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Background  Scant genomic information from non-avian reptile sex chromosomes is available, and for only a few lizards, several snakes and one turtle species, and it represents only a small fraction of the total sex chromosome sequences in these species.    Results  We report a 352 kb of contiguous sequence from the sex chromosome of a squamate reptile,  Pogona vitticeps,  with a ZZ/ZW sex microchromosome system. This contig contains five protein coding genes ( oprd1, rcc1, znf91, znf131 ,  znf180 ), and major families of repetitive sequences with a high number of copies of LTR and non-LTR retrotransposons, including the CR1 and Bov-B LINEs. The two genes,  oprd1  and  rcc1  are part of a homologous syntenic block, which is conserved among amniotes. While  oprd1  and  rcc1  have no known function in sex determination or differentiation in amniotes, this homologous syntenic block in mammals and chicken also contains  R-spondin 1  ( rspo1 ), the ovarian differentiating gene in mammals. In order to explore the probability that  rspo1  is sex determining in dragon lizards, genomic BAC and cDNA clones were mapped using fluorescence  in situ  hybridisation. Their location on an autosomal microchromosome pair, not on the ZW sex microchromosomes, eliminates  rspo1  as a candidate sex determining gene in  P. vitticeps .    Conclusion  Our study has characterized the largest contiguous stretch of physically mapped sex chromosome sequence (352 kb) from a ZZ/ZW lizard species. Although this region represents only a small fraction of the sex chromosomes of  P. vitticeps , it has revealed several features typically associated with sex chromosomes including the accumulation of large blocks of repetitive sequences.

Sequence and gene content of a large fragment of a lizard sex chromosome and evaluation of candidate sex differentiating gene R-spondin 1