Integrated Transcriptomics and Proteomics Reveal Amino Acid Composition and Protein Expression Profiles of Crassostrea hongkongensis and Crassostrea ariakensis.
5 affiliations
- 1Laboratory of Quality & Safety Risk Assessment on Agro-Products Processing (Zhanjiang), Ministry of Agriculture and Rural Affairs, Agricultural Products Processing Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524001, China.
- 2School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden.
- 3Turku Centre for Biotechnology, University of Turku, FI-20520 Turku, Finland.
- 4Turku Centre for Biotechnology, Abo Akademi University, FI-20520 Turku, Finland.
- 5Department of Life Technologies, University of Turku, FI-20014 Turku, Finland.
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.
Related
- Effects of Rhizobium inoculation and integrated fertilization on the nutritional composition of maize (Zea mays L.) in northwest Ethiopia
- Measuring atmospheric microplastic composition and occurrence from an uncrewed aerial system
- Microplastic contamination in commercially important marine fishes from the Sohar Coast, Sea of Oman: occurrence, characterization, and polymer composition
- Influence of fluid chemical composition on fracture toughness and frictional strength weakening: Sandstone brittle and ductile strength constraints
- Mineral Matrix Composition Controls the Redistribution of Soil Organic Carbon Fractions and Microbial Functioning in Constructed Technosols Under Semi‐Arid Conditions
BibTeX
@article{liu2026integrated,
title = {{Integrated Transcriptomics and Proteomics Reveal Amino Acid Composition and Protein Expression Profiles of Crassostrea hongkongensis and Crassostrea ariakensis.}},
author = {Shaojuan Liu and Huifang Ma and Ling Lin and Shaodong Zeng and Saihao Ren and Donghong Zhu and Matej Orešič and Xiaowei Pan and Jianzhi Ye},
journal = {Foods (Basel, Switzerland)},
year = {2026},
month = oct,
doi = {10.3390/foods15203606},
url = {https://europepmc.org/article/MED/42940242},
note = {CC BY},
}
RIS
TY - JOUR
TI - Integrated Transcriptomics and Proteomics Reveal Amino Acid Composition and Protein Expression Profiles of Crassostrea hongkongensis and Crassostrea ariakensis.
AU - Shaojuan Liu
AU - Huifang Ma
AU - Ling Lin
AU - Shaodong Zeng
AU - Saihao Ren
AU - Donghong Zhu
AU - Matej Orešič
AU - Xiaowei Pan
AU - Jianzhi Ye
PY - 2026
DA - 2026/10/10
JO - Foods (Basel, Switzerland)
DO - 10.3390/foods15203606
UR - https://europepmc.org/article/MED/42940242
AB - 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.
SN - 2304-8158
ER -