Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Heat Stress Experiment and Sample Collection
2.2. RNA Extraction, Library Construction, and Sequencing
2.3. Sequencing Quality Detection and Comparison
2.4. Differential Gene Expression Analysis
2.5. STEM Analysis
2.6. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) Validation of mRNA Expression Patterns
3. Results
3.1. Transcriptome Sequencing
3.2. Differential Gene Expression Analysis
3.3. Expression Trend and Enrichment Analysis of DEGs
3.4. Validation of Gene Expression Patterns by qRT-PCR
4. Discussion
4.1. Protein Homeostasis
4.1.1. HSPs and Correct Folding of Proteins
4.1.2. Ubiquitin-Proteasome System (UPS) and Protein Degradation
4.2. Adaptation to Hypoxia and Transition of Energy Metabolism
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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Primer Name | Forward Primer (5′ to 3′) | Reverse Primer (5′ to 3′) |
---|---|---|
PFKL | CATGTGTGCTTGGCCTCAAC | GGCCGCAGATTATACCACCA |
HSP90AB1 | CATTTCTCAGTGGAGGGCCA | GAGATGTTGAGGGGCAGGTC |
ENO1 | CTGACGACCCTAACCGCTAC | TCACCCACCACCTGGATACT |
EPO | CTCAGCTTGCTACGGTCCTC | CACCGTCCATGTTCCCTCAA |
GAPDH | TCGGAGTCGCAAGACAGACA | AACCTTCTTGGAGTGGAAAGCA |
ALDOCB | TATCCCGCACTGACTCCTGA | TGTGTTCTCAACCCCGATGG |
MKNK2 | CTGTGGCTGGGAATTAGGGG | GGTTTTTGGCATCCCGAACC |
PSMB3 | TACATCGAGCCCGTGATTGC | CACACATGCCGTACATCTGC |
HIF1A | GACACATTGGCATCACGCAG | TGTCTGCGGCTTCTTACTCG |
PSMC5 | CCCAAGGGTGTGCTGTTGTA | GCACCCTCTCCGATGAACTT |
PSMD1 | TGGCCTAGCAGTGGGAATTG | AGTGTACATTCCAGAGCGCC |
Sample | Raw Reads Number | Clean Reads Number | Raw Bases (bp) | Clean Bases (bp) | Error Rate (%) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|---|---|
CT1 | 45,449,954 | 45,392,066 | 6,817,493,100 | 6,779,000,457 | 0.13 | 97.97 | 94.1 | 50.71 |
CT2 | 44,500,604 | 44,444,572 | 6,675,090,600 | 6,639,750,913 | 0.13 | 98.04 | 94.24 | 50.21 |
CT3 | 46,646,638 | 46,596,420 | 6,996,995,700 | 6,948,044,496 | 0.11 | 98.02 | 94.18 | 50.19 |
HT31-1 | 37,526,202 | 37,480,302 | 5,628,930,300 | 5,593,758,917 | 0.12 | 97.81 | 93.71 | 50.67 |
HT31-2 | 40,355,502 | 40,304,816 | 6,053,325,300 | 6,014,917,041 | 0.13 | 97.88 | 93.92 | 50.12 |
HT31-3 | 39,904,620 | 39,857,718 | 5,985,693,000 | 5,949,485,580 | 0.12 | 97.99 | 94.16 | 50.78 |
HT34-1 | 43,571,734 | 43,524,904 | 6,535,760,100 | 6,493,798,692 | 0.11 | 98.11 | 94.38 | 51.23 |
HT34-2 | 45,659,610 | 45,602,954 | 6,848,941,500 | 6,798,784,900 | 0.12 | 97.94 | 94 | 52.84 |
HT34-3 | 43,264,302 | 43,214,412 | 6,489,645,300 | 6,448,179,655 | 0.12 | 98.09 | 94.38 | 51.07 |
Sample | High Quality Clean Reads Number (%) | Unmapped (%) | Unique Mapped (%) | Multiple Mapped (%) | Total Mapped (%) |
---|---|---|---|---|---|
CT1 | 45,161,002 (99.49%) | 3,409,069 (7.55%) | 38,298,481 (84.80%) | 3,453,452 (7.65%) | 41,751,933 (92.45%) |
CT2 | 44,019,362 (99.04%) | 3,303,947 (7.51%) | 37,445,636 (85.07%) | 3,269,779 (7.43%) | 40,715,415 (92.49%) |
CT3 | 46,521,200 (99.84%) | 2,776,762 (5.97%) | 39,787,437 (85.53%) | 3,957,001 (8.51%) | 43,744,438 (94.03%) |
HT31-1 | 37,301,710 (99.52%) | 2,670,282 (7.16%) | 31,797,678 (85.24%) | 2,833,750 (7.60%) | 34,631,428 (92.84%) |
HT31-2 | 40,179,202 (99.69%) | 3,327,393 (8.28%) | 33,573,047 (83.56%) | 3,278,762 (8.16%) | 36,851,809 (91.72%) |
HT31-3 | 39,515,610 (99.14%) | 3,218,708 (8.15%) | 33,369,322 (84.45%) | 2,927,580 (7.41%) | 36,296,902 (91.85%) |
HT34-1 | 43,441,596 (99.81%) | 2,913,743 (6.71%) | 37,249,288 (85.75%) | 3,278,565 (7.55%) | 40,527,853 (93.29%) |
HT34-2 | 41,427,788 (90.84%) | 9,231,820 (22.28%) | 29,895,198 (72.16%) | 2,300,770 (5.55%) | 32,195,968 (77.72%) |
HT34-3 | 42,779,862 (98.99%) | 3,236,432 (7.57%) | 36,188,522 (84.59%) | 3,354,908 (7.84%) | 39,543,430 (92.43%) |
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Li, Q.-Q.; Zhang, J.; Wang, H.-Y.; Niu, S.-F.; Wu, R.-X.; Tang, B.-G.; Wang, Q.-H.; Liang, Z.-B.; Liang, Y.-S. Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress. Animals 2023, 13, 2053. https://doi.org/10.3390/ani13132053
Li Q-Q, Zhang J, Wang H-Y, Niu S-F, Wu R-X, Tang B-G, Wang Q-H, Liang Z-B, Liang Y-S. Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress. Animals. 2023; 13(13):2053. https://doi.org/10.3390/ani13132053
Chicago/Turabian StyleLi, Qian-Qian, Jing Zhang, Hong-Yang Wang, Su-Fang Niu, Ren-Xie Wu, Bao-Gui Tang, Qing-Hua Wang, Zhen-Bang Liang, and Yan-Shan Liang. 2023. "Transcriptomic Response of the Liver Tissue in Trachinotus ovatus to Acute Heat Stress" Animals 13, no. 13: 2053. https://doi.org/10.3390/ani13132053