Comparison of single-cell sequencing technologies for allele-specific expression analysis in rabbit spermatids

Gene drives are transmission distorters that can transmit specific alleles to >90% of the progeny, e.g., the naturally occurring t-haplotype in mice. The hypothesised mechanism involves biased allele expression with impaired transcript sharing between developing spermatids. For invasive pest species, there is interest in co-opting naturally occurring gene drives. It is unknown whether similar natural gene drives exist in the European rabbit, a detrimental pest species in Australia. Here, we analysed the allele-specific expression (ASE) in rabbit spermatids to identify candidate genes for future investigation in genetic biocontrol applications. We utilised short-read and long-read technologies and performed a comparative analysis. Illumina sequencing was deemed unsuitable, whereas both long-read sequencing platforms demonstrated similar performance. The SPINK2 gene that plays an important role in fertility, consistently showed ASE towards one of the alleles. Furthermore, two kinases displayed bimodal allele expression. Future work is warranted to assess suitability of these genes for genetic biocontrol.