apicoplast is a vestigial plastid homologous to the chloroplasts of algae and plants. Apicoplasts are present in the majority of parasites from Phylum apicomplexa [189]. The apicoplast is of secondary endosymbiotic origin (please see the “The origins of eukaryotic cells” subchapter) and contains a circular genome around 0.035 Mb (35 kb; Table 2.3) [190]. The plastid encodes RNAs and proteins [191].
Table 2.3 The average genome size in different eukaryotic organelles.
Source: Refs. [190, 198].
| Genome size average (Mb) | |||||||
|---|---|---|---|---|---|---|---|
| Apicoplast | Chloroplast | Chromatophore | Cyanelle | Kinetoplast | Mitochondrion | Other plastids | |
| AV | 0.035 | 0.152 | 1.022 | 0.136 | 0.031 | 0.034 | 0.15 |
| SD | ±0.008 | ±0.028 | — | — | ±0.01 | ±0.463 | ±0.038 |
| Average GC% content | |||||||
| Apicoplast | Chloroplast | Chromatophore | Cyanelle | Kinetoplast | Mitochondrion | Other plastids | |
| AV | 15.5 | 37.04 | 37.99 | 30.47 | 21.58 | 35.71 | 36.74 |
| SD | ±3.09 | ±2.61 | - | - | ±2.96 | ±9.28 | ±2.95 |
| Samples | 54 | 4247 | 1 | 1 | 3 | 11 144 | 938 |
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). For instance, 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 0.035 Mb is 35 kb. The last row (samples) indicates how many sequenced genomes have been used for these computations.
2.4.3 Chromatophores
Chromatophores are photosynthetic organelles discovered in species of freshwater amoeboids from Paulinella genus. Evidence shows that primary endosymbiosis of chromatophores occurred relatively recently (90–140 million years ago) compared to the