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Background   Scylla paramamosain  is one of the commercially crucial marine crustaceans belonging to the genus  Scylla , which is commonly distributed along the coasts of China, Vietnam, and Japan. Genomic and transcriptomic data are scarce for the mud crab. Light intensity is one of the ecological factors that affect  S. paramamosain  during indoor overwintering. To understand the energy metabolism mechanism adapted to light intensity, we analyzed the transcriptome of  S. paramamosain  hepatopancreas in response to different light intensities (0, 1.43, 40.31 μmol·m − 2 ·s − 1 ).    Results  A total of 5052 differentially expressed genes were identified in low light group (LL group, 3104 genes were up-regulated and 1948 genes were down-regulated). A total of 7403 differentially expressed genes were identified in high light group (HL group, 5262 genes were up-regulated and 2141 genes were down-regulated).  S. paramamosain  adapts to different light intensity environments through the regulation of amino acids, fatty acids, carbon and energy metabolism. Different light intensities had a strong impact on the energy generation of  S. paramamosain  by influencing oxygen consumption rate, aerobic respiration, glycolysis/gluconeogenesis pathway, the citrate cycle (TCA cycle) and fatty acid degradation.    Conclusion  Low light is more conducive to the survival of  S. paramamosain , which needs to produce and consume relatively less energy to sustain physiological activities. In contrast,  S. paramamosain  produced more energy to adapt to the pressure of high light intensities. The findings of the study add to the knowledge of regulatory mechanisms related to  S. paramamosain  metabolism under different light intensities.    Supplementary Information   Supplementary information  accompanies this paper at 10.1186/s12864-020-07190-w.

bmc genomics

Transcriptome analysis of genes and pathways associated with metabolism in Scylla paramamosain under different light intensities during indoor overwintering