Transcriptome-Based Identification of Genes Responding to the Organophosphate Pesticide Phosmet in Danio rerio
Abstract
:1. Introduction
2. Results
2.1. Effects of Phosmet on ZF Development
2.2. Transcriptome Analysis
2.3. Gene Ontology Term Enrichment
2.4. Functional Annotation of DEGs
2.5. qPCR Validation of Randomly Selected DEGs
3. Discussion
4. Materials and Methods
4.1. Ethics Statement
4.2. ZF Maintenance and Embryo Collection
4.3. Pesticide Treatment and Deformities Scoring
4.4. Heartbeat Survey
4.5. TEER and VMER
4.6. Body Length Survey
4.7. RNA Sequencing Preparations
4.8. Transcriptome Alignment and Analysis of DEGs
4.9. Gene Ontology and Pathway Enrichment Analysis
4.10. Quantitative Real-Time PCR
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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Time | Deformity (%) | NTZF | PTZF |
---|---|---|---|
24 hpf | Mortality | 0 | 17.50 ± 2.89 * |
Edema symptoms | 2.50 ± 1.44 | 19.54 ± 7.11 * | |
Abnormal somites | 2.50 ± 1.25 | 69.76 ± 8.02 * | |
48 hpf | Mortality | 0 | 32.50 ± 2.89 * |
Low retina pigment | 0 | 63.07 ± 8.99 * | |
Abnormal tail blood flow | 1.25 ± 1.25 | 53.85 ± 7.97 * | |
Hyperemia | 0 | 44.22 ± 10.84 * | |
72 hpf | Mortality | 2.50 ± 1.44 | 43.75 ± 6.29 * |
Unhatched embryos | 1.25 ± 1.25 | 78.22 ± 6.05 * | |
Pericardial edema | 3.88 ± 1.30 | 61.63 ± 11.05 * | |
Yolk sac edema | 2.57 ± 1.48 | 48.11 ± 9.31 * | |
96 hpf | Mortality | 2.50 ± 1.44 | 52.50 ± 3.23 * |
Unhatched embryos | 0 | 82.29 ± 8.01 * | |
Body curvature | 0 | 80.21 ± 5.15 * | |
VMER | 25.00 ± 5.00 | 100.00 * | |
TEER | 10.00 ± 5.77 | 90.00 ± 5.77 * |
Samples | Total Reads | Clean Reads | Mapped Reads | Mapped Rate (%) | Q20 (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|---|---|
NTZF-1 | 72,783,012 | 71,783,716 | 60,458,452 | 84.22 | 98.91 | 96.05 | 43.62 |
NTZF-2 | 61,925,392 | 60,857,682 | 51,896,692 | 85.28 | 98.91 | 96.06 | 44.95 |
NTZF-3 | 60,878,020 | 59,726,314 | 51,603,485 | 86.4 | 98.85 | 95.87 | 46.00 |
PTZF-1 | 69,410,088 | 68,273,094 | 45,753,478 | 67.02 | 98.89 | 96.11 | 53.24 |
PTZF-2 | 66,557,046 | 65,493,004 | 55,524,220 | 84.78 | 98.92 | 96.13 | 49.44 |
PTZF-3 | 74,253,266 | 73,041,798 | 61,232,206 | 83.83 | 98.97 | 96.27 | 47.69 |
Term | Genes | p-Value | FDR |
---|---|---|---|
