A single-nucleus transcriptomic atlas of early marine shrimp embryogenesis reveals cell-type specification and eye pigment transport mechanisms

Early embryogenesis and their underlying regulatory mechanisms in crustaceans remains unclear at the cellular level. Here, we mapped the early developmental stages of marine shrimp Palaemon carinicauda using single nucleus RNA sequencing (snRNA-seq), spanning the transitional stages of blastula to protozoea. Profiling over 60,000 nuclei, we identify six distinct embryonic cell types, including the multiple neuronal subtypes, extracellular matrix- producing cells, cuticle-forming cells, and an eye-related cells that emerged during protozoea development. Cell-type identities were validated using selected marker genes expression and spatial expression patterns via fluorescent in situ hybridization (FISH). PcWhite and PcScarlet contain a highly conserved nucleotide-binding domain (NBD) motif, including Walker A, ABC signature sequence and Walker B domain and a conserved six transmembrane domain (TMD). RNA interference (RNAi) analysis targeting the ABC transporter genes White (W) and Scarlet (St) demonstrated that these genes are essential for eye pigment precursor transport, morphogenesis, and embryonic viability. Collectively, this integrative approach demonstrates the robustness of snRNA-seq for dissecting early embryogenesis in non-model species, linking cell-type-specific gene expression to key developmental processes that enables comparative evolutionary genomics across crustaceans.