Genome-wide identification of FTZ-F1 genes in Chlamys farreri and analysis of ChIP-seq-based binding sites and potential target genes

FTZ-F1 (Fushi tarazu factor-1) is a crucial member of the monomeric orphan nuclear receptor family, playing essential roles in reproductive development, steroidogenesis, and metabolism. However, studies on the function of FTZ-F1 and its target genes in bivalve mollusks remain limited. In this study, we conducted a genome-wide analysis of Chlamys farreri and identified two FTZ-F1 family members, designated as Cf FTZ-F1 and Cf FTZ-F1b. We characterized their sequence features, evolutionary relationships, and protein structures. To elucidate its potential regulatory roles, we employed chromatin immunoprecipitation sequencing (ChIP-seq) to identify potential target genes, revealing 22,570 binding peaks. Motif analysis identified three conserved motifs consistent with the known binding characteristics of FTZ-F1. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses indicated that the target genes associated with these motifs are primarily involved in phospholipid metabolism, carbohydrate metabolism, steroid hormone biosynthesis, and key signaling pathways such as the PI3K-Akt pathway. Notably, genes involved in steroid hormone biosynthesis (CYP17A1, Srd5a1), gonadal differentiation (DAX-1, Dmrta2), and metabolic regulation (fumA, Adcy1) were identified as putative targets, suggesting that Cf FTZ-F1 may play a crucial role in these physiological processes. ChIP-qPCR further validated the binding sites of several target genes. This study sheds insights into the regulatory roles of FTZ-F1 in C. farreri, particularly its potential involvement in steroidogenesis, gonadal development, and metabolic regulation, laying the foundation for future functional investigations.