Metabolic pathways | gls2a, gls2b, gpx9, gda, hacd1, chia.2, gyg1b, tecrl2b, zgc:153896, elovl4b, zgc:153704, cyp7a1, zgc:103586, pgam2, pde6g, lpin1, ATP8, aoc1, LOC559107, ndufa4l2a, zgc:109982, pts, tyr, si:ch211-214p16.3, gch2, ampd1, mdh1ab, ND4L, tecrl2a, dhrs3a, atpv0e2, agxta, chs1, cyp21a2, aldoab, gal3st1a, ckmt2b, th2, si:dkey-78a14.5, dpm3, spam1, csgalnact1b, nat8l, ptges, atp5ia, nme2a, ND1, ND3, ND5, gpx8, ND2, si:dkey-78a14.4, aanat2, ndufa1, adssl1, si:ch211-217a12.1, ATP6, entpd8, alpi.2, tymp, ndufa4, elovl8a, entpd5a, zgc:112320, pigw, haao, CYTB, ckma, cel.1, gstk4, hao2, nme2b.2, pigh, pfkma, hpda, pnp4b, ND4, aldh3b2, smyd1a, b3gnt5a, mocs1, uox, st3gal7, si:ch211-106j24.1, pde6c, ndufa2, ugt5e1, fhit, sdhdb, acot19, agxtb, cyp2r1, COX3, COX1, COX2, tyrp1b, pde6d, acp5a *, sgpp2 *, galnt6 *, pik3c2g *, gal3st1b *, ugt5a1 *, atic *, glulc *, sqlea *, alp3 *, aldh3b1 *, p4ha1b *, paics *, elovl6l *, ethe1 *, plcd1a *, zgc:100864 *, zgc:154054 *, ugt1a5 *, cmasb *, aldob *, gstm.3 *, cyp24a1 *, ugt1a7 *, cbr1l *, zgc:123275 *, fut9d *, zgc:112332 *, b4galnt3b *, hao1 *, ugt1a1 *, mthfd1l *, si:ch73-337l15.2 *, ugt5a4 *, ptgs2b *, cmbl *, mgst1.2 *, rdh12l *, dao.1 *, zgc:163121 *, nansb *, si:ch211-276a23.5 *, cox4i1l *, pla2g4f.1 *, ugt1a2 *, ugt1a6 *, cyp3a65 *, cyp17a1 *, alas2 *, ptgs2a *, bhmt *, sqrdl *, nqo1 *, LOC565422 *, ptgis *, gstp1 *, ugt2a4 *, gstp2 * | 1.14402 × 10−53 | 1.61306 × 10−51 |
Calcium signaling pathway | slc25a4, adrb2b, atp2a1l, mylk4b, stim2a, mylk4a, camk1gb, fgf4, ednraa, casq1a, trdn, tnnc2, p2rx5, avpr1aa, p2rx8, si:rp71-17i16.4, cacna1sb, casq2, calm1b, egf, ednrba, zgc:56235, casq1b, orai1a, si:dkey-247m21.3, fgf1a, p2rx3a, ryr3, atp2a1, phkg1b, tacr3a *, mcoln3a *, plcd1a *, p2rx1 *, si:dkey-251i10.1 *, cxcr4a *, ltb4r2a *, gna15.1 *, gna14 * | 2.39485 × 10−15 | 1.68837 × 10−13 |
Phototransduction | opn1mw2, gngt1, opn1mw1, guca1c, gnat1, guca1d, pde6g, rhol, gnat2, rho, guca1e, rcvrnb, rcvrn2, grk7a, rcvrn3, calm1b, zgc:112320, cnga1 | 6.05641 × 10−15 | 2.84651 × 10−13 |
Cardiac muscle contraction | atp2a1l, si:ch211-139a5.9, cacng6b, zgc:163073, zgc:86725, cacng1a, trdn, tnnt2d, atp1b1a, tpm4b, tnnt2e, cacna1sb, casq2, atp1b2b, CYTB, atp1a3b, atp1b4, smyhc1, atp2a1, atp1b2a, COX3, COX1, COX2, cox4i1l *, atp1a1a.2 * | 2.86244 × 10−14 | 1.00901 × 10−12 |
Drug metabolism—other enzymes | zgc:103586, si:dkey-78a14.5, nme2a, si:dkey-78a14.4, gstk4, nme2b.2, aldh3b2, ugt5e1, ugt5a1 *, tpmt.1 *, tpmt.2 *, aldh3b1 *, ugt1a5 *, gstm.3 *, ugt1a7 *, ugt1a1 *, ugt5a4 *, mgst1.2 *, ugt1a2 *, ugt1a6 *, gstp1 *, ugt2a4 *, gstp2 * | 4.12652 × 10−13 | 1.16368 × 10−11 |
