Читать книгу Algorithms in Bioinformatics - Paul A. Gagniuc - Страница 70

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).