Physiological and Transcriptome Analyses of Gill and Hepatopancreas of Potamocorbula ustulata Under Ammonia Exposure
Abstract
1. Introduction
2. Materials and Methods
2.1. Clam Culture and Sample Collection
2.2. Physiological Parameters Determination
2.3. Transcriptome Analysis
2.3.1. RNA Extraction and Transcriptome Sequencing
2.3.2. Transcriptome Assembly and Differential Expression Analysis
2.3.3. Functional Annotation and Enrichment of Differentially Expressed Genes
2.4. Statistical Analyses
3. Results
3.1. Enzyme Activity Determination
3.2. Characterization of Transcriptome Data
3.3. Analysis of DEGs
3.4. Functional Annotation of Unigenes
3.4.1. GO Functional Annotation
3.4.2. KEGG Functional Annotation
3.5. Functional Enrichment Analysis of GO and KEGG Pathways
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Enzyme | Gill | Hepatopancreas |
---|---|---|
CAT | 0.934 | 0.888 |
SOD | 0.557 | 0.412 |
GSH-Px | 0.821 | 0.679 |
MDA | 0.429 | 0.681 |
GS | / | 0.409 |
GDH | / | 0.663 |
ARG | / | 0.757 |
Urea | / | 0.909 |
Sample | Sequence | Bases | Q30 (%) | Q20 (%) | Error Rate (%) | GC (%) |
---|---|---|---|---|---|---|
D0H1 | 22,842,296 | 6.9 | 92.74 | 97.30 | 0.03 | 46.29 |
D0H2 | 23,273,599 | 7.0 | 92.32 | 97.12 | 0.03 | 42.37 |
D0H3 | 27,418,945 | 8.2 | 92.55 | 97.21 | 0.03 | 45.26 |
D0H4 | 23,860,226 | 7.2 | 92.48 | 97.18 | 0.03 | 45.64 |
D1H1 | 23,994,308 | 7.2 | 91.53 | 96.79 | 0.03 | 46.80 |
D1H2 | 22,670,194 | 6.8 | 91.83 | 96.86 | 0.03 | 46.40 |
D1H3 | 23,711,368 | 7.1 | 92.57 | 97.20 | 0.03 | 45.68 |
D1H4 | 23,714,877 | 7.1 | 92.33 | 97.10 | 0.03 | 45.83 |
D4H1 | 22,935,647 | 6.9 | 92.52 | 97.20 | 0.03 | 46.42 |
D4H2 | 23,685,353 | 7.1 | 92.52 | 97.16 | 0.03 | 46.04 |
D4H3 | 25,613,052 | 7.7 | 92.73 | 97.28 | 0.03 | 45.89 |
D4H4 | 23,934,056 | 7.2 | 92.66 | 97.28 | 0.03 | 45.23 |
D0G1 | 23,564,918 | 7.1 | 92.23 | 97.14 | 0.03 | 39.38 |
D0G2 | 23,949,276 | 7.2 | 92.54 | 97.24 | 0.03 | 42.89 |
D0G3 | 22,637,216 | 6.8 | 92.55 | 97.22 | 0.03 | 43.49 |
D0G4 | 23,608,151 | 7.1 | 92.44 | 97.21 | 0.03 | 40.29 |
D1G1 | 23,043,652 | 6.9 | 92.02 | 97.04 | 0.03 | 36.88 |
D1G2 | 22,836,559 | 6.9 | 92.62 | 97.28 | 0.03 | 39.80 |
D1G3 | 27,259,303 | 8.2 | 92.82 | 97.36 | 0.03 | 40.51 |
D1G4 | 25,161,300 | 7.5 | 92.74 | 97.32 | 0.03 | 40.52 |
D4G1 | 23,078,351 | 6.9 | 92.12 | 97.06 | 0.03 | 41.31 |
D4G2 | 23,594,571 | 7.1 | 92.55 | 97.23 | 0.03 | 42.58 |
D4G3 | 23,397,638 | 7.0 | 91.50 | 96.76 | 0.03 | 42.71 |
D4G4 | 23,971,951 | 7.2 | 92.45 | 97.22 | 0.03 | 43.32 |
Group | Category | GO ID | Description | GeneRatio |
---|---|---|---|---|
D1G vs. D0G | BP | GO:0008219 | Cell death | 12 |
BP | GO:0055085 | Transmembrane transport | 43 | |
MF | GO:0022857 | Transmembrane transporter activity | 53 | |
BP | GO:0006520 | Cellular amino acid metabolic process | 28 | |
D4G vs. D0G | BP | GO:0055085 | Transmembrane transport | 67 |
BP | GO:0005975 | Carbohydrate metabolic process | 36 | |
MF | GO:0016874 | Ligase activity | 16 | |
