Comparative sequence analysis of the mouse pseudoautosomal region from three inbred strains reveals it to be the most rapidly evolving ‘chromosome’

The pseudoautosomal region (PAR) of mammalian sex chromosomes is a small region of sequence identity shared by the X and Y chromosomes that allows pairing, crossover, recombination, and proper segregation of sex chromosomes. Although the mouse PAR sequence was largely a mystery, we have recently obtained the complete PAR sequences of the C57BL/6J and CAST/EiJ strains. Here, we report the complete PAR sequence of a Japanese wild mouse-derived strain, MSM/Ms, and compare the PARs of the three strains. There are considerable differences in the size of PARs between strains (MSM/Ms PAR is only about 20% the length of C57BL/6J PAR) and numerous amino acid substitution variants were found in the PAR genes. High GC-content exons and short introns are common features of the PAR genes and are likely a consequence of maintaining the functions of the encoded proteins during rapid evolution of the mouse PAR, whose recombination frequency in male meiosis is ∼100 times higher than the autosomal average.