An Integrated Transcriptomic and Proteomic Approach Uncovers the Molecular Mechanisms of Hypoosmotic Adaptation in Megalopa.

Salinity is a pivotal environmental factor that governs crustacean survival and development through its regulatory effects on key physiological processes, including osmoregulation and metabolic homeostasis. In the mud crab , salinity tolerance of the megalopa plays an important role in larval survival rates and aquaculture yield. Here, we employed a combined transcriptomic and proteomic strategy to comprehensively dissect the molecular adaptive mechanisms of megalopa exposed to acute and prolonged low-salinity stress (8‱) compared to control condition (17‱). Illumina-based transcriptome sequencing generated 81.71 Gb of high-quality clean data, which were assembled into 42,210 unigenes. LC-MS/MS-based proteomic profiling identified 51,390 unique peptides, corresponding to 5909 confidently quantified proteins. Transcriptomic profiling identified 2627 differentially expressed genes (DEGs) under acute low-salinity stress, comprising 1332 upregulated and 1295 downregulated genes compared to the control group. In contrast, a total of 733 DEGs were identified under prolonged low-salinity exposure, including 390 upregulated and 343 downregulated genes. Parallel proteomic analysis identified 199 differentially expressed proteins (DEPs) in the acute stress group, with 105 upregulated and 94 downregulated relative to the control group. Under prolonged stress, 206 DEPs were detected, including 124 upregulated and 82 downregulated proteins compared to the control group. Significant GO term and KEGG pathway enrichments contained metal ion binding, oxidoreductase activity, nucleus, apoptotic process, innate immune response, and amino acid metabolism, suggesting that megalopa employ coordinated regulatory mechanisms involving metabolic reprogramming, immunity system modulation, ion homeostasis maintenance and cell cycle regulation to adapt to hypoosmotic stress. Integrated multi-omics analysis identified 17 genes displaying significant concordant differential expression at both mRNA and protein levels during acute hypoosmotic stress, versus only 5 gene-protein pairs during prolonged stress exposure, indicating extensive post-transcriptional regulation and protein turnover mechanisms in sustained hypoosmotic condition. To the best of our knowledge, this study established the first integrative transcriptome-proteome framework elucidating hypoosmotic adaptation (8‱) mechanisms in megalopa. The identified molecular signatures offer actionable targets for selective breeding of salinity-tolerant strains and precision management of megalopa culture under suboptimal salinity condition, while fundamentally advancing our mechanistic understanding of osmoregulatory plasticity across decapod crustaceans.