Dynamic transcriptome analysis during early development of black rockfish (Sebastes schlegelii)

The black rockfish (Sebastes schlegelii), an important species in aquaculture, has experienced significant population declines due to habitat degradation and overfishing. Despite its rapid growth making it attractive for aquaculture, larval rearing remains challenging, as high-density culture conditions frequently lead to skeletal deformities and slowed growth. To elucidate the molecular mechanisms supporting this fast growth and developmental transitions, we profiled transcriptomic changes across three developmental stages (n = 3 per stage): larval (5 days post-hatching, dph), post-larval (21 dph), and juvenile (45 dph). RNA-Seq generated 56.77 Gb of clean data, resulting in 21,837 annotated unigenes. Differential expression analysis (|log₂FC|≥ 1.2, FDR < 0.05) identified dynamic transcriptomic changes, with 3532 upregulated and 3383 downregulated genes in the 21 vs. 5 dph comparison, and 3789 upregulated and 4582 downregulated genes in the 45 vs. 21 dph comparison. GO enrichment revealed stage-specific pathways, including antigen processing in larvae and autophagy in post-larvae. KEGG pathway analysis underscored notable changes in metabolic processes, including long-term potentiation (21 vs. 5 dph) and proteasome-mediated protein degradation (45 vs. 21 dph). Hub genes, including haao, sec61a1, and vcp, were implicated in energy metabolism, protein synthesis, and cell cycle regulation, supporting rapid growth and tissue differentiation. This study provides fundamental transcriptomic data for exploring early development in S. schlegelii. The identified genes and pathways may facilitate further investigations into growth mechanisms and offer a molecular basis for improving larval survival and aquaculture performance.