Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.)
Abstract
:1. Introduction
2. Results
2.1. Identification of C3H Gene Family in Potato
2.2. Location Analysis of C3H Gene Family Members on the Chromosome in Potato
2.3. Multiple Sequence Alignment and Phylogenetic Analysis of C3H Gene Family in Potato
2.4. Analysis of Gene and Protein Structure and Function Prection of C3H Family in Potato
2.5. Collinearity Analysis of C3H Gene Family
2.6. Cis-Acting Elements Analysis
2.7. Expression Analysis of C3H Gene Family in Potato
2.8. RT-qPCR Verification of Expression Level of StC3H Gene Family in Potato
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Identification of C3H Gene Family in Potato
4.3. Location Analysis of C3H Gene Family Members on the Chromosome in Potato
4.4. Multiple Sequence Alignment and Phylogenetic Analysis of C3H Gene Family in Potato
4.5. Analysis of Gene and Protein Structure and Function Prection of C3H Family in Potato
4.6. Collinearity Analysis of StC3H Genes in Potato
4.7. Cis-Acting Elements Analysis
4.8. Expression of StC3H Genes in Different Tissues and Its Response to Different Stress
4.9. Total RNA Extraction and RT-qPCR
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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Gene Name | Gene ID | Protein | Subcellular Location | |||
---|---|---|---|---|---|---|
Number of Amino Acids (aa) | Molecular Weight (Da) | Theoretical pI | Grand Average of Hydropathicity | |||
StC3H-1 | PGSC0003DMG400016400 | 707 | 79,152.04 | 5.80 | −1.060 | Nucleus |
StC3H-2 | PGSC0003DMG400010493 | 650 | 71,922.33 | 6.00 | −0.570 | Nucleus |
StC3H-3 | PGSC0003DMG400024054 | 223 | 23,792.81 | 9.01 | −0.480 | Nucleus |
StC3H-4 | PGSC0003DMG400022651 | 492 | 51,506.80 | 8.41 | −0.390 | Nucleus |
StC3H-5 | PGSC0003DMG400006828 | 739 | 80,448.74 | 5.93 | −0.503 | Nucleus |
StC3H-6 | PGSC0003DMG400006803 | 730 | 79,277.70 | 6.02 | −0.468 | Nucleus |
StC3H-7 | PGSC0003DMG400006330 | 289 | 30,656.69 | 9.33 | −0.438 | Nucleus |
StC3H-8 | PGSC0003DMG400002748 | 129 | 14,562.29 | 8.61 | −0.888 | Cytoplasm |
StC3H-9 | PGSC0003DMG400020705 | 761 | 89,133.84 | 6.62 | −1.436 | Peroxisome |
StC3H-10 | PGSC0003DMG400001658 | 702 | 77,141.25 | 6.67 | −0.512 | Nucleus |
StC3H-11 | PGSC0003DMG400010434 | 477 | 53,542.39 | 5.78 | −0.882 | Nucleus |
StC3H-12 | PGSC0003DMG400013655 | 338 | 38,113.47 | 7.12 | −1.036 | Nucleus |
StC3H-13 | PGSC0003DMG400003622 | 858 | 91,533.33 | 5.48 | −0.722 | Nucleus |
StC3H-14 | PGSC0003DMG400030591 | 341 | 38,323.55 | 6.02 | −0.748 | Nucleus |
StC3H-15 | PGSC0003DMG400009821 | 284 | 30,014.31 | 9.57 | −0.381 | Cytoplasm |
StC3H-16 | PGSC0003DMG400014305 | 430 | 47,162.96 | 7.88 | −0.374 | Chloroplast |
StC3H-17 | PGSC0003DMG400026471 | 349 | 38,383.75 | 6.19 | −0.690 | Nucleus |
StC3H-18 | PGSC0003DMG400015168 | 518 | 58,326.50 | 5.14 | −1.168 | Nucleus |
StC3H-19 | PGSC0003DMG400000604 | 224 | 24,991.78 | 8.80 | −0.724 | Nucleus |
StC3H-20 | PGSC0003DMG400038576 | 212 | 24,095.85 | 6.14 | −0.979 | Nucleus |
StC3H-21 | PGSC0003DMG400005636 | 352 | 41,316.02 | 8.51 | −1.540 | Nucleus |
