Asymptotically increasing compliance of genomes with Chargaff's second parity rules through inversions and inverted transpositions

Chargaff's second parity rules for mononucleotides and oligonucleotides (C^II_mono and C^II_oligo rules) state that a sufficiently long (> 100 kb) strand of genomic DNA that contains N copies of a mono-or oligonucleotide, also contains N copies of its reverse complementary mono- or oligonucleotide on the same strand. There is very strong support in the literature for the validity of the rules in coding and noncoding regions, especially for the C^II_mono rule. Because the experimental support for the C^II_oligo rule is much less complete, the present article, focusing on the special case of trinucleotides (triplets), examined several gigabases of genome sequences from a wide range of species and kingdoms including organelles such as mitochondria and chloroplasts. I found that all genomes, with the only exception of certain mitochondria, complied with the C^II_triplet rule at a very high level of accuracy in coding and noncoding regions alike. Based on the growing evidence that genomes may contain up to millions of copies of interspersed repetitive elements, I propose in this article a quantitative formulation of the hypothesis that inversions and inverted transposition could be a major contributing if not dominant factor in the almost universal validity of the rules.