Directional magnitude and intricacy of minimal repeat-mediated recombination across mouse and primates

Background Crossover and recombination may be crucially linked to evolution and speciation, because they create genetic diversity in a large spectrum of genomes. We recently reported that minimal repeats (MRs), such as dinucleotide two- and three-repeat units (D2Us and D3Us, respectively) are ubiquitous sites of unequal crossover and recombination and consequent colonization across the human genome. However, this phenomenon remains largely unexplored at the cross-species level. Methods On a genome-wide scale, we mapped and compared the magnitude and intricacy of AT/TA and CG/GC D3U recombination and colonization in seven species of common ancestry, including mouse (rodent), marmoset (New World monkeys), macaque (Old World monkeys), gibbon (lesser apes), and gorilla, chimpanzee, and human (great apes). Moreover, we studied the largest colony of each species as a prototype for MR-mediated intricacy comparison across the seven species. Results The AT/TA D3U colonies were significantly more abundant, larger, and more intricate than CG/GC colonies across all selected species. In these colonies, D2Us and D3Us were the sites of unequal crossover and recombination, which resulted in primary and secondary recombinants. The primary recombinants overlapped, and subsequent non-overlapping recombination of these recombinants created secondary recombinants. In a positive slope, the AT/TA D3U colony counts were in increasing order in primates in comparison to mouse, and the great apes had the highest counts. With respect to intricacy, the largest D3U colony in mouse consisted of primary recombinants only. Primary recombinants were longer in marmoset, and secondary recombinants were also rare in these monkeys. In macaque, the largest colony predominantly consisted of periodic secondary recombinants. The intricacy of recombinants increased in gibbon, and reached its maximum in the great apes. Conclusions The magnitude and intricacy of AT/TA MR-mediated recombination are directional, bearing positive slope from mouse to great apes. These directional events may link to natural selection and adaptivity across these species.