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Comparison of human and chimpanzee genomes has received much attention,because of paramount role for understanding evolutionary step distinguishing usfrom our closest living relative. In order to contribute to insight into Ychromosome evolutionary history, we study and compare tandems, higher orderrepeats (HORs), and regularly dispersed repeats in human and chimpanzee Ychromosome contigs, using robust Global Repeat Map algorithm. We find a newtype of long-range acceleration, human-accelerated HOR regions. In peripheraldomains of 35mer human alphoid HORs, we find riddled features with tenadditional repeat monomers. In chimpanzee, we identify 30mer alphoid HOR. Weconstruct alphoid HOR schemes showing significant human-chimpanzee difference,revealing rapid evolution after human-chimpanzee separation. We identify andanalyze over 20 large repeat units, most of them reported here for the firsttime as: chimpanzee and human ~1.6 kb 3mer secondary repeat unit (SRU) and~23.5 kb tertiary repeat unit (~0.55 kb primary repeat unit, PRU); human 10848,15775, 20309, 60910, and 72140 bp PRUs; human 3mer SRU (~2.4 kb PRU); 715merand 1123mer SRUs (5mer PRU); chimpanzee 5096, 10762, 10853, 60523 bp PRUs; andchimpanzee 64624 bp SRU (10853 bp PRU). We show that substantialhuman-chimpanzee differences are concentrated in large repeat structures, atthe level of as much as ~70% divergence, sizably exceeding previous numericalestimates for some selected noncoding sequences. Smeared over the wholesequenced assembly (25 Mb) this gives ~14% human--chimpanzee divergence. Thisis significantly higher estimate of divergence between human and chimpanzeethan previous estimates.

journal of molecular evolution

Large Tandem, Higher Order Repeats and Regularly Dispersed Repeat Units  Contribute Substantially to Divergence Between Human and Chimpanzee Y  Chromosomes