| Summary: | <i>Eriocheir sinensis</i> is an aquatic species found distributed worldwide. It is found in the Yangtze River of China, where the commercial fishing of this valuable catadromous aquatic species has been banned. As an important member of the phylum Arthropoda, <i>E. sinensis</i> grows by molting over its whole lifespan. The central nervous system of <i>Eriocheir sinensis</i> plays an important regulatory role in molting growth. Nevertheless, there are no reports on the regulatory mechanisms of the nervous system in <i>E. sinensis</i> during the molting cycle. In this study, a comparative transcriptome analysis of <i>E. sinensis</i> thoracic ganglia at post-molt and inter-molt stages was carried out for the first time to reveal the key regulatory pathways and functional genes operating at the post-molt stage. The results indicate that pathways and regulatory genes related to carapace development, tissue regeneration, glycolysis and lipolysis and immune and anti-stress responses were significantly differentially expressed at the post-molt stage. The results of this study lay a theoretical foundation for research on the regulatory network of the <i>E. sinensis</i> nervous system during the post-molt developmental period. Detailed knowledge of the regulatory network involved in <i>E. sinensis</i> molting can be used as a basis for breeding improved <i>E. sinensis</i> species, recovery of the wild <i>E. sinensis</i> population and prosperous development of the <i>E. sinensis</i> artificial breeding industry.
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