A comparative transcriptomics reveals stage-specific molecular mechanisms during early zoeal development in the Chinese mitten crab, Eriocheir sinensis

Abstract

This study systematically analyzed the molecular expression patterns across the zoeal stages (ZI to ZV) of the Chinese mitten crab (Eriocheir sinensis) using comparative transcriptomics. It focused on core biological processes, including metabolism, organelle structure, and signal transduction, to reveal the molecular mechanisms underlying the crab's early development. Based on trend analysis, the differentially expressed genes (DEGs) profile of the ZI stage was significantly distinct from that of the other four developmental stages. Genes enriched and highly expressed in ZI were primarily associated with transmembrane signaling and calcium signaling pathways, which support the transition of early larvae from embryonic development to a free-living life. Meanwhile, enzyme activity analysis indicated that ZI activated the body's antioxidant defense system and nonspecific immune capacity. In the ZII-ZIII stages, DEGs were mainly related to endoplasmic reticulum (ER) structural components and pathways (e.g., ER protein processing and proteasome), suggesting the activation of ER-associated degradation to maintain protein homeostasis during morphological and dietary transitions. In the ZIV-ZV stages, DEGs were predominantly enriched in metabolic pathways (e.g., organic acid metabolism, tyrosine metabolism) and peroxisome/lysosome pathways, which enhance energy supply, exoskeleton sclerotization, immunity, and cell remodeling to facilitate megalopa metamorphosis. Overall, this study sheds new light on the molecular mechanisms underlying zoeal development in E. sinensis and provides theoretical support for aquaculture practices.