Congruent evolution of different classes of non-coding DNA in prokaryotic genomes

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Abstract
Prokaryotic genomes are considered to be ‘wall‐to‐wall’ genomes, which consist largely of genes for proteins and structural RNAs, with only a small fraction of the genomic DNA allotted to intergenic regions, which are thought to typically contain regulatory signals. The majority of bacterial and archaeal genomes contain 6–14% non‐coding DNA. Significant positive correlations were detected between the fraction of non‐coding DNA and inter‐ and intra‐operonic distances, suggesting that different classes of non‐coding DNA evolve congruently. In contrast, no correlation was found between any of these characteristics of non‐coding sequences and the number of genes or genome size. Thus, the non‐coding regions and the gene sets in prokaryotes seem to evolve in different regimes. The evolution of non‐coding regions appears to be determined primarily by the selective pressure to minimize the amount of non‐functional DNA, while maintaining essential regulatory signals, because of which the content of non‐coding DNA in different genomes is relatively uniform and intra‐ and inter‐operonic non‐coding regions evolve congruently. In contrast, the gene set is optimized for the particular environmental niche of the given microbe, which results in the lack of correlation between the gene number and the characteristics of non‐coding regions.