Detoxification, Apoptosis, and Immune Transcriptomic Responses of the Gill Tissue of Bay Scallop Following Exposure to the Algicide Thiazolidinedione 49
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal Maintenance and TD49 Exposure
2.2. RNA Preparation
2.3. Library Preparation and Illumina Sequencing
2.4. De Novo Transcriptome Assembly
2.5. Gene Annotation and Analysis
2.6. Enrichment Analysis of DEGs
2.7. Quantitative Real-Time PCR Verification
2.8. Statistical Analysis
3. Results
3.1. Analysis of DGE Libraries
3.2. Functional Annotation and Species Distribution
3.3. DEG Analysis
3.4. Enrichment and Pathway Analysis
3.5. Genes Related to TD49-Induced Stress Response
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample | Total Raw Reads (Mb) | Total Clean Reads (Mb) | Total Clean Bases (Gb) | Clean Reads Q20 (%) | Clean Reads Q30 (%) | Clean Reads Ratio (%) |
---|---|---|---|---|---|---|
CN | 45.92 | 45.76 | 4.58 | 98.21 | 95.30 | 99.65 |
TD | 45.92 | 45.85 | 4.58 | 98.30 | 95.52 | 99.84 |
Sample | Total Number | Total Length | Mean Length | N50 | N70 | N90 | GC (%) |
---|---|---|---|---|---|---|---|
CN | 78,376 | 52,817,747 | 673 | 1231 | 568 | 252 | 39.12 |
TD | 71,899 | 45,492,111 | 632 | 1093 | 518 | 245 | 39.23 |
Sample | Total Number | Total Length | Mean Length (bp) | N50 | N70 | N90 | GC (%) |
---|---|---|---|---|---|---|---|
CN | 51,394 | 40,985,988 | 797 | 1410 | 702 | 302 | 39.48 |
TD | 48,654 | 36,217,952 | 744 | 1266 | 637 | 288 | 39.54 |
All-unigene | 57,882 | 50,329,144 | 869 | 1594 | 827 | 321 | 39.36 |
Values | Total | Nr- Annotated | Nt- Annotated | SwissProt- Annotated | KEGG- Annotated | COG- Annotated | Interpro- Annotated | GO- Annotated | Overall |
---|---|---|---|---|---|---|---|---|---|
Number | 57,882 | 25,267 | 9983 | 19,555 | 18,931 | 8729 | 19,017 | 4032 | 28,172 |
Percentage | 100% | 43.65% | 17.25% | 33.78% | 32.71% | 15.08% | 32.85% | 6.97% | 48.67% |
Description | Transcript | Log2 Fold Change (RNAseq) | Regulation |
---|---|---|---|
Downregulated | |||
Immune system | CLEC 4M | −1.62 | Down |
CLEC 4F | −2.69 | Down | |
FIBCD 1 | −2.00 | Down | |
ACP 5 | −2.94 | Down | |
ACP 6 | −2.40 | Down | |
PAPL | −1.27 | Down | |
HSP70 | −2.00 | Down | |
Apoptosis | Bcl-2 | −1.90 | Down |
BIRC 2 | −2.51 | Down | |
BIRC 3 | −4.97 | Down | |
BIRC 6 | −4.25 | Down | |
BIRC 7A | −1.33 | Down | |
BIRC 7B | −1.61 | Down | |
Transmembrane proteins | ABC A3 | −5.01 | Down |
ABC A5 | −2.80 | Down | |
ABC B1 | −2.11 | Down | |
ABC B10 | −4.27 | Down | |
ABC C1 | −1.16 | Down | |
ABC D3 | −1.32 | Down | |
ABC G2 | −1.95 | Down | |
Antioxidant system | NQO1 | −5.10 | Down |
CAT | −3.06 | Down | |
Mn SOD | −1.30 | Down | |
Cu/Zn SOD | −1.56 | Down | |
GR | −5.08 | Down | |
GPx | −2.55 | Down | |
Nrf2 | −1.61 | Down | |
Metabolism of xenobiotics | CREBP 3 | −1.39 | Down |
MOA | −1.79 | Down | |
NOX3 | −1.55 | Down | |
GSTω | −11.18 | Down | |
Upregulated | |||
Apoptosis | Cas3 | 2.29 | Up |
Cas6 | 2.79 | Up | |
FADD | 1.68 | Up | |
Immune system | TLR 2 | 4.18 | Up |
TRAF 6 | 1.17 | Up | |
Metabolism of xenobiotics | CYP 1A1 | 2.45 | Up |
CYP 2C8 | 8.52 | Up | |
GST ζ1 | 8.40 | Up | |
GST 1 | 3.08 | Up | |
GSTσ3 | 3.20 | Up | |
GST A | 3.41 | Up | |
GSTκ1 | 1.74 | Up |
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Chi, C.; Giri, S.S.; Jun, J.W.; Kim, H.J.; Yun, S.; Kim, S.W.; Kang, J.W.; Park, S.C. Detoxification, Apoptosis, and Immune Transcriptomic Responses of the Gill Tissue of Bay Scallop Following Exposure to the Algicide Thiazolidinedione 49. Biomolecules 2019, 9, 310. https://doi.org/10.3390/biom9080310
Chi C, Giri SS, Jun JW, Kim HJ, Yun S, Kim SW, Kang JW, Park SC. Detoxification, Apoptosis, and Immune Transcriptomic Responses of the Gill Tissue of Bay Scallop Following Exposure to the Algicide Thiazolidinedione 49. Biomolecules. 2019; 9(8):310. https://doi.org/10.3390/biom9080310
Chicago/Turabian StyleChi, Cheng, Sib Sankar Giri, Jin Woo Jun, Hyoun Joong Kim, Saekil Yun, Sang Wha Kim, Jeong Woo Kang, and Se Chang Park. 2019. "Detoxification, Apoptosis, and Immune Transcriptomic Responses of the Gill Tissue of Bay Scallop Following Exposure to the Algicide Thiazolidinedione 49" Biomolecules 9, no. 8: 310. https://doi.org/10.3390/biom9080310