Читать книгу Algorithms in Bioinformatics - Paul A. Gagniuc - Страница 62

Eukaryotic organisms show an average genome size of 434 Mb and prokaryotic organisms show an average genome size of 3.7 Mb. DNA-containing organelles (70 kb) and viruses (40 kb) show mildly close values for the average genome size. On the other hand, plasmids (110 kb) contain almost twice as much genetic material when compared to the average genome size of organelles and viruses. Out of curiosity, a calculation can be made here on the reductive evolution of organelles. Considering the ancestry of the organelles, the average genome of prokaryotes (3.74 Mb) was taken as the reference system in this approach:

where average prokaryote genome (ARG) is the average size of the reference genome and average organellar genome (AOG) is the average size of the organelle genome. AOG% represents the size of AOG expressed as a percentage from ARG. The AOG represents 1.8% from the ARG. Thus, the reductive evolution is then represented by the reference (the average genome of prokaryotes) percentage value of 100% minus 1.8%:

where REv represents the reduction of the AOG since first endosymbiosis occurred (2 billion – 1.5 billion years ago). Thus, during this period, the AOG underwent a reductive evolution of 98%. Note that genomes fluctuate in size over long periods of time and the reductive evolution is not necessarily a “one-way street” [181]. The average GC% content was also calculated. The average GC% shows a fairly large difference between prokaryotes and eukaryotes. Plasmids and viruses show a close GC% average of ∼ 45% (Table 2.1).

This observation is not entirely surprising since plasmid-to-virus transition scenarios have been proposed in the past [182]. Prokaryotic and eukaryotic ssDNA viruses have their origin in bacterial and archaeal plasmids [183]. Plasmid propagation by virus-like particles was observed in the saline waters of cold environments. For instance, a plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells [184]. The average GC% of organellar genomes is somewhat close to the average GC% value observed in the eukaryotic genomes, but very far from the GC% average value observed in the prokaryotic genomes. In prokaryotes, the average genome size and the average GC% content was also calculated separately for bacteria and archaea (Table 2.2).

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.