ABSTRACT Crustaceans, such as shrimp and crabs, are pivotal to global aquaculture, yet their productivity is severely impacted by low‐temperature stress. This study employs comparative transcriptomic and genomic analyses to elucidate the molecular mechanisms underlying crustacean responses to cold stress across five economically significant species: Litopenaeus vannamei , Penaeus indicus , Eriocheir sinensis , Cherax quadricarinatus , and Macrobrachium rosenbergii . We identified 4711 conserved orthogroups and analyzed differential gene expression under low‐temperature conditions. Results revealed species‐specific responses, with 25 orthogroups shared across all five species and 113 orthogroups common to at least four species. Functional enrichment highlighted pathways such as oxidation–reduction, hormone metabolism, immune regulation, and spliceosomes. Key genes, including EcKL , CYP2W1 , HSPA5 , and SLCs , were implicated in signaling, metabolic, immunological, and developmental adaptations. Phylogenetic analysis was used to trace the evolutionary origins of stress‐responsive genes, enabling the identification of both ancient conserved genes and lineage‐specific genes. The results indicated that “younger” genes tend to exhibit greater transcriptional plasticity than ancient conserved genes. These findings provide critical insights into shared and species‐specific low‐temperature adaptation mechanisms, offering a foundation for breeding cold‐tolerant crustacea strains to enhance aquaculture resilience.
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