An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (Micropterus salmoides) Under MS-222 (Tricaine Methanesulfonate) Exposure
Abstract
1. Introduction
2. Materials and Methods
2.1. Fish Husbandry
2.2. Experimental Design and Sampling
2.3. Transcriptomic Analysis
2.3.1. RNA Extraction
2.3.2. Library Preparation for Transcriptomic Sequencing
2.3.3. Clustering and Sequencing
2.3.4. Data Processing
2.4. Metabolomic Analysis
2.4.1. Sample Preparation and Extraction
2.4.2. HPLC Conditions
2.4.3. MS Conditions (AB)
2.4.4. Data Processing
3. Results
3.1. Transcriptomic Analysis
3.1.1. Transcriptomic Sequence Assembly
3.1.2. Annotation and Functional Analyses
3.1.3. Differentially Expressed Genes
3.2. Metabolomic Analysis
3.2.1. Gill
3.2.2. Liver
4. Discussion
4.1. Transcriptomic Response Profiles
4.1.1. Global Gene Expression Patterns
4.1.2. Gill-Specific Responses
4.1.3. Liver-Specific Responses
4.2. Metabolomic Remodeling Characteristics
4.2.1. Overall Metabolite Alterations
4.2.2. Amino Acid-Centric Adaptations
4.2.3. Tissue-Specific Energy Strategies
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Sample | Raw Reads | Clean Reads | Clean Base (G) | Error Rate (%) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|---|
GCA12_1 | 47,779,856 | 45,645,160 | 6.85 | 0.03 | 97.6 | 93.24 | 47.33 |
GCA12_2 | 48,091,768 | 46,731,910 | 7.01 | 0.03 | 97.32 | 92.62 | 46.16 |
GCA12_3 | 46,402,036 | 45,195,964 | 6.78 | 0.03 | 97.34 | 92.6 | 46.76 |
GMA12_1 | 46,078,140 | 43,466,010 | 6.52 | 0.03 | 96.39 | 91.37 | 46.54 |
GMA12_2 | 46,143,790 | 44,027,190 | 6.60 | 0.03 | 96.94 | 92.37 | 45.40 |
GMA12_3 | 47,919,228 | 46,176,644 | 6.93 | 0.03 | 97.3 | 92.8 | 47.41 |
LCA12_1 | 54,554,562 | 53,317,498 | 8.00 | 0.03 | 97.45 | 92.82 | 47.88 |
LCA12_2 | 54,862,588 | 53,770,872 | 8.07 | 0.03 | 97.29 | 92.45 | 47.59 |
LCA12_3 | 50,456,582 | 49,470,860 | 7.42 | 0.03 | 97.58 | 93.05 | 47.43 |
LMA12_1 | 51,634,666 | 50,452,610 | 7.57 | 0.03 | 97.52 | 92.89 | 48.88 |
LMA12_2 | 50,587,374 | 49,199,952 | 7.38 | 0.03 | 97.85 | 93.65 | 48.64 |
LMA12_3 | 52,125,768 | 50,729,502 | 7.61 | 0.03 | 97.2 | 92.4 | 46.22 |
Sample | Total Reads | Reads Mapped | Unique Mapped | Multi Mapped |
---|---|---|---|---|
GCA12_1 | 45,645,160 | 43,950,315 (96.29%) | 40,734,042 (89.24%) | 3,216,273 (7.05%) |
GCA12_2 | 46,731,910 | 44,782,783 (95.83%) | 41,196,719 (88.16%) | 3,586,064 (7.67%) |
GCA12_3 | 45,195,964 | 43,526,886 (96.31%) | 40,055,401 (88.63%) | 3,471,485 (7.68%) |
GMA12_1 | 43,466,010 | 40,121,249 (92.30%) | 36,667,547 (84.36%) | 3,453,702 (7.95%) |
GMA12_2 | 44,027,190 | 41,029,375 (93.19%) | 38,306,518 (87.01%) | 2,722,857 (6.18%) |
GMA12_3 | 46,176,644 | 44,052,857 (95.40%) | 39,506,689 (85.56%) | 4,546,168 (9.85%) |
LCA12_1 | 53,317,498 | 51,649,052 (96.87%) | 46,284,750 (86.81%) | 5,364,302 (10.06%) |
LCA12_2 | 53,770,872 | 51,762,201 (96.26%) | 45,014,672 (83.72%) | 6,747,529 (12.55%) |
LCA12_3 | 49,470,860 | 47,830,869 (96.68%) | 41,344,771 (83.57%) | 6,486,098 (13.11%) |
LMA12_1 | 50,452,610 | 48,712,746 (96.55%) | 42,378,751 (84.00%) | 6,333,995 (12.55%) |
LMA12_2 | 49,199,952 | 47,719,632 (96.99%) | 43,063,660 (87.53%) | 4,655,972 (9.46%) |
LMA12_3 | 50,729,502 | 48,694,832 (95.99%) | 44,096,718 (86.93%) | 4,598,114 (9.06%) |
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Gao, P.; Chen, R.; Ma, D.; Lin, S.; Yu, H.; Zhang, X. An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (Micropterus salmoides) Under MS-222 (Tricaine Methanesulfonate) Exposure. Metabolites 2025, 15, 349. https://doi.org/10.3390/metabo15060349
Gao P, Chen R, Ma D, Lin S, Yu H, Zhang X. An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (Micropterus salmoides) Under MS-222 (Tricaine Methanesulfonate) Exposure. Metabolites. 2025; 15(6):349. https://doi.org/10.3390/metabo15060349
Chicago/Turabian StyleGao, Ping, Rimeng Chen, Deyun Ma, Shanshan Lin, Haodong Yu, and Xuezhen Zhang. 2025. "An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (Micropterus salmoides) Under MS-222 (Tricaine Methanesulfonate) Exposure" Metabolites 15, no. 6: 349. https://doi.org/10.3390/metabo15060349
APA StyleGao, P., Chen, R., Ma, D., Lin, S., Yu, H., & Zhang, X. (2025). An Integrated Analysis of Transcriptomic and Metabolomic Effects Reveals Insights into Stress Responses in Largemouth Bass (Micropterus salmoides) Under MS-222 (Tricaine Methanesulfonate) Exposure. Metabolites, 15(6), 349. https://doi.org/10.3390/metabo15060349