Genome-wide identification and expression analysis of carbohydrate catabolism pathway genes in crustaceans with special reference to Chinese mitten crab Eriocheir sinensis.

Carbohydrate catabolism is essential for energy production and environmental adaptation in crustaceans. However, it largely remains unclear regarding the identification and expression pattern of key genes involved in carbohydrate catabolism pathway. Therefore, this study was conducted to comprehensively identify and analyze the key genes involved in crustacean carbohydrate catabolism pathway based on genomic and transcriptomic datasets of representative crustaceans. Most core metabolic genes are conserved across phyla in copy number. However, decapods exhibit expansion of the α-amylase (AMY) and triosephosphate isomerase (TPI) families, typically harboring four or more copies, whereas pyruvate metabolism genes (PDH, PDK, PDP) show contraction, frequently reduced to single copies. Synteny and chromosomal localization analyses revealed distinct evolutionary patterns underlying the expansion of AMY and TPI, while the contracted pyruvate metabolism-related genes exhibited high syntenic conservation. Phylogenetic analysis showed that phosphoglycerate mutase (PGAM) formed distinct evolutionary clades, while transcriptomic data revealed clade-specific high expression patterns across tissues and in the hepatopancreas at different molting stages, suggesting potential functional divergence. Transcription factor binding site analysis of representative species with contrasting dietary tendencies demonstrated enrichment of carbohydrate-related transcription factors, including ChREBP, in AMY promoters, suggesting a potential association between gene expansion, cis-regulatory architecture, and dietary adaptation. Notably, promoters of multiple glycolysis-related genes harbored six or more HIF-1α binding sites, exceeding those of most other transcription factors, implicating HIF-1α in the transcriptional regulation of hypoxia-induced glycolytic adaptation. Overall, this study provides new insights into the evolution, functional divergence, and regulation of carbohydrate catabolic genes in crustaceans.