Argopecten scallops are hermaphroditic bivalves and commercially important in aquaculture. Up to now, the molecular mechanism of sex differentiation and gonad growth/maturation in hermaphroditic animals is still largely unknown. In this study, we analyzed the transcriptome of the gonads at different stages of the QN Orange scallop, a new scallop strain selected from the hybrids between the bay scallop and the Peruvian scallop. Among sex differentiation-related genes, 5 transcription factors (TFs) (1 SOX, 2 FOXL and 2 GATA) and 2 TGF-beta s (2 BMP) were mainly expressed in the male part and 2 TFs (1 FOXL and 1GATA) and 2 TGF-beta s (2 BMP) were mainly expressed in the female part of the gonads. Among gonad growth/maturation related genes, 1 ...