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 origin of canonical Archaeplastida 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