D1H vs. D0H | MF | GO:0003700 | DNA-binding transcription factor activity | 20 |
CC | GO:0005654 | Nucleoplasm | 12 | |
BP | GO:0048856 | Anatomical structure development | 13 | |
BP | GO:0032196 | Transposition | 6 | |
BP | GO:0071554 | Cell wall organization or biogenesis | 5 | |
BP | GO:0006457 | Protein folding | 5 | |
CC | GO:0005634 | Nucleus | 35 | |
D4H vs. D0H | MF | GO:0016810 | Hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds | 5 |
BP | GO:0005975 | Carbohydrate metabolic process | 18 | |
D4H vs. D0H | MF | GO:0003700 | DNA-binding transcription factor activity | 16 |
MF | GO:0003677 | DNA binding | 46 | |
BP | GO:0071554 | Cell wall organization or biogenesis | 5 | |
BP | GO:0051301 | Cell division | 7 |
Gene ID | Gill Log2FoldChange | Hepatopancreas Log2FoldChange | Gene Description |
---|---|---|---|
Cluster-22753.63857 | 2.8233 | 1.345 | V-type proton ATPase subunit B |
Cluster-22753.75873 | 1.895 | 0.23366 | V-type H+-transporting ATPase subunit a |
Cluster-22753.36771 | −0.63368 | −0.82744 | Na/K-ATPase alpha-subunit |
Cluster-22753.62202 | 3.3914 | 1.9668 | Glutathione S-transferase |
Cluster-22753.59646 | 12.094 | 10.949 | NADH dehydrogenase subunit 2 |
Cluster-22753.15118 | 2.7716 | 1.7348 | Glutamine synthetase |
Cluster-22753.77275 | 0.94146 | 0.57256 | Glutamate dehydrogenase |
Cluster-22753.98962 | 2.4491 | −0.48522 | Argininosuccinate synthase |
Cluster-16686.0 | 0.7397 | Ammonium transporter 3 | |
Cluster-22753.117320 | 0.19705 | 0.24848 | Ammonium transporter 1 |
Cluster-22753.129763 | 1.8164 | −0.46276 | Ammonium transporter Rh type |
Cluster-22753.133859 | −2.8919 | 2.1372 | Carbonic anhydrase |
Cluster-22753.2946 | −0.47581 | −2.9762 | Carbonic anhydrase 6 |
Cluster-22753.70938 | 0.39958 | 0.39334 | Catalase |
Cluster-21163.0 | −0.54152 | −0.41775 | Cu/Zn superoxide dismutase |
Cluster-22753.11717 | 0.67884 | 0.14033 | Glutathione peroxidase |
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He, J.; Wang, X.; Wu, M.; Lin, Z.; He, L.; Zheng, X. Physiological and Transcriptome Analyses of Gill and Hepatopancreas of Potamocorbula ustulata Under Ammonia Exposure. Fishes 2025, 10, 200. https://doi.org/10.3390/fishes10050200
He J, Wang X, Wu M, Lin Z, He L, Zheng X. Physiological and Transcriptome Analyses of Gill and Hepatopancreas of Potamocorbula ustulata Under Ammonia Exposure. Fishes. 2025; 10(5):200. https://doi.org/10.3390/fishes10050200
Chicago/Turabian StyleHe, Jing, Xinhui Wang, Mingyu Wu, Zhihua Lin, Lin He, and Xiafei Zheng. 2025. "Physiological and Transcriptome Analyses of Gill and Hepatopancreas of Potamocorbula ustulata Under Ammonia Exposure" Fishes 10, no. 5: 200. https://doi.org/10.3390/fishes10050200
APA StyleHe, J., Wang, X., Wu, M., Lin, Z., He, L., & Zheng, X. (2025). Physiological and Transcriptome Analyses of Gill and Hepatopancreas of Potamocorbula ustulata Under Ammonia Exposure. Fishes, 10(5), 200. https://doi.org/10.3390/fishes10050200