Universal Genome Strand Parity Across Evolution

The structural complexity of eukaryotic genomes remains a major open challenge in molecular biology. Genome architecture operates across multiple scales—from chromatin loops that mediate regulatory interactions, to isochores, chromatin domains and spatial territories. Genes within these regions are differentially distributed, replicated and expressed, underscoring the importance of long-range correlations for coordinated cellular functions. Here, we describe a previously unrecognized and evolutionarily conserved structural feature, the DNA strand parity, of eukaryotic genome. This principle governs the distribution of virtually all major genomic components. Across eleven evolutionary distant animal and plant species genes, exons, introns and all major transposable element (TE) classes occur in nearly equal number on the plus and minus DNA strands and display highly similar length distributions. The parity also extends to the start positions of TE fragments and to local sequence composition, as illustrated for LINE elements. This property provides a unifying explanation for longstanding observations of sequence-level symmetry, including the symmetry described by Chargaff’s second rule for single DNA strands. We further show that gene and TE lengths follow power-law-like distributions identical on either strand, with correlated scaling exponents across species, suggesting conserved fractal-like constraints during genome evolution. Together, these results establish strand parity as a universal principle of eukaryotic genome organization and support the view that it is an emergent property of the global fractal architecture of the genome.