Using a handful of transcriptomes to detect sex-linked markers and develop molecular sexing assays in a species with homomorphic sex chromosomes.

To understand the biology of a species it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many non-model species sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays is challenging without additional genomic resources. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has 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 lizard genome, and readily designed multiple single locus PCR primers to sex C. ocellatus and related species. Our approach also facilitated valuable comparisons of sex determining systems on a broad taxonomic scale.

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© The Author(s) 2024. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.