Sex-linked markers in an Australian frog Platyplectrum ornatum with a small genome and homomorphic sex chromosomes

Abstract Amphibians have highly diverse sex-determining modes leading to a notable interest in vertebrate sex determination and sex chromosome evolution. The identification of sex-determining systems in amphibians, however, is often difficult as a vast majority consist of homomorphic sex chromosomes making them hard to distinguish. In this study, we used Diversity Array Technology sequencing (DArTseq™) to identify the sex-determining system in the ornate burrowing frog from Australia, Platyplectrum ornatum . We applied DArTseq™ to 44 individuals, 19 males and 25 females, collected from two locations to develop sex-linked markers. Unexpectedly, these 44 individuals were classified into two distinct population clusters based on our SNP analyses, 36 individuals in cluster-1, and 8 individuals in cluster-2. We then performed sex-linkage analyses separately in each cluster. We identified 35 sex-linked markers from cluster-1, which were all associated with maleness. Therefore, P. ornatum cluster-1 is utilising a male heterogametic (XX/XY) sex-determining system. On the other hand, we identified 210 sex-linked markers from cluster-2, of which 89 were male specific, i.e., identifying XX/XY sex determining system and 111 were female specific, i.e., identifying ZZ/ZW sex determining system, suggesting existence of either male or female heterogametic sex determining system in cluster-2. We also performed cytogenetic analyses in 1 male and 1 female from cluster-1; however, we did not detect any visible differentiation between the X and Y sex chromosomes. We also mapped sex-linked markers from the two clusters against the P. ornatum genome and our comparative analysis indicated that the sex chromosomes in both clusters shared homologies to chromosome 10 (autosome) of Rana temporaria and ZWY sex chromosome of Xenopus tropicalis . It is plausible that the cluster-2 has a potential to be either male or female heterogamety in sex determination, requiring further investigation.