The Iwagaki oyster Crassostrea nippona is an important aquaculture species with significant potential for large-scale oyster farming. It is susceptible to the fluctuated salinity in the coastal area. In this study, we compared the transcriptome of Crassostrea nippona larvae under variant conditions with low-salinity stress (28, 20, 15, 10, and 5 practical salinity units (psu)) for 24 h. KEGG enrichment analysis of differentially expressed genes (DEGs) from pairwise comparisons identified several free amino acid metabolism pathway (taurine and hypotaurine, arginine and proline, glycine, and beta-alanine) contributing to the salinity change adaptation and activated “lysosome” and “apoptosis” pathway in response to the low-salinity stress (10 and 5 psu). Trend analysis revealed sustained upregulation of transmembrane transport–related genes (such as SLC family) and downregulation of ribosomal protein synthesis genes faced with decreasing salinities. In addition, 9 biomarkers in response to low-salinity stress were identified through weighted gene co-expression network analysis (WGCNA) and validated by qRT-PCR. Our transcriptome analysis provides a comprehensive view of the molecular mechanisms and regulatory networks underlying the adaptive responses of oyster larvae to hypo-salinity conditions. These findings contribute to our understanding of the complex biological processes involved in oyster resilience and adaptation to changing environmental conditions.

岩垣牡蛎（Crassostrea nippona）是重要的水产养殖品种，具有大规模牡蛎养殖的巨大潜力。它很容易受到沿海地区盐度波动的影响。在本研究中，我们比较了低盐胁迫（28、20、15、10 和 5 个实际盐度单位 (psu)）不同条件下日本巨牡蛎幼虫 24 小时的转录组。通过配对比较对差异表达基因（DEG）进行 KEGG 富集分析，确定了几种有助于盐度变化适应并激活“溶酶体”和“细胞凋亡”的游离氨基酸代谢途径（牛磺酸和亚牛磺酸、精氨酸和脯氨酸、甘氨酸和 β-丙氨酸） ” 响应低盐度胁迫（10 和 5 psu）的途径。趋势分析显示，随着盐度的降低，跨膜运输相关基因（例如SLC家族）持续上调，核糖体蛋白合成基因下调。此外，通过加权基因共表达网络分析 (WGCNA) 鉴定了 9 个响应低盐胁迫的生物标志物，并通过 qRT-PCR 进行了验证。我们的转录组分析提供了牡蛎幼虫对低盐度条件适应性反应的分子机制和调控网络的全面视图。这些发现有助于我们了解牡蛎恢复力和适应不断变化的环境条件所涉及的复杂生物过程。