Cell adhesion molecules | cldn7a, cldn19, mpz, cldn5b, mag, si:ch211-286o17.1, cldnj, cdh15, itgb1a, cd99l2, cldnf, cdh1, cldnc, cldn8, itgb1b.1, oclnb, zgc:110333, cldn7b, cldnb, oclna, cldn1, cldne, si:ch211-95j8.5, cldni, zgc:136892 | 2.61473 × 10−12 | 6.14462 × 10−11 |
Aminoacyl-tRNA biosynthesis | trnS2, trnA, trnH, trnD, trnE, trnG, trnK, trnN, trnM, trnY, trnP, trnQ, trnC, trnR, trnI, trnL1, trnS1 | 4.82031 × 10−12 | 9.70947 × 10−11 |
Biosynthesis of cofactors | pts, gch2, dhrs3a, nme2a, adssl1, alpi.2, haao, nme2b.2, hpda, mocs1, ugt5e1, ugt5a1, alp3, ugt1a5, ugt1a7, zgc:112332, ugt1a1, mthfd1l, ugt5a4, rdh12l, ugt1a2, ugt1a6, alas2, nqo1, ugt2a4 | 2.2858 × 10−11 | 3.55548 × 10−10 |
Metabolism of xenobiotics by cytochrome P450 | gstk4, aldh3b2, ugt5e1, ugt5a1,aldh3b1, ugt1a5, gstm.3, ugt1a7, cbr1l, ugt1a1, ugt5a4, mgst1.2, ugt1a2, ugt1a6, gstp1, ugt2a4, gstp2 | 2.50462 × 10−11 | 3.55548 × 10−10 |
Regulation of actin cytoskeleton | cfl2, cxcl12b, mylk4b, mylk4a, fgf4, mylpfb, cxcl12a, LOC101885790, si:dkey-44g17.6, itga10, egf, tmsb, scinla, pfn2l, itgb1a, fgf1a, si:ch73-116o1.2, brk1, itga2.2, itgb1b.1, cxcr4a, rac2, zgc:86896, myh9a, fn1b, itgb3a, gsnb, pfn1, cfl1l, zgc:101810 | 2.52162 ×10−11 | 3.55548 ×10−10 |
Gene Symbol | Fold Change (RNA-Seq) | Fold Change (qPCR) (Mean ± SD) |
---|---|---|
gna14 | 6.13 | 4.17 ± 0.14 |
fn1b | 4.14 | 2.13 ± 0.21 |
gstp2 | 12.09 | 5.15 ± 1.28 |
gls2b | −7.25 | −4.40 ± 0.56 |
cnga1 | −2.07 | −2.84 ± 0.55 |
adrb2b | −4.27 | −3.91 ± 1.02 |
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Vasamsetti, B.M.K.; Chon, K.; Kim, J.; Oh, J.-A.; Yoon, C.-Y.; Park, H.-H. Transcriptome-Based Identification of Genes Responding to the Organophosphate Pesticide Phosmet in Danio rerio. Genes 2021, 12, 1738. https://doi.org/10.3390/genes12111738
Vasamsetti BMK, Chon K, Kim J, Oh J-A, Yoon C-Y, Park H-H. Transcriptome-Based Identification of Genes Responding to the Organophosphate Pesticide Phosmet in Danio rerio. Genes. 2021; 12(11):1738. https://doi.org/10.3390/genes12111738
Chicago/Turabian StyleVasamsetti, Bala Murali Krishna, Kyongmi Chon, Juyeong Kim, Jin-A Oh, Chang-Young Yoon, and Hong-Hyun Park. 2021. "Transcriptome-Based Identification of Genes Responding to the Organophosphate Pesticide Phosmet in Danio rerio" Genes 12, no. 11: 1738. https://doi.org/10.3390/genes12111738
APA StyleVasamsetti, B. M. K., Chon, K., Kim, J., Oh, J.-A., Yoon, C.-Y., & Park, H.-H. (2021). Transcriptome-Based Identification of Genes Responding to the Organophosphate Pesticide Phosmet in Danio rerio. Genes, 12(11), 1738. https://doi.org/10.3390/genes12111738