StC3H-22 | PGSC0003DMG400031374 | 708 | 79,259.80 | 5.93 | −1.084 | Nucleus |
StC3H-23 | PGSC0003DMG402025318 | 159 | 17,809.09 | 6.43 | −0.834 | Chloroplast |
StC3H-24 | PGSC0003DMG400024801 | 858 | 96,138.64 | 9.10 | −1.114 | Nucleus |
StC3H-25 | PGSC0003DMG400014565 | 832 | 91,063.68 | 6.40 | −0.707 | Nucleus |
StC3H-26 | PGSC0003DMG400030567 | 338 | 37,972.62 | 7.72 | −0.684 | Nucleus |
StC3H-27 | PGSC0003DMG400005333 | 397 | 43,110.49 | 8.51 | −0.455 | Nucleus |
StC3H-28 | PGSC0003DMG400030758 | 396 | 42,133.40 | 6.10 | −0.380 | Nucleus |
StC3H-29 | PGSC0003DMG402027067 | 603 | 67,135.00 | 5.15 | −0.862 | Nucleus |
StC3H-30 | PGSC0003DMG400026937 | 357 | 39,088.35 | 6.79 | −0.743 | Nucleus |
StC3H-31 | PGSC0003DMG400030361 | 668 | 73,112.19 | 5.97 | −0.434 | Nucleus |
StC3H-32 | PGSC0003DMG400032829 | 427 | 47,977.30 | 7.59 | −0.725 | Nucleus |
StC3H-33 | PGSC0003DMG400025459 | 350 | 39,389.36 | 6.46 | −0.579 | Nucleus |
StC3H-34 | PGSC0003DMG400014784 | 495 | 55,654.30 | 5.53 | −0.779 | Nucleus |
StC3H-35 | PGSC0003DMG400011383 | 435 | 46,976.53 | 8.81 | −0.315 | Nucleus |
StC3H-36 | PGSC0003DMG400024171 | 336 | 36,065.91 | 7.59 | −0.534 | Nucleus |
StC3H-37 | PGSC0003DMG400023710 | 294 | 30,815.82 | 9.30 | −0.499 | Cytoplasm |
StC3H-38 | PGSC0003DMG400023719 | 697 | 76,264.47 | 6.83 | −0.478 | Nucleus |
StC3H-39 | PGSC0003DMG400008150 | 701 | 76,411.82 | 6.61 | −0.444 | Nucleus |
StC3H-40 | PGSC0003DMG400011414 | 301 | 31,381.47 | 9.35 | −0.503 | Chloroplast |
StC3H-41 | PGSC0003DMG400016236 | 433 | 47,084.25 | 8.85 | −0.463 | Nucleus |
StC3H-42 | PGSC0003DMG400029993 | 701 | 76,760.82 | 5.82 | −0.489 | Nucleus |
StC3H-43 | PGSC0003DMG400026524 | 331 | 38,988.95 | 9.62 | −1.358 | Nucleus |
StC3H-44 | PGSC0003DMG400025515 | 335 | 38,362.12 | 6.76 | −0.885 | Nucleus |
StC3H-45 | PGSC0003DMG400002893 | 425 | 45,207.41 | 8.58 | −0.687 | Nucleus |
StC3H-46 | PGSC0003DMG400000350 | 372 | 42,312.18 | 5.84 | −0.815 | Nucleus |
StC3H-47 | PGSC0003DMG400046840 | 215 | 24,845.06 | 6.50 | −0.899 | Cytoplasm |
StC3H-48 | PGSC0003DMG400005394 | 385 | 43,943.14 | 6.08 | −0.497 | Cytoskeleton |
StC3H-49 | PGSC0003DMG400045292 | 414 | 47,260.84 | 6.08 | −0.710 | Nucleus |
StC3H-50 | PGSC0003DMG400043565 | 281 | 32,097.45 | 6.56 | −0.702 | Cytoskeleton |
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Deng, Z.; Yang, Z.; Liu, X.; Dai, X.; Zhang, J.; Deng, K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.). Int. J. Mol. Sci. 2023, 24, 12888. https://doi.org/10.3390/ijms241612888
Deng Z, Yang Z, Liu X, Dai X, Zhang J, Deng K. Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.). International Journal of Molecular Sciences. 2023; 24(16):12888. https://doi.org/10.3390/ijms241612888
Chicago/Turabian StyleDeng, Zeyi, Zhijiang Yang, Xinyan Liu, Xiumei Dai, Jiankui Zhang, and Kexuan Deng. 2023. "Genome-Wide Identification and Expression Analysis of C3H Zinc Finger Family in Potato (Solanum tuberosum L.)" International Journal of Molecular Sciences 24, no. 16: 12888. https://doi.org/10.3390/ijms241612888