Salinity Stress Mechanisms in Sepia esculenta Larvae Revealed by Integrated Biochemical and Transcriptome Analyses
Abstract
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Acquisition and Processing of Experimental Samples
2.2. Determination of Enzyme Activity and Related Product Content
2.3. Transcriptome Data Processing and Analysis
2.4. Analysis of DEGs
2.5. Functional Analysis of DEGs
2.6. Protein-Protein Interaction Networks Analysis
2.7. qRT-PCR Validation
2.8. Statistical Analysis
3. Results
3.1. Sequencing Results
3.2. Enzyme Activity and Peroxide Content
3.3. Identification of DEGs
3.4. Clustering Heatmap Analysis
3.5. Functional Analysis of DEGs
3.6. GSEA Analysis
3.7. Analysis of PPI
3.8. qRT-PCR Validation of DEGs
4. Discussion
4.1. Expression and Functional Enrichment Analysis of DEGs
4.2. Discussion on Enzyme Activity and Peroxide Content
4.3. Chemokine Signaling Pathway
4.4. MAPK Signaling Pathway
4.5. Cell Cycle Pathway
4.6. Review of Key Gene Sets and Genes Under Different Salinity Stress
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
S. esculenta | Sepia esculenta |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
DEGs | Differentially expressed genes |
qRT-PCR | quantitative Reverse Transcription Polymerase Chain Reaction |
PPI | Protein-Protein Interaction |
GSEA | Gene Set Enrichment Analysis |
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Gene Name | Forward Primer (5′-3′) | TM (°C) | Reverse Primer (5′-3′) | TM (°C) | Amplicon Length (bp) |
---|---|---|---|---|---|
CDC16 | TAGCAAAGCGACCACATTAG | 60 | CTGGGAGGCAGTGAAATAAG | 60 | 118 |
CDC25B | CTGCCAATAAAGACTGCTATCC | 61 | CTCACACATTTCCGTTCCAC | 61 | 101 |
CDC42 | GTTGTGGTTGGTGATGGT | 60 | GCCCTGCAGTATCAAAGAG | 60 | 163 |
CDC45 | CCCGATGATGATGTCTGTTT | 60 | CTGGGATGTCTCTCATTTCTTC | 60 | 121 |
CDC6 | CAGGTGGCAGCCTTTATATT | 60 | CTCACTCCCATGCAGTTAAG | 60 | 130 |
CDK1 | GCCAGGAGTAACCTCATTAC | 60 | AAGTCCTGCGTCATCTAATC | 59 | 100 |
CHEK1 | CTTGGAGAAGGTGCTTATGG | 60 | CCCTGACAGAAACCTCTTTATC | 60 | 106 |
DUSP1 | GCAGACGTAGCGTCATTT | 60 | GGGAGTGATGATGTCCTAAAC | 60 | 172 |
DUSP10 | CGGTGCGAATATCCTTATCC | 60 | CGCTTCTGTTTCACGTATCT | 60 | 126 |
DUSP7 | CCCTTAACGTCCTTGGTATT | 59 | GCTGGATGGATTCTCGTTTA | 60 | 125 |
ESPL1 | AGCACCACCAGTAGAGATAA | 60 | CTCTTGGCAGTCCTTTAGTG | 60 | 117 |
FLNA | TGACAGAAGTGCTGCTAAAC | 60 | GGTTCGAGAGGCATGTAATC | 60 | 123 |
GSK3B | TGTGCCTGAGACTGTGTA | 60 | CTCCTTGGGAATGGATGTATG | 60 | 128 |
JUN | ATGTGACCGAAGAACAAGAG | 60 | GTGGAGGCGATGTAGAATTT | 60 | 102 |
MAD2L1 | GGCTTATAGAGATGGTGTTGG | 60 | CCAGTGTCATCTTCCACATC | 60 | 103 |
MAP2K1 | CCATGACTGGGAAACCTTTA | 60 | AGGGTGGAGGCTCATTTA | 60 | 129 |
MAPKAPK2 | GCCCAAATCACGAAGAGAA | 60 | CAACAAGGAAGGCACACT | 60 | 112 |
MRAS | CTTGCCGCTCACCTTAAT | 60 | GTGGCTGCTCTCGAATAAT | 60 | 109 |
MYC | CACCTGGAACGAGAAAGAAG | 60 | TCGTAGCCTCATCCACAA | 60 | 121 |
NFKB1 | GCCTGCATAAAGCTGTTAGA | 60 | AGAGCAGTCTGGGACTTT | 60 | 127 |
NFKBIA | CTGCCCTCCAGAAACATTAC | 60 | CCCATGTTCAGCAGCATAA | 60 | 116 |
PIK3CA | GCAGGTGATCAGGATTATGG | 60 | GCAGCAGGAACAACTTCA | 60 | 120 |
PIK3CD | GGTGTTGTACGTGATAGAGTG | 60 | CGGCTGCTGGAACAAATA | 60 | 131 |
PIK3R1 | GGCGAGTTATCAAGAGAAGAG | 60 | TCTAAGGGTCAGAGTGTAGTC | 60 | 108 |
PTK2 | GAAGTCACGAGAAAGCTACTG | 60 | CCGAAGTTCATACCTCCATTC | 60 | 106 |
RAC2 | AGGCAATTGGTGGGTTAG | 59 | CGCAGAACACTCCATGTAT | 60 | 107 |
ROCK1 | TTGTATGCGGATGGATGTG | 60 | CATCACCACCTTGGGATTT | 60 | 101 |
