FoxL2 exhibits two-stage expression and maintains the ovarian niche in a lophotrochozoan

The genetic pathways governing sex determination remain a key enigma in lophotrochozoans, a major branch of bilaterian animals, hindering a comprehensive understanding of their evolution. Here, we enable genetic analysis in the gonochoristic scallop Chlamys farreri by developing robust female-specific DNA markers for accurate molecular sex identification. Leveraging this, we perform a systematic dissection of a female sex-determination pathway in this major bilaterian clade. We reveal a regulatory program centered on the transcription factor FoxL2 that controls ovarian fate. This program involves a cis-regulatory code that may contribute to ovarian-specific expression of FoxL2 through the integration of activating and repressive elements. FoxL2 itself exhibits a two-stage expression pattern, initially expressed during early gonad formation before switching to a sustained, female-specific expression that commits the gonad to ovarian fate. Functionally, FoxL2 is essential for maintaining the ovarian cellular niche, including germ cells and a specific somatic lineage. Our work thus provides a framework for a female sex-determination pathway in a lophotrochozoan, establishing the two-stage FoxL2 regulatory program as a candidate model to explore the evolution of this process across metazoans.