Antioxidant Capacity, Enzyme Activities Related to Energy Metabolism, and Transcriptome Analysis of Crassostrea hongkongensis Exposed to Hypoxia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Hypoxia Experiment
2.2. Antioxidant Capacity and Enzyme Activity Determination
2.3. RNA Extraction and Sequencing
2.4. Sequence Processing and Functional Annotation
2.5. Analysis of DEGs
2.6. Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR)
3. Results
3.1. Antioxidant Capacity, Glycogen Content, and Enzyme Activities
3.2. Sequencing, Sequence Assembly, and Annotation
3.3. Candidate Genes under Hypoxic Conditions
3.4. Functional Annotation of DEGs under Hypoxic Conditions in C. hongkongensis
3.5. KEGG Pathway Network Enriched by DEGs
3.6. RT-qPCR Confirmation of DEGs
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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mRNA | Sequence (5′–3′) | Length (bp) | |
---|---|---|---|
CH1000250 | Fwd | AAGGTGACTTCAACACATCCG | 220 |
Rev | CCTACTTGGTTTTGCTCGTTAT | ||
CH1001282 | Fwd | AGAAATGGGGTCAAGGTCG | 119 |
Rev | TAGCAGGTTCAGGTAACATACAA | ||
CH0900166 | Fwd | TCCACCATAGGGTCCACG | 242 |
Rev | CCATTTCCAAAGGTCCGTC | ||
CH0502591 | Fwd | GGTTATTTAGAAGTGGCGTCA | 102 |
Rev | GTGTGTACCAGTCCTACTGTCCT | ||
CH0200562 | Fwd | CAACAATAGAGAGATTCCCGAT | 210 |
Rev | CTACCTTAAAGTCCTCCGAGC | ||
GAPDH | Fwd | GGATTGGCGTGGTGGTAGAG | 184 |
Rev | GTATGATGCCCCTTTGTTGAGTC |
Sample | Number of Clean Reads | Number of Clean Bases | GC (%) | % ≥ Q30 |
---|---|---|---|---|
N1 | 25,206,800 | 7,511,666,510 | 40.8 | 95.56 |
N2 | 19,802,452 | 5,893,526,304 | 41.43 | 95.32 |
N3 | 20,465,606 | 6,087,523,020 | 41.01 | 95.31 |
H1 | 20,647,843 | 6,150,256,584 | 41.19 | 95.32 |
H2 | 24,095,305 | 7,170,772,744 | 41.7 | 95.47 |
H3 | 24,502,902 | 7,288,089,524 | 41.72 | 95.65 |
R1 | 20,244,717 | 6,033,282,358 | 41.11 | 95.45 |
R2 | 21,361,892 | 6,362,961,796 | 40.9 | 95.26 |
R3 | 21,484,903 | 6,389,008,412 | 41.5 | 95.75 |
ID | Gene Description | Log2.Fold Change (H/N) | Log2.Fold Change (R/N) | Log2.Fold Change (R/H) |
---|---|---|---|---|
CH0900239 | cytochrome P450 3A11 isoform X2 | 2.07 | - | −1.08 |
CH0603576 | egl nine homolog 1 isoform X2 (EGLN1) | 2.4 | - | −2.50 |
CH1000250 | transient receptor potential cation channel subfamily M member 2 (TRPM2) | −2.41 | −2.23 | - |
CH1001282 | tyramine beta-hydroxylase (TBH) | 1.23 | 2.05 | - |
CH0900166 | superoxide dismutase (SOD) | −1.09 | −1.27 | - |
CH0502591 | alternative oxidase, mitochondrial (AOX) | 1.75 | - | - |
CH0200562 | globin isoform X3 | 4.16 | - | −4.22 |
CH0502351 | glutathione S-transferase (GST) | - | 1.39 | 1.95 |
CH0202054 | S-crystallin SL11 | 1.21 | 1.24 | - |
CH0202058 | S-crystallin SL11-like | - | 1.19 | - |
CH0102986 | glutathione S-transferase P 1 isoform X1 (GST) | - | −1.01 | - |
CH0403890 | Phosphoenolpyruvate carboxykinase (PEPCK) | - | - | −1.05 |
CH0301448 | methionine adenosyltransferase 2 subunit beta (MAT2A) | −1.38 | - | - |
CH0900455 | asparagine synthetase (ASNS) | 1.55 | - | |
CH1000346 | cytoplasmic aconitate hydratase isoform X2 | 1.04 | - | −1.52 |
CH0403169 | carbonyl reductase (CR) | 1.34 | - | |
CH0201309 | xanthine dehydrogenase/oxidase-like | 1.641 | - | −1.65 |
CH0302869 | uricase-like | 1.18 | - | −1.11 |
CH0303655 | senecionine N-oxygenase (SNO) | - | 1.03 | - |
CH0601326 | xanthine dehydrogenase/oxidase | - | −1.33 | - |
CH0203696 | xanthine dehydrogenase | - | - | −1.83 |
Pathway ID | Pathway Term | DEGs Name |
---|---|---|
Hypoxia (H) vs. Normoxia (N) | ||
ko01230 | biosynthesis of amino acids | MAT2A; ASNS; cytoplasmic aconitate hydratase isoform X2 |
ko00232 | caffeine metabolism | xanthine dehydrogenase/oxidase-like; uricase-like |
ko00980 | metabolism of xenobiotics by cytochrome P450 | S-crystallin SL11; CR |
ko04066 | HIF-1 signaling pathway | EGLN1 |
Reoxygenation (R) vs. Normoxia (N) | ||
ko00982 | drug metabolism-cytochrome P450 | glutathione S-transferase P 1 isoform X1; S-crystallin SL11; S-crystallin SL11-like; SNO; glutathione S-transferase |
ko00980 | metabolism of xenobiotics by cytochrome P450 | glutathione S-transferase P 1 isoform X1; S-crystallin SL11; S-crystallin SL11-like; glutathione S-transferase |
ko00232 | caffeine metabolism | xanthine dehydrogenase/oxidase |
Reoxygenation (R) vs. Hypoxia (H) | ||
ko00232 | caffeine metabolism | xanthine dehydrogenase/oxidase-like; xanthine dehydrogenase; uricase-like |
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He, P.; Li, W.; Wei, P.; Jiang, L.; Guan, J.; Ma, Y.; Zhang, L.; Chen, Y.; Zheng, Y.; Zhang, X.; et al. Antioxidant Capacity, Enzyme Activities Related to Energy Metabolism, and Transcriptome Analysis of Crassostrea hongkongensis Exposed to Hypoxia. Antioxidants 2024, 13, 1063. https://doi.org/10.3390/antiox13091063
He P, Li W, Wei P, Jiang L, Guan J, Ma Y, Zhang L, Chen Y, Zheng Y, Zhang X, et al. Antioxidant Capacity, Enzyme Activities Related to Energy Metabolism, and Transcriptome Analysis of Crassostrea hongkongensis Exposed to Hypoxia. Antioxidants. 2024; 13(9):1063. https://doi.org/10.3390/antiox13091063
Chicago/Turabian StyleHe, Pingping, Wei Li, Pinyuan Wei, Linyuan Jiang, Junliang Guan, Yuan Ma, Li Zhang, Yongxian Chen, Yusi Zheng, Xingzhi Zhang, and et al. 2024. "Antioxidant Capacity, Enzyme Activities Related to Energy Metabolism, and Transcriptome Analysis of Crassostrea hongkongensis Exposed to Hypoxia" Antioxidants 13, no. 9: 1063. https://doi.org/10.3390/antiox13091063