Genome-Wide Identification and Analysis of the Aux/IAA Gene Family in Rosa hybrida—“The Fairy”: Evidence for the Role of RhIAA25 in Adventitious Root Development
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Identification of the Aux/IAA Gene Family in R. hybrida
2.3. Analysis of the Phylogenetic Tree, Conserved Domain, Motif, and Gene Structure of RhAux/IAA
2.4. Chromosomal Localization and Collinearity Analysis of RhAux/IAA
2.5. Analysis of Cis-Acting Elements in RhAux/IAA Genes
2.6. Analysis of Expression of RhAux/IAA Genes during Rooting Based on RNA-Seq
2.7. Quantitative Real-Time PCR
2.8. Subcellular Localization
2.9. Yeast Self-Activation Analysis of RhIAA25
2.10. Genetic Transformation and Identification of Transgenic RhIAA25 in A. thaliana
2.11. Statistical Analyses
3. Results
3.1. Identification of RhAux/IAA Genes
3.2. Phylogenetic Analysis of RhAux/IAA Genes
3.3. Gene Structure Analysis of RhAux/IAA Family Members
3.4. The Chromosomal Localization and Collinearity Analysis of the RhAux/IAA Genes
3.5. Cis-Elements in the Promoters of RhAux/IAA Genes
3.6. The Expression Pattern of RhAux/IAA Genes during Adventitious Root Development
3.7. The Expression Pattern and Molecular Characteristics of RhIAA25
3.8. The Effect of Overexpressing RhIAA25 on Arabidopsis Root Development
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Name | Gene ID | Isoelectric Point (pl) | Molecular Weight (Da) | Instability Index | Aliphatic Index | Grand Average of Hydropathicity | Subcellular Localization |
---|---|---|---|---|---|---|---|
RhIAA1 | Chr1g0360041 | 6.57 | 76,056.96 | 52.02 | 70.87 | −0.444 | Nucleus |
RhIAA2 | Chr2g0087791 | 8.40 | 24,832.97 | 47.94 | 70.51 | −0.780 | Nucleus |
RhIAA3 | Chr2g0089801 | 8.71 | 36,549.63 | 40.36 | 63.03 | −0.678 | Nucleus |
RhIAA4 | Chr2g0091261 | 7.59 | 33,159.66 | 45.32 | 69.00 | −0.427 | Nucleus |
RhIAA5 | Chr2g0095551 | 6,22 | 130,207.21 | 69,93 | 69.70 | −0.707 | Nucleus |
RhIAA6 | Chr2g0109881 | 8.09 | 40,175.07 | 48.94 | 61.08 | −0.601 | Nucleus |
RhIAA7 | Chr2g0137301 | 6.60 | 21,507.46 | 58.19 | 71.95 | −0.457 | Nucleus |
RhIAA8 | Chr2g0137311 | 5.15 | 12,409.52 | 46.65 | 78.91 | −0.112 | Nucleus |
RhIAA9 | Chr2g0139301 | 8.09 | 37,084.92 | 47.92 | 62.90 | −0.615 | Nucleus |
RhIAA10 | Chr2g0140681 | 9.16 | 36,783.42 | 52.43 | 68.39 | −0.699 | Nucleus |
RhIAA11 | Chr2g0152951 | 6.00 | 101,532.47 | 66.77 | 72.86 | −0.490 | Nucleus |
RhIAA12 | Chr3g0451071 | 6.05 | 27,871.51 | 33.99 | 67.83 | −0.596 | Nucleus |
RhIAA13 | Chr3g0451081 | 8.24 | 20,409.43 | 45.62 | 60.88 | −0.646 | Nucleus |
RhIAA14 | Chr3g0487771 | 5.79 | 94,404.83 | 66.83 | 69.33 | −0.509 | Nucleus |
RhIAA15 | Chr4g0389611 | 6.41 | 21,983.12 | 41.43 | 75.98 | −0.531 | Nucleus |
RhIAA16 | Chr4g0389621 | 8.59 | 26,427.61 | 42.17 | 67.47 | −0.470 | Nucleus |
RhIAA17 | Chr4g0395511 | 8.18 | 39,694.86 | 38.55 | 72.41 | −0.301 | Nucleus |
RhIAA18 | Chr4g0397771 | 6.24 | 124,586.58 | 64.85 | 70.86 | −0.598 | Nucleus |
RhIAA19 | Chr4g0402441 | 9.65 | 18,232.67 | 65.45 | 86.91 | −0.478 | Nucleus |
RhIAA20 | Chr4g0428011 | 7.19 | 23,209.94 | 50.72 | 79.38 | −0.505 | Nucleus |
RhIAA21 | Chr4g0428791 | 5.76 | 11,445.23 | 20.32 | 89.49 | −0.249 | Nucleus |
RhIAA22 | Chr4g0434391 | 5.00 | 21,066.55 | 49.22 | 81.08 | −0.481 | Nucleus |
RhIAA23 | Chr5g0014961 | 6.04 | 98,764.09 | 65.78 | 73.67 | −0.434 | Nucleus |
RhIAA24 | Chr6g0286601 | 6.34 | 32,064.59 | 39.66 | 66.08 | −0.394 | Nucleus |
RhIAA25 | Chr6g0289571 | 6.46 | 26,908.69 | 42.57 | 62.08 | −0.629 | Nucleus |
RhIAA26 | Chr6g0289581 | 5.22 | 21,129.74 | 49.08 | 59.10 | −0.748 | Nucleus |
RhIAA27 | Chr6g0292551 | 5.83 | 75,288.01 | 60.28 | 70.36 | −0.411 | Nucleus |
RhIAA28 | Chr6g0297821 | 5.93 | 26,495.80 | 37.58 | 72.01 | −0.712 | Nucleus |
RhIAA29 | Chr6g0302551 | 5.22 | 100,600.14 | 57.27 | 74.22 | −0.391 | Nucleus |
RhIAA30 | Chr6g0306631 | 8.21 | 34,123.51 | 54.45 | 70.59 | −0.721 | Nucleus |
RhIAA31 | Chr7g0186081 | 6.52 | 74,700.30 | 51.15 | 72.81 | −0.482 | Nucleus |
RhIAA32 | Chr7g0188911 | 6.15 | 93,554.81 | 53.60 | 65.06 | −0.656 | Nucleus |
RhIAA33 | Chr7g0219771 | 6.03 | 75,041.53 | 60.25 | 70.89 | −0.488 | Nucleus |
RhIAA34 | Chr7g0233101 | 7.05 | 39,188.39 | 47.89 | 71.21 | −0.578 | Nucleus |
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Zhang, W.; Zhang, Y.; Huangfu, M.; Fan, Y.; Zhang, J.; Yang