Genome-Wide Identification of the Soybean AlkB Homologue Gene Family and Functional Characterization of GmALKBH10Bs as RNA m6A Demethylases and Expression Patterns under Abiotic Stress
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Identification of the GmALKBH Genes in Soybean
2.2. Chromosomal Localization and Duplication Analysis of Soybean ALKBH Family Genes
2.3. Gene Structure and Conserved Motifs of the GmALKBH Family of Genes
2.4. Cis-Element Analysis of the GmALKBH Family of Genes
2.5. GmALKBH10Bs Are RNA N6-Methyladenosine Demethylases in Soybean
2.6. Spatiotemporal Expression and Subcellular Localization of GmALKBH10B Subfamily Members
2.7. Expression Patterns of GmALKBH10B Genes in Response to Abiotic Stress
3. Discussion
4. Method
4.1. Plant Materials and Abiotic Treatment
4.2. Identification of GmALKBH Gene Family Members and Construction of the Phylogenetic Tree of the ALKBH Family
4.3. Chromosomal Location and Duplication Analysis of the GmALKBH Gene Family
4.4. Gene Structure, Conserved Domain, Motif Analysis, and Cis-Element Analysis of GmALKBH Genes in Soybean
4.5. RNA Isolation, cDNA Synthesis and Quantitative Real-Time PCR (qRT–PCR)
4.6. Cloning and Vector Construction
4.7. Soybean Hairy Root Transformation
4.8. Subcellular Localization and Tissue-Specific Expression of GmALKBH10B Genes
4.9. Quantitative Analysis with LC–MS/MS
4.10. Statistics
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene ID (Phytozome) | Amino Acid Length | Isoelectric Point | Molecular Weight (kDa) | Subcellular Localization Prediction |
---|---|---|---|---|---|
GmALKBH1A1 | Glyma.11G250800 | 396 | 7.13 | 45.05 | chloroplast |
GmALKBH1A2 | Glyma.18G006200 | 358 | 5.89 | 40.53 | nucleus |
GmALKBH1B | Glyma.19G263000 | 314 | 9.33 | 34.62 | nucleus |
GmALKBH1C | Glyma.20G056000 | 311 | 8.72 | 34.37 | nucleus |
GmALKBH1D | Glyma.01G129600 | 488 | 8.94 | 54.13 | mitochondrion |
GmALKBH2A | Glyma.09G014800 | 236 | 9.14 | 27.12 | nucleus |
GmALKBH2B | Glyma.15G120500 | 125 | 9.86 | 14.32 | extracellular space |
GmALKBH6A | Glyma.09G156400 | 263 | 6.26 | 30.03 | nucleus |
GmALKBH6B | Glyma.16G207100 | 263 | 6.20 | 29.79 | nucleus |
GmALKBH7 | Glyma.14G026500 | 229 | 5.91 | 25.75 | nucleus |
GmALKBH8 | Glyma.09G217100 | 342 | 6.83 | 38.34 | nucleus |
GmALKBH9A | Glyma.08G186500 | 423 | 6.29 | 48.00 | nucleus |
GmALKBH9B | Glyma.14G106000 | 523 | 6.22 | 58.58 | nucleus |
GmALKBH9C | Glyma.17G220300 | 553 | 7.60 | 62.19 | nucleus |
GmALKBH10B1 | Glyma.02G149900 | 514 | 5.95 | 56.37 | nucleus |
GmALKBH10B2 | Glyma.03G149900 | 520 | 5.88 | 57.46 | nucleus |
GmALKBH10B3 | Glyma.10G023900 | 511 | 5.71 | 56.08 | nucleus |
GmALKBH10B4 | Glyma.19G152900 | 362 | 8.66 | 40.24 | nucleus |
GmALKBH10C1 | Glyma.05G138600 | 681 | 6.79 | 73.69 | nucleus |
GmALKBH10C2 | Glyma.07G175300 | 664 | 6.61 | 71.74 | nucleus |
GmALKBH10C3 | Glyma.08G093800 | 683 | 7.12 | 73.46 | nucleus |
GmALKBH10C4 | Glyma.20G012100 | 626 | 6.73 | 68.04 | nucleus |
Duplicated 1 | Duplication 2 | Duplication Event |
---|---|---|
GmALKBH1A1 | GmALKBH1A2 | whole genome duplication |
GmALKBH1B | GmALKBH1D | transposed duplication |
GmALKBH1C | GmALKBH1D | transposed duplication |
GmALKBH2A | GmALKBH2B | whole genome duplication |
GmALKBH6A | GmALKBH6B | whole genome duplication |
GmALKBH9A | GmALKBH9B | transposed duplication |
GmALKBH9B | GmALKBH9C | whole genome duplication |
GmALKBH10B1 | GmALKBH10B2 | whole genome duplication |
GmALKBH10B1 | GmALKBH10B3 | whole genome duplication |
GmALKBH10B2 | GmALKBH10B3 | whole genome duplication |
GmALKBH10B2 | GmALKBH10B4 | whole genome duplication |
GmALKBH10C1 | GmALKBH10C2 | whole genome duplication |
GmALKBH10C1 | GmALKBH10C3 | whole genome duplication |
GmALKBH10C1 | GmALKBH10C4 | whole genome duplication |
GmALKBH10C2 | GmALKBH10C3 | whole genome duplication |
GmALKBH10C2 | GmALKBH10C4 | whole genome duplication |
GmALKBH10C3 | GmALKBH10C4 | whole genome duplication |
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Zhao, J.; Yang, T.; Liu, P.; Liu, H.; Zhang, H.; Guo, S.; Liu, X.; Chen, X.; Chen, M. Genome-Wide Identification of the Soybean AlkB Homologue Gene Family and Functional Characterization of GmALKBH10Bs as RNA m6A Demethylases and Expression Patterns under Abiotic Stress. Plants 2024, 13, 2491. https://doi.org/10.3390/plants13172491
Zhao J, Yang T, Liu P, Liu H, Zhang H, Guo S, Liu X, Chen X, Chen M. Genome-Wide Identification of the Soybean AlkB Homologue Gene Family and Functional Characterization of GmALKBH10Bs as RNA m6A Demethylases and Expression Patterns under Abiotic Stress. Plants. 2024; 13(17):2491. https://doi.org/10.3390/plants13172491
Chicago/Turabian StyleZhao, Jie, Tengfeng Yang, Peng Liu, Huijie Liu, Hui Zhang, Sichao Guo, Xiaoye Liu, Xiaoguang Chen, and Mingjia Chen. 2024. "Genome-Wide Identification of the Soybean AlkB Homologue Gene Family and Functional Characterization of GmALKBH10Bs as RNA m6A Demethylases and Expression Patterns under Abiotic Stress" Plants 13, no. 17: 2491. https://doi.org/10.3390/plants13172491
APA StyleZhao, J., Yang, T., Liu, P., Liu, H., Zhang, H., Guo, S., Liu, X., Chen, X., & Chen, M. (2024). Genome-Wide Identification of the Soybean AlkB Homologue Gene Family and Functional Characterization of GmALKBH10Bs as RNA m6A Demethylases and Expression Patterns under Abiotic Stress. Plants, 13(17), 2491. https://doi.org/10.3390/plants13172491