Integrated Transcriptomics and Proteomics Reveal Amino Acid Composition and Protein Expression Profiles of Crassostrea hongkongensis and Crassostrea ariakensis

Abstract

Crassostrea hongkongensis and Crassostrea ariakensis are commercially and nutritionally important oysters. However, species-specific differences in amino acid composition and protein expression profiles, and underlying mechanisms, remain poorly understood. Here, we integrated high-performance liquid chromatography (HPLC), transcriptomic, and proteomic analysis to address these objectives. C. ariakensis exhibited significantly higher total hydrolyzed amino acid contents than C. hongkongensis, with glycine, alanine, glutamic acid, proline and serine being the predominant amino acids in both species. Proteomic analysis identified 1371 differentially expressed proteins (DEPs) that were primarily enriched in proteasome, spliceosome, ribosome, and amino acid metabolism. Transcriptomic analysis screened 16,747 differentially expressed genes (DEGs), which were significantly enriched in the Notch signaling pathway, Ubiquitin mediated proteolysis, Neuroactive ligand-receptor interaction and Phagosome pathways. The integration of proteomics and transcriptomics jointly identified five common KEGG pathways, among which gene set enrichment analysis (GSEA) showed ECM–receptor interaction and folate biosynthesis to be significantly downregulated in C. hongkongensis, suggesting their potential involvement in shaping amino acid composition and protein abundance. Collectively, these findings provide a foundation for the further investigation of species-specific nutritional differences and their potential implications for oyster aquaculture.