Guanine and Cytosine Exhibit a Consistent Linear Gradient Skew Across Each Chromosome in the Malaria Genome

Abstract

It is empirically known that the numbers of thymine and adenine, as well as guanine and cytosine, are nearly equal on a single strand of each chromosome in genomes, a phenomenon referred to as Chargaff's Second Parity Rule (CSPR). An investigation of how this CSPR is achieved in the Plasmodium genome, which is a eukaryotic genome with an extremely low GC content, revealed that although the numbers of guanine and cytosine are nearly equal on each chromosome, their local ratio is skewed in a linear gradient depending on the position along each chromosome. This suggests local deviations from CSPR as a function of chromosome position. While CSPR has traditionally been explained by the equivalence of base substitution ratios, the consistent gradient skew of guanine and cytosine across all 14 chromosomes in malaria suggests a more complex underlying mechanism shaping CSPR.