A Draft Male Genome Assembly of the Slipper Lobster (Thenus australiensis) Reveals an XY System and a Validated Diagnostic Marker for Monosex Aquaculture.

The slipper lobster (Thenus australiensis) is rapidly emerging as a high-potential species for commercial aquaculture. Because females exhibit superior growth characteristics due to less frequent moulting after sexual maturity, developing monosex breeding strategies is highly desirable for industry profitability. However, the lack of genomic resources and early sex-identification tools has hindered this development. Here, we report the first draft male genome assembly for T. australiensis, generated using a combination of whole-genome shotgun sequencing, DArT-seq, and multi-tissue transcriptomics. The curated assembly spans 0.913 Gbp with high functional completeness (93.0% BUSCO), providing a robust repertoire of 30,100 protein-coding genes. Through k-mer subtraction and population-level DArT-seq genotyping, we provide definitive evidence that T. australiensis utilizes an XX/XY sex-determination system. Crucially, by identifying male-specific structural variations within a neo-Y locus, we developed a diagnostic PCR assay targeting a male-exclusive sequence. This 171 bp marker achieved 100% accuracy in phenotypic sex identification across wild-caught populations. Ultimately, these foundational genomic resources, combined with a highly reliable molecular sexing tool, provide the critical framework necessary for early sex sorting, broodstock management, and the commercial advancement of monosex slipper lobster farming. HighlightsO_LIFirst draft genome of slipper lobster (0.913 Gbp) assembled. C_LIO_LIMulti-omics approach confirms an XX/XY sex-determination system. C_LIO_LIDeveloped a 171 bp diagnostic PCR sex marker with 100% accuracy. C_LIO_LIFacilitates early sex sorting for profitable monosex aquaculture. C_LI