Two Independently Comparative Transcriptome Analyses of Hemocytes Provide New Insights into Understanding the Disease-Resistant Characteristics of Shrimp against Vibrio Infection
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Experimental Animals
2.2. VIE Fluorescent Labeling and Hemolymph Collection
2.3. V. parahaemolyticus Immersion and Hepatopancreas Collection
2.4. DNA Extraction and Bacteria Load Detection
2.5. RNA Extraction and Transcriptome Sequencing
2.6. Clean Data Mapping and Annotations
2.7. Differential Expression and Enrichment Analysis
2.8. Quantitative Real-Time PCR
3. Results
3.1. The Loads of V. parahaemolyticus in Hepatopancreas of Infected Shrimp
3.2. The Correlation of the Transcriptome Data from All Samples
3.3. DEGs between Two Populations and between V. parahaemolyticus Resistant and Susceptible Shrimp
3.4. Enriched GO Items and KEGG Pathways between V. parahaemolyticus-Resistant and Susceptible Shrimp
3.5. Detailed Analysis of DEGs between V. parahaemolyticus-Resistant and Susceptible Shrimp
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AHPND | acute hepatopancreatic necrosis disease |
DEGs | differentially expressed genes |
HIF-1 | hypoxia-inducible factor 1 |
PI3K/Akt | phosphoinositide 3-kinase/protein kinase B |
NF-KappaB | nuclear factor kappa-B |
VIE | visible implant elastomer |
EDTA | ethylene diamine tetraacetic acid |
PCR | polymerase chain reaction |
cDNA | complementary DNA |
NR | non-redundant protein |
KEGG | kyoto encyclopedia of genes and genomes |
COG | clusters of orthologous genes |
FPKM | fragment per kliobase of transcript per million mapped reads |
FDR | false discovery rate |
GO | gene ontology |
PCA | principal component analysis |
WSSV | white spot syndrome virus |
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Gene ID | HcS1_fpkm | HcD1_fpkm | log2(HcD1/HcS1) | FDR | Description |
---|---|---|---|---|---|
ncbi_113820920 | 0.40 | 0.00 | −8.63 | 0.0376 | structural maintenance of chromosomes protein 2-like |
ncbi_113815624 | 0.71 | 0.08 | −3.13 | 0.0154 | vang-like protein 2 |
MSTRG.1662 | 5.77 | 1.38 | −2.07 | 0.0017 | APC membrane recruitment protein 1-like |
ncbi_113812130 | 67.07 | 109.46 | 0.71 | 0.0499 | 4-coumarate—CoA ligase 1 isoform X1 |
ncbi_113824615 | 186.25 | 373.56 | 1.00 | 0.0001 | spermatogonial stem-cell renewal factor |
MSTRG.4583 | 11.36 | 42.55 | 1.91 | 0.0154 | arasin-like protein |
ncbi_113807541 | 51.35 | 197.85 | 1.95 | 0.0397 | immune-associated nucleotide-binding protein 13-like |
ncbi_113817613 | 5.39 | 25.35 | 2.23 | 0.0027 | E3 ubiquitin-protein ligase TRIM32 |
ncbi_113824399 | 82.06 | 388.92 | 2.24 | 0.0023 | Septin-4-like protein |
ncbi_113813611 | 0.34 | 3.21 | 3.24 | 0.0373 | troponin I |
ncbi_113805465 | 0.66 | 6.27 | 3.25 | 0.0017 | myosin light chain 2 |
ncbi_113822686 | 0.65 | 7.58 | 3.55 | 0.0001 | myosin light chain |
ncbi_113820123 | 5.27 | 68.89 | 3.71 | 0.0000 | glyceraldehyde-3-phosphate-dehydrogenase |
ncbi_113819252 | 0.12 | 2.74 | 4.50 | 0.0154 | actin 2 |
ncbi_113816511 | 0.04 | 0.95 | 4.64 | 0.0035 | myosin heavy chain, muscle-like isoform X4 |
MSTRG.15220 | 0.18 | 7.35 | 5.34 | 0.0002 | Retrovirus-related Pol polyprotein from transposon 297 |
ncbi_113807016 | 0.01 | 0.43 | 6.44 | 0.0411 | myosin heavy chain, muscle-like isoform X8 |
ncbi_113823028 | 0.00 | 2.97 | 11.53 | 0.0000 | alpha-(1,6)-fucosyltransferase-like |
ncbi_113829244 | 0.00 | 10.32 | 13.33 | 0.0000 | MAM and LDL-receptor class A domain-containing protein 2-like |
Gene ID | HcS2_fpkm | HcD2_fpkm | log2(HcD2/HcS2) | FDR | Description |
---|---|---|---|---|---|
ncbi_113815990 | 11.16 | 3.46 | −1.69 | 0.0184 | dihydropyrimidinase-like isoform X3 |
ncbi_113825784 | 13.80 | 5.06 | −1.45 | 0.0473 | prohibitin |
ncbi_113824882 | 5.22 | 2.06 | −1.34 | 0.0184 | iroquois-class homeodomain protein IRX-2-like |
ncbi_113829145 | 6.34 | 2.66 | −1.25 | 0.0402 | diacylglycerol kinase 1 |
ncbi_113813376 | 1.43 | 6.81 | 2.26 | 0.0142 | tubulin alpha-3 chain-like |
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Li, S.; Zhang, K.; Du, W.; Li, F. Two Independently Comparative Transcriptome Analyses of Hemocytes Provide New Insights into Understanding the Disease-Resistant Characteristics of Shrimp against Vibrio Infection. Biology 2023, 12, 977. https://doi.org/10.3390/biology12070977
Li S, Zhang K, Du W, Li F. Two Independently Comparative Transcriptome Analyses of Hemocytes Provide New Insights into Understanding the Disease-Resistant Characteristics of Shrimp against Vibrio Infection. Biology. 2023; 12(7):977. https://doi.org/10.3390/biology12070977
Chicago/Turabian StyleLi, Shihao, Keke Zhang, Wenran Du, and Fuhua Li. 2023. "Two Independently Comparative Transcriptome Analyses of Hemocytes Provide New Insights into Understanding the Disease-Resistant Characteristics of Shrimp against Vibrio Infection" Biology 12, no. 7: 977. https://doi.org/10.3390/biology12070977