Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation
Abstract
1. Introduction
2. Results
2.1. Identification and Phylogenetic Analysis of ARF Gene Family in Phoebe bournei
2.2. Protein Motif and Gene Structure Analysis of PbARF Genes
2.3. Cis-Acting Element Analysis of PbARF Gene Family
2.4. Synteny Analysis of PbARF Gene Family
2.5. Expression Analysis of PbARF Gene in Different Tissues of Phoebe bournei
2.6. Expression Analysis of the PbARF Gene Under Different Treatments
3. Discussion
4. Materials and Methods
4.1. Genome Data and Plant Material Source
4.2. Identification and Analysis of Physical and Chemical Properties
4.3. Chromosomal Distribution and Gene Duplication of PbARF1 Genes
4.4. Collinearity Analysis of PbARF1 Genes
4.5. Phylogenetic Analysis
4.6. Analysis of Conserved Motifs and Gene Structures
4.7. Multiple Sequence Alignment and Promoter Cis-Element Analysis of PbARF1 Genes
4.8. Different Plant Tissues and Abiotic Stress Treatments
4.9. qRT-PCR Analysis
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 | Gene ID | AA/aa | MW/kDa | pI | II | AI | GRAVY | Subcelluar Localization | CLASS |
---|---|---|---|---|---|---|---|---|---|
OF09010 | PbARF1 | 715 | 80,305.10 | 6.04 | 58.31 | 73.61 | −0.470 | Nucleus | V |
OF01795 | PbARF2 | 1059 | 117,250.14 | 5.57 | 57.40 | 73.98 | −0.485 | Nucleus | III |
OF13500 | PbARF3 | 571 | 62,566.62 | 7.56 | 44.58 | 71.84 | −0.337 | Nucleus | II |
OF12274 | PbARF4 | 490 | 53,867.87 | 9.27 | 56.49 | 81.41 | −0.324 | Nucleus | IV |
OF00399 | PbARF5 | 826 | 91,562.44 | 6.33 | 43.97 | 73.16 | −0.434 | Nucleus | IV |
OF14335 | PbARF6 | 720 | 80,909.46 | 6.07 | 57.04 | 73.50 | −0.502 | Nucleus | V |
OF02341 | PbARF7 | 561 | 62,376.75 | 8.02 | 50.82 | 70.91 | −0.466 | Nucleus | V |
OF14461 | PbARF8 | 674 | 74,422.02 | 7.01 | 50.77 | 71.31 | −0.413 | Nucleus | II |
OF14278 | PbARF9 | 1444 | 165,759.74 | 6.70 | 46.97 | 76.20 | −0.467 | Nucleus | V |
OF15166 | PbARF10 | 1057 | 117,517.64 | 6.22 | 61.66 | 77.31 | −0.477 | Peroxisome | III |
OF14282 | PbARF11 | 680 | 75,645.98 | 5.99 | 58.56 | 67.81 | −0.553 | Nucleus | V |
OF21754 | PbARF12 | 787 | 87,876.70 | 6.56 | 52.77 | 72.35 | −0.459 | Nucleus | V |
OF09049 | PbARF13 | 511 | 56,529.57 | 8.04 | 49.50 | 88.18 | −0.221 | Chloroplast | IV |
OF05709 | PbARF14 | 707 | 77,550.83 | 7.56 | 46.17 | 74.61 | −0.350 | Nucleus | II |
OF05094 | PbARF15 | 899 | 99,896.26 | 6.06 | 63.09 | 78.08 | −0.471 | Nucleus | III |
OF07141 | PbARF16 | 705 | 77,183.54 | 6.56 | 50.96 | 75.80 | −0.301 | Nucleus | II |
OF20357 | PbARF17 | 662 | 73,604.32 | 6.60 | 51.51 | 72.73 | −0.410 | Peroxisome | IV |
OF20735 | PbARF18 | 856 | 95,038.56 | 5.82 | 55.64 | 64.68 | −0.620 | Nucleus | V |
OF22918 | PbARF19 | 828 | 93,545.12 | 6.11 | 60.73 | 71.11 | −0.505 | Nucleus | III |
OF26137 | PbARF20 | 1113 | 122,852.38 | 6.13 | 60.47 | 74.59 | −0.518 | Nucleus | III |
OF14279 | PbARF21 | 311 | 35,145.69 | 6.40 | 63.31 | 71.45 | −0.430 | Nucleus | V |
OF18244 | PbARF22 | 815 | 91,853.67 | 5.88 | 60.23 | 75.24 | −0.437 | Nucleus | III |
OF15400 | PbARF23 | 910 | 100,774.16 | 6.06 | 71.90 | 76.27 | −0.449 | Nucleus | III |
OF24604 | PbARF24 | 738 | 81,011.35 | 7.35 | 54.56 | 70.26 | −0.437 | Nucleus | IV |
OF01686 | PbARF25 | 900 | 99,660.42 | 6.17 | 63.19 | 80.14 | −0.383 | Nucleus | III |
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Zheng, K.; Feng, Y.; Liu, R.; Zhang, Y.; Fan, D.; Zhong, K.; Tang, X.; Zhang, Q.; Cao, S. Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation. Int. J. Mol. Sci. 2025, 26, 3701. https://doi.org/10.3390/ijms26083701
Zheng K, Feng Y, Liu R, Zhang Y, Fan D, Zhong K, Tang X, Zhang Q, Cao S. Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation. International Journal of Molecular Sciences. 2025; 26(8):3701. https://doi.org/10.3390/ijms26083701
Chicago/Turabian StyleZheng, Kehui, Yizhuo Feng, Ronglin Liu, Yanlin Zhang, Dunjin Fan, Kai Zhong, Xinghao Tang, Qinghua Zhang, and Shijiang Cao. 2025. "Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation" International Journal of Molecular Sciences 26, no. 8: 3701. https://doi.org/10.3390/ijms26083701
APA StyleZheng, K., Feng, Y., Liu, R., Zhang, Y., Fan, D., Zhong, K., Tang, X., Zhang, Q., & Cao, S. (2025). Bioinformatics Analysis Reveals the Evolutionary Characteristics of the Phoebe bournei ARF Gene Family and Its Expression Patterns in Stress Adaptation. International Journal of Molecular Sciences, 26(8), 3701. https://doi.org/10.3390/ijms26083701