Structure and ampliconic sequence content of bull, mouse, and primate Y Chromosomes. (A) Phylogenetic relationships among five species with SHIMS-assembled MSY sequences. Branch lengths are drawn to scale to indicate species divergence times. Nonhuman photos from Unsplash.com. (B–D) Triangular dot plots, to scale, of DNA sequence identities within the euchromatic MSYs of bull (B), mouse (C), and primates (human, chimpanzee, and rhesus) (D). Each dot represents 100% intrachromosomal identity within a 200-bp window. Direct repeats appear as horizontal lines, inverted repeats as vertical lines, and palindromes as vertical lines that nearly intersect the baseline. Below plots, schematic representations of chromosomes are shown. Sequence classes are color coded as indicated. (Other) Single-copy male-specific sequences that are not homologous to the X Chromosome. (E) Bull and mouse MSYs are represented as spiral diagrams drawn to scale. Major repeat units in bull and mouse long-arm amplicons are color coded as indicated. Repeat units between species are unrelated.