SOS1 | CAGGAAGCAAGTGGAGAAAG | 61 | GAACTGTAAGTGGTGAGGAATG | 61 | 125 |
TFDP1 | GACACATCCTACCTCCTTTATG | 60 | CAACATTTGGGCTTTGATCC | 60 | 133 |
VAV1 | CAGTGATGACGAGGACATCTA | 61 | CTTCCTCTTCGTACACAACATC | 61 | 101 |
Sample | Raw Reads | Raw Bases | Clean Reads | Clean Bases | Q20 (%) | Q30 (%) | Total Mapping |
---|---|---|---|---|---|---|---|
C_0h_1 | 461,138,06 | 6.92G | 449,821,04 | 6.75G | 97.07 | 92.32 | 39456868 (87.72%) |
C_0h_2 | 505,451,56 | 7.58G | 493,877,00 | 7.41G | 97.44 | 93.02 | 44052010 (89.20%) |
C_0h_3 | 475,155,46 | 7.13G | 463,599,16 | 6.95G | 97.27 | 92.68 | 41025164 (88.49%) |
C_4h_1 | 461,799,90 | 6.93G | 451,241,90 | 6.77G | 96.77 | 91.61 | 39813899 (88.23%) |
C_4h_2 | 464,091,28 | 6.96G | 449,101,60 | 6.74G | 97.27 | 92.62 | 40048934 (89.18%) |
C_4h_3 | 443,214,76 | 6.65G | 430,526,24 | 6.46G | 96.27 | 90.81 | 37441672 (86.97%) |
C_24h_1 | 447,868,92 | 6.72G | 431,101,54 | 6.47G | 95.85 | 90.05 | 37201612 (86.29%) |
C_24h_2 | 449,431,88 | 6.74G | 433,935,64 | 6.51G | 95.83 | 90.02 | 37413049 (86.22%) |
C_24h_3 | 457,950,96 | 6.87G | 448,865,64 | 6.73G | 97.42 | 92.92 | 39924459 (88.95%) |
SAL20_4h_1 | 460,619,26 | 6.91G | 448,902,60 | 6.73G | 97.06 | 92.29 | 39336186 (87.63%) |
SAL20_4h_2 | 459,147,26 | 6.89G | 445,807,56 | 6.69G | 97.22 | 92.65 | 39383060 (88.34%) |
SAL20_4h_3 | 501,220,24 | 7.52G | 486,853,20 | 7.30G | 95.69 | 89.74 | 42000224 (86.27%) |
SAL20_24h_1 | 426,766,10 | 6.40G | 415,836,98 | 6.24G | 97.26 | 92.68 | 36631715 (88.09%) |
SAL20_24h_2 | 476,870,56 | 7.15G | 463,630,26 | 6.95G | 97.36 | 92.84 | 40997032 (88.43%) |
SAL20_24h_3 | 464,417,70 | 6.97G | 451,153,78 | 6.77G | 97.41 | 92.91 | 39895803 (88.43%) |
SAL40_4h_1 | 466,644,44 | 7.00G | 448,498,10 | 6.73G | 97.45 | 93.00 | 39852403 (88.86%) |
SAL40_4h_2 | 412,505,16 | 6.19G | 401,588,60 | 6.02G | 95.80 | 89.92 | 34776949 (86.60%) |
SAL40_4h_3 | 455,434,02 | 6.83G | 440,828,56 | 6.61G | 97.33 | 92.81 | 39194280 (88.91%) |
SAL40_24h_1 | 459,581,10 | 6.89G | 447,316,52 | 6.71G | 97.52 | 93.10 | 39903972 (89.21%) |
SAL40_24h_2 | 477,382,44 | 7.16G | 465,891,80 | 6.99G | 97.49 | 93.38 | 41137815 (88.30%) |
SAL40_24h_3 | 476,587,96 | 7.15G | 465,246,48 | 6.98G | 97.21 | 92.51 | 41317022 (88.81%) |
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Zhao, Y.; Zhu, X.; Zhang, J.; Wang, W.; Cui, C.; Tan, X.; Liu, X.; Xu, X.; Li, Z.; Yang, J. Salinity Stress Mechanisms in Sepia esculenta Larvae Revealed by Integrated Biochemical and Transcriptome Analyses. Biology 2025, 14, 1338. https://doi.org/10.3390/biology14101338
Zhao Y, Zhu X, Zhang J, Wang W, Cui C, Tan X, Liu X, Xu X, Li Z, Yang J. Salinity Stress Mechanisms in Sepia esculenta Larvae Revealed by Integrated Biochemical and Transcriptome Analyses. Biology. 2025; 14(10):1338. https://doi.org/10.3390/biology14101338
Chicago/Turabian StyleZhao, Yancheng, Xueyu Zhu, Jingzhao Zhang, Weijun Wang, Cuiju Cui, Xin Tan, Xiumei Liu, Xiaohui Xu, Zan Li, and Jianmin Yang. 2025. "Salinity Stress Mechanisms in Sepia esculenta Larvae Revealed by Integrated Biochemical and Transcriptome Analyses" Biology 14, no. 10: 1338. https://doi.org/10.3390/biology14101338
APA StyleZhao, Y., Zhu, X., Zhang, J., Wang, W., Cui, C., Tan, X., Liu, X., Xu, X., Li, Z., & Yang, J. (2025). Salinity Stress Mechanisms in Sepia esculenta Larvae Revealed by Integrated Biochemical and Transcriptome Analyses. Biology, 14(10), 1338. https://doi.org/10.3390/biology14101338