Deep Sequencing of Fosmid Clones Indicates Gene Conversion in the Male-Specific Region of the Giant Panda Y Chromosome

The giant panda (Ailuropoda melanoleuca) is popular around the world and is widely recognized as a symbol of nature conservation. A draft genome of the giant panda is now available, but its Y chromosome has not been sequenced. Y chromosome data are necessary for study of sex chromosome evolution, male development, and spermatogenesis. Thus, in the present study, we sequenced two parts of the giant panda Y chromosome utilizing a male giant panda fosmid library. The sequencing data were assembled into two contigs, each ∼100 kb in length with no gaps, providing high-quality resources for studying the giant panda Y chromosome. Annotation and transposable element comparison indicates varied evolutionary pressure in different regions of the Y chromosome. Two genes, zinc finger protein, Y-linked (ZFY) and lysine demethylase 5D (KDM5D), were annotated and gene conversion was observed for ZFY exon 7. Phylogenetic analysis also revealed that this gene conversion event happened independently in multiple mammalian lineages, indicating a putative mechanism to maintain the function of this particular gene on the Y chromosome. Furthermore, a transposition event, discovered through comparative alignment with the giant panda X chromosome sequence, may be involved in the process of gaining new genes on the Y chromosome. Thus, these newly obtained Y chromosome sequences provide valuable insights into the genomic patterns of the giant panda.