Understanding gene regulation during the development of the sea cucumber Apostichopus japonicus using comparative transcriptomics

Embryonic development, especially metamorphosis and settlement, has a major impact on the life history of marine invertebrates. Apostichopus japonicus is an economically important species of sea cucumber. In this study, we performed RNA sequencing on six key stages of A. japonicas development: fertilized eggs, blastula, gastrula, auricularia, doliolaria, and pentactula. A total of 32,353 genes were identified and annotated as a reference gene set for subsequent pairwise comparison analysis. After filtering out low-quality genes, the dynamic molecular responses to development were revealed by WGCNA. The results showed that of the 20 modules, genes in the blue, yellow, and darkslateblue modules were highly correlated with the gastrula, auricularia, and blastula stages, respectively. GO terms for "RNA" and "proteasome complex" were most significantly enriched in the blue module. In the darkslateblue and yellow module, receptors of signaling pathways and metabolic processes were significantly enriched, respectively. All DEGs were categorized into 34 terms, mainly associated with signal transduction and cellular immunity. The expression pattern of genes associated with adhesion, cell cycle, signal, transcription factor, extracellular matrix (ECM), and cytoskeleton was analyzed according to gene function. The results of this study facilitated a more comprehensive understanding of the molecular characteristics of sea cucumber embryonic development and will provide theoretical guidance for larva rearing in sea cucumber culture.