Transcriptome analysis of gene expression patterns during embryonic development in golden cuttlefish (Sepia esculenta)

Li Bian, Changlin Liu, Siqing Chen, Fazhen Zhao, Jianlong Ge, Jie Tan

Golden cuttlefish (Sepia esculenta) is an important economic species in China. Because of the rapid decline of its natural resource, researchers are exploring breeding technique for this species. The major obstacle that hinders artificial breeding of S. esculenta is the low larvae survival rate. Mortality is especially high during the mouth-opening stage. Investigating the embryogenesis before the first feed could provide theoretical guidance for reproduction control and breeding of S. esculenta and other Sepia species. In this study, we analyzed the dynamics of the S. esculenta transcriptome along different stages of embryonic development by mRNA-sEq. Our bioinformatics protocol identified 1492 differentially expressed genes (DEGs) across the early developmental stages. Gene ontology enrichment analysis showed that the DEGs were significantly involved in developmental processes and molecular functions, including chitin metabolic process, peptidase activity, catalytic activity, and calcium ion binding. Our results indicated that genes related to cuttlebone development and gene regulation functions were active during the early life phase of S. esculenta. Hierarchical clustering of the DEGs reflected the successiveness of the developmental stages, revealing that gene expression patterns of neighboring stages were similar. The DEG analysis allowed us to identify specific genes and relevant biological pathways to better understand the molecular mechanisms during each developmental stage. This study provides novel insights into the processes underlying the early developmental stages of S. esculenta. The transcriptomic data and identified genes will serve as valuable references for the developmental biology of this species and will help promote its aquaculture research.