Using a handful of transcriptomes to detect sex-linked markers in a lizard with homomorphic sex chromosomes

To understand the biology of a species it is often crucial to be able to differentiate males and females. Many species lack distinguishable sexually dimorphic traits, but in those that possess sex chromosomes, molecular sexing offers a good alternative. Designing molecular sexing assays is typically achieved through the comparison of male and female genomic sequences, often from reduced-representation sequencing. However, in many non-model species sex chromosomes are poorly differentiated, and identifying sex-limited sequences and developing PCR-based sexing assays is challenging without additional genomic resources. Here we highlight a simple procedure for detection of sex-linked markers based on transcriptomes that circumvents limitations of other approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a lizard with homomorphic XY chromosomes that also experiences environmentally-induced sex reversal. With transcriptomes from 3 males and 3 females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related genome, and readily design PCR primers to sex C. ocellatus and related species. In addition to providing an important molecular sexing tool for these species, this approach also facilitated valuable comparisons of sex determining systems on a large taxonomic scale.