Combinatory crossover and recombination at CG-only minimal repeats create versatile genomic constituents across primate and mouse genomes

Background: Crossover and recombination have significant outcomes in genomic diversity and evolution. We previously reported that minimal repeats (MRs) such as AT-only trinucleotide two-repeat units (T2Us) are primary sites of unequal crossover and recombination across the human genome, the combinatory impact of which result in intricate colonies (distance between consecutive T2Us <500 bp) of biological and evolutionary implications. Methods: We studied the combinatory impact and landscape of all types of CG-only T2Us on crossover and recombination in the human genome. To this end, we mapped CCGCCG, CGGCGG, CGCCGC, GGCGGC, GCGGCG, and CGCCGC. Subsequently, we performed a comparative genomics study of several colonies of diverse sizes in other primates and mouse. Results: Most CG-only T2Us formed colonies that were primarily distributed in genic intervals. These colonies were predominantly larger than the colonies in the intergenic intervals. Dense arrays of combinatory overlapping and non-overlapping recombinants of the T2Us in the same colony indicated unequal crossover and recombination at these units. The colonies formed versatile genomic constituents, including gene parts (promoters, untranslated regions, and exonic/intronic sequences), microsatellites, and minisatellites. Cross-species analysis of several colonies revealed that some of the colonies were dynamically shared as phylogenetically distant as in mouse. These colonies were mainly of maximum complexity and size in human. Conclusions: CG-only T2Us are crossover and recombination hotspots across the genomes of primates and mouse. The combinatory recombination of these MRs creates versatile genomic elements of evolutionary and biological relevance across these genomes. Because of their high CG content, propensity for unequal crossover and recombination, enrichment in genic regions, and cross-species occurrence, CG-only MRs may partly contribute to the formation, architecture, and evolution of euchromatic genomic regions.