Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Identification and Phylogenetic Analysis of the CBF and ICE Gene Family in Three Walnut Genomes
2.2. Chromosomal Distribution and Duplication Patterns of Juglans regia and Juglans sigillata
2.3. Protein Domain and Gene Structure Analysis
2.4. Collinearity Analysis and Selective Pressure
2.5. Cis-Acting Elements Analysis of Promoters
2.6. Gene Expression Patterns Analysis
2.7. Protein–Protein and Protein-microRNA Interaction Predictions
2.8. Evolution of CBF1 and ICE1 in Angiosperms
3. Discussion
3.1. Characteristics of CBF and ICE1 in Three Walnut Genomes
3.2. Conserved Domain and Cis-Acting Elements of CBF and ICE1 in Three Walnut Genomes
3.3. Gene Expression Profiles of CBF and ICE1 in Response to Cold Stress
3.4. Protein–Protein and Protein Interactions, and the Putative microRNA Interaction Predictions
4. Materials and Methods
4.1. Plant Materials and RNA Sequencing
4.2. Identification of the Gene Members in Three Juglans Regia Cultivars
4.3. Construction of Phylogenetic Tree and Analysis of Gene Structure, Conserved Motif
4.4. Chromosomal Location, Collinearity of Transcription Factors, and Selective Pressure Analysis in Juglans Regia
4.5. Analysis of Subcellular Localization and Protein Physicochemical Properties
4.6. Cis-Acting Elements Analysis of Promoter and Gene Expression
4.7. Protein–Protein Interactions and microRNA Targeting Analysis
4.8. Evolution of CBF1 and ICE1 Genes in Angiosperms
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name 1 | No. of Amnio Acids | Mol. Wt (kDa) | Isoelectric Point (pI) | Instability Index (II) | Aliphatic Index | Grand Average of Hydropathicity (GRAVY) | Subcellular Localization |
---|---|---|---|---|---|---|---|
JrCBF1 | 212 | 23,251.1 | 5.26 | 52.72 | 61.37 | −0.503 | Nucleus |
JrCBF2 | 214 | 23,955.9 | 6.20 | 56.34 | 66.17 | −0.563 | Nucleus |
JrCBF3 | 218 | 24,001.2 | 8.59 | 54.02 | 71.24 | −0.477 | Nucleus |
JrCBF4 | 249 | 27,626.1 | 5.53 | 57.99 | 72.13 | −0.482 | Nucleus |
JreCBF1 | 249 | 27,626.1 | 5.53 | 57.99 | 72.13 | −0.482 | Nucleus |
JreCBF2 | 253 | 28,821.2 | 5.42 | 56.81 | 65.61 | −0.743 | Nucleus |
JreCBF3 | 266 | 29,507.2 | 6.19 | 55.73 | 70.49 | −0.538 | Nucleus |
JreCBF4 | 212 | 23,251.1 | 5.26 | 52.72 | 61.37 | −0.503 | Nucleus |
JreCBF5 | 150 | 16,684.8 | 10.00 | 59.52 | 60.60 | −0.744 | Nucleus |
JreCBF6 | 265 | 29,260.9 | 6.19 | 60.5 | 68.94 | −0.486 | Nucleus |
JreCBF7 | 218 | 24,001.2 | 8.59 | 54.02 | 71.24 | −0.477 | Nucleus |
JsCBF1 | 212 | 23,251.1 | 5.26 | 52.72 | 61.37 | −0.503 | Nucleus |
JsCBF2 | 214 | 24,026.0 | 6.75 | 54.69 | 62.52 | −0.581 | Nucleus |
JsCBF3 | 253 | 28,893.2 | 5.33 | 56.32 | 65.61 | −0.755 | Nucleus |
JsCBF4 | 250 | 27,799.2 | 5.21 | 56.64 | 70.28 | −0.516 | Nucleus |
JsCBF5 | 218 | 24,011.3 | 8.59 | 54.9 | 71.24 | −0.481 | Nucleus |
JrICE1a | 534 | 57,836.5 | 5.36 | 46.26 | 74.01 | −0.516 | Nucleus |
JrICE1b | 539 | 58,329.4 | 5.03 | 56.61 | 78.89 | −0.423 | Nucleus |
JrICE1c | 537 | 58,102.2 | 4.98 | 56.64 | 78.99 | −0.420 | Nucleus |
JrICE1d | 540 | 58,754.7 | 5.16 | 56.23 | 72.46 | −0. 542 | Nucleus |
JrICE1e | 552 | 60,506.9 | 5.73 | 57.26 | 72.30 | −0. 530 | Nucleus |
JrICE1f | 492 | 54,205.0 | 5.77 | 46.78 | 77.36 | −0. 515 | Nucleus |
JreICE1 | 645 | 70,822.6 | 6.35 | 49.98 | 83.32 | −0. 305 | Nucleus |
JreICE1a | 541 | 58,832.7 | 5.76 | 48.38 | 72.87 | −0.563 | Nucleus |
JreICE1b | 560 | 61,275.6 | 5.22 | 58.34 | 75.09 | −0.521 | Nucleus |
JreICE1c | 648 | 70,913.0 | 5.18 | 59.24 | 83.98 | −0.330 | Nucleus |
JsICE1a | 539 | 58,395.5 | 5.14 | 55.74 | 78.89 | −0.441 | Nucleus |
JsICE1b | 542 | 59,042.0 | 5.22 | 55.92 | 72.20 | −0.550 | Nucleus |
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Zhou, H.; Ma, J.; Liu, H.; Zhao, P. Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions. Int. J. Mol. Sci. 2024, 25, 25. https://doi.org/10.3390/ijms25010025
Zhou H, Ma J, Liu H, Zhao P. Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions. International Journal of Molecular Sciences. 2024; 25(1):25. https://doi.org/10.3390/ijms25010025
Chicago/Turabian StyleZhou, Huijuan, Jiayu Ma, Hengzhao Liu, and Peng Zhao. 2024. "Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions" International Journal of Molecular Sciences 25, no. 1: 25. https://doi.org/10.3390/ijms25010025
APA StyleZhou, H., Ma, J., Liu, H., & Zhao, P. (2024). Genome-Wide Identification of the CBF Gene Family and ICE Transcription Factors in Walnuts and Expression Profiles under Cold Conditions. International Journal of Molecular Sciences, 25(1), 25. https://doi.org/10.3390/ijms25010025