| Summary: | <p>Abstract</p> <p>Background</p> <p>Mammalian sex-chromosomes originated from a pair of autosomes. A step-wise cessation of recombination is necessary for the proper maintenance of sex-determination and, consequently, generates a four strata structure on the X chromosome. Each stratum shows a specific per-site nucleotide sequence difference (<it>p-</it>distance) between the X and Y chromosomes, depending on the time of recombination arrest. Stratum 4 covers the distal half of the human X chromosome short arm and the <it>p</it>-distance of the stratum is ~10%, on average. However, a 100-kb region, which includes <it>KALX </it>and <it>VCX</it>, in the middle of stratum 4 shows a significantly lower <it>p</it>-distance (1-5%), suggesting frequent sequence exchanges or gene conversions between the X and Y chromosomes in humans. To examine the evolutionary mechanism for this low <it>p</it>-distance region, sequences of a corresponding region including <it>KALX</it>/<it>Y </it>from seven species of non-human primates were analyzed.</p> <p>Results</p> <p>Phylogenetic analysis of this low <it>p</it>-distance region in humans and non-human primate species revealed that gene conversion like events have taken place at least ten times after the divergence of New World monkeys and Catarrhini (<it>i.e</it>., Old World monkeys and hominoids). A <it>KALY</it>-converted <it>KALX </it>allele in white-handed gibbons also suggests a possible recent gene conversion between the X and Y chromosomes. In these primate sequences, the proximal boundary of this low <it>p</it>-distance region is located in a <it>LINE </it>element shared between the X and Y chromosomes, suggesting the involvement of this element in frequent gene conversions. Together with a palindrome on the Y chromosome, a segmental palindrome structure on the X chromosome at the distal boundary near <it>VCX</it>, in humans and chimpanzees, may mediate frequent sequence exchanges between X and Y chromosomes.</p> <p>Conclusion</p> <p>Gene conversion events between the X and Y homologous regions have been suggested, mainly in humans. Here, we found frequent gene conversions in the evolutionary course of primates. An insertion of a <it>LINE </it>element at the proximal end of the region may be a cause for these frequent conversions. This gene conversion in humans may also be one of the genetic causes of Kallmann syndrome.</p>
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