Universal Rules Governing Genome Evolution Expressed by Linear Formulas

Codon evolution is influenced by an organelle-specific bias existing within cellular compartments. The discovery of evidence that codon evolution is controlled by different factors among nuclei, mitochondria and chloroplasts, indicates the existence of biases based on what we term organelle biases . In plant chloroplasts and mitochondria, nucleotide substitutions, based on the correlations among nucleotides, were governed by the linear formula, y = ax + b, where y and x represent nucleotide contents, and a and b are constants. In animal mitochondria, with respect to the correlations between each nucleotide, only the correlations between purines (A versus G) or pyrimidines (C versus T) were almost linear, while the other correlations between purine and pyrimidine (A or G versus T or C) were not. However, nucleotide substitutions, based on the correlations of the same nucleotide between complete single-strand DNA and its coding or non-coding region, were always linear, y = ax + b, in any organelle. Linear correlations of the same nucleotide were also obtained between coding and non-coding region DNAs. The present results clearly reveal evidence that genome evolution is governed by universal linear formulas, although different rules are apparently observed in the different organelle fields formed by nuclei, mitochondria and chloroplasts. This report quantitatively demonstrates the existence of factors controlling genome evolution that are expressed by linear formulas.