A single locus carrying modified oogenesis genes underlies the switch to asexuality in Artemia brine shrimp

Transitions from sexual to asexual reproduction are well-documented across different taxa. However, despite extensive efforts, the regulatory changes underlying the emergence of asexuality remain largely undiscovered in the majority of species studied. Artemia brine shrimp have multiple closely related sexual and obligate parthenogenetic lineages, making them a promising model for addressing this question. While earlier work suggested that asexuals use a modified meiosis, and inferred a likely role for the Z-chromosome in its transmission, no master regulator or genetic changes have been put forward as the root causes for the shift. Here, we generate single-nucleus RNAseq data of the female reproductive system of individuals from the Aibi lake population of Artemia parthenogenetica and its closely related obligate sexual species Artemia sp. Kazakhstan. We identify the germline cell clusters in the female reproductive system and perform differential expression analysis to infer substantial transcriptional differences at genes putatively involved in cell cycle and oocyte development between the meiotic cells of the two species. Additionally, we use whole-genome sequencing of 32 individuals from two backcrossing experiments to narrow down the genomic regions associated with the transmission of asexuality to an 8 megabase region of the Z chromosome. Within the identified regions, two adjacent genes with known functions in oogenesis, ITPR and USP8, show differential expression and genetic differentiation between sexuals and asexuals, making them promising candidate drivers of asexuality in this species.