Transcriptome Analysis of The Whole Body Provides Novel Insights Into The Molecular Mechanisms of Growth, Immunity, and Metabolism During The Molting Cycle of The Juvenile Mud Crab Scylla Paramamosain

Abstract Background: Molting is an inherent cyclic process that occurs in all crustaceans and is essential for growth, metamorphosis, and reproduction. Recent studies have shown that many organs and systems are involved in molting regulation, including the hepatopancreas, the immune system, and production of ecdysteroids by Y-organs. However, the molecular mechanisms underlying the dynamic process of crab molting remain poorly understood at the whole-individual level. Therefore, we investigated global expression changes in the transcriptomes of the mud crab Scylla paramamosain, the most cultured crab species worldwide. We revealed a cascade of sequential expression events of molting-related genes involved in various aspects of the molting process by using whole-body sequencing of juvenile crabs. Results: RNA-sequencing (RNA-seq) produced 139.49 Gb of clean reads and 20,436 differentially expressed genes (DEGs) among different molting stages. The expression patterns for genes involved in several molecular events critical for molting, such as cuticle reconstruction, cytoskeletal structure remodeling, hormone regulation, immune responses, and metabolism, were characterized and considered as mechanisms underlying molting in S. paramamosain. Among these genes, we identified 10,695 DEGs in adjacent molting stages. In further GO and KEGG analyses, the significantly enriched pathways included structural constituents of cuticle, binding and chitin metabolic processes, steroid hormone biosynthesis, insulin resistance, and amino sugar metabolic processes. The expression profiles of 12 functional genes detected via RNA-Seq were corroborated via real-time RT-PCR assays. The results indicated gene expression profiles across the molting cycle and identified possible activation pathways for future investigation of the underlying molecular mechanisms. Conclusions: This study establishes a comprehensive transcriptomic repertoire for the molting process in S. paramamosain. The data generated in this study will serve as an important transcriptomic resource for the crab research community to facilitate gene and genome annotation and provide fundamental support for future research on molecular mechanisms in this species. Furthermore, the comprehensive analysis results will improve our understanding of morphological variation in the molting cycle and serve as a potential blueprint for future research on molting in crustaceans and other animals.