Sterile or non-reproductive shellfish are both a market driven need and an ecologically
sustainable approach to increasing food production via aquaculture. Current methods for inducing sterility in bivalve shellfish focus on ploidy manipulation. An alternative approach is the induction of sterility by inactivation of genes essential for germ cell (future gamete) formation and development. The power of this biotechnological approach has been realized recently in several finfish species, where suppression of a critical germ-cell specific gene, dead end (dnd), results in germ cell-free, sterile fish. The shellfish industry is now poised to adopt these technological advances. Unfortunately, the use of this technology in shellfish is hampered by a lack of knowledge of the gene(s) essential for primordial germ cell (PGC) specification in bivalves. To overcome this challenge, we used single-cell RNA-Seq (scRNA-seq), a cutting-edge approach that uses high-throughput sequencing to identify genes expressed in individual cells, to identify genes involved in PGC specification. Using expression of the marker gene vasa, we were able to identify cells in cleavage stage and blastula cells likely to represent the germ cell lineage, but had yet to fully differentiate. At the gastrula stage, vasa expression was limited primarily to a single cluster. Genes uniquely expressed in the vasa+ gastrula cells include those with functions in transcriptional repression, chromatin architecture and DNA repair. Interestingly, genes with no known homology in other species are also uniquely expressed in this cluster, perhaps indicating novel germ cell specification genes in the bivalve lineage. In addition to the elucidation of genes specific to the earliest germ cells in bivalves, this effort also produced a transcriptional atlas of cell states in early bivalve embryos providing a wealth of information on genes contributing to growth and shell production. This is the earliest developmental stage examined via single-cell RNA sequencing in a lophotrochozoan.