Energy metabolism and the transcriptome provide new insights into the response mechanism of Manila clam (Rudiatapes philippinarum) between Southern and Northern China populations under high-temperature stress.

Marine heatwaves (MHWs) pose an existential threat to global aquaculture, inflicting severe economic repercussions on bivalve fisheries. While Manila clams (Ruditapes philippinarum), a key species of aquaculture systems, exhibit pronounced geographic variation in temperature tolerance, the underlying molecular mechanisms governing this adaptation remain obscure. This study compared the temperature resilience disparities between southern (Lianjiang) and northern (Laizhou) Chinese populations under simulated heat stress (33℃), integrating physiological, energetic, and transcriptomic analyses. Survival kinetics reveal a striking divergence: Southern populations maintain an 84.44 ± 1.56% survival rate at 96 h, significantly outperforming northern populations (71.11 ± 1.33%, p < 0.01). Energy budget analysis showed that the southern population superior energy utilization, as evidenced by lower consumption energy (C), fecal energy (F), and higher scope for growth (P) values. Transcriptomics revealed 1,022 differentially expressed genes (DEGs) in southern populations (383 up/639 down), predominantly enriched in amino acid metabolism and biosynthesis pathways. Key energy metabolism and amino acid-related genes were upregulated in this population, indicating enhanced thermotolerance. These integrated results demonstrate that southern populations prioritize efficient energy allocation to growth and activate amino acid metabolic pathways for thermal resilience. Our findings provide mechanistic insights into geographic adaptation and support breeding thermotolerant Manila clams strains.