Integrated Survival Assessment and mRNA/miRNA Transcriptomics Reveal Heat Stress Response and Recovery Mechanisms in Cultured Razor Clam Sinonovacula constricta

Abstract

Intertidal burrowing bivalves, such as razor clam Sinonovacula constricta, are economically significant aquaculture species in coastal China. However, they exhibit high susceptibility to heat stress under global warming, which poses a substantial challenge to aquaculture sustainability and production. While several studies have identified genes responsive to heat stress in S. constricta, the regulatory mechanisms and core networks underlying these responses remain poorly understood. Non-coding RNAs (ncRNAs) play a crucial role in gene regulation. To investigate the function of ncRNAs and their associated regulatory networks during both heat stress and recovery, this study employed transcriptomic and miRNA transcriptomic analyses, enrichment analysis of key responsive genes, network construction, and dual-luciferase reporter assays. The results showed that, in contrast to other species, more than 7 of the top 10 most significantly responsive genes in S. constricta during heat stress were heat shock protein 70 (HSP70) genes, while the number of HSP genes sharply decreased (to 3 or 0) during recovery. Enrichment analysis revealed that protein stability and folding were critical response processes during heat stress, whereas catabolism dominated during the recovery phase. Network analysis identified Bcl-2-associated athanogene 3 (BAG3), miR-m0017-5p, and lnc9737 as the core genes, in the heat stress response. Dual-luciferase reporter assays demonstrated that lnc9737 might act as a ceRNA in the miR-m0017-5p/BAG3 axis during heat stress. This research enhances our understanding of heat stress responses in these key aquaculture species and identifies molecular targets for selective breeding to improve thermal tolerance in razor clam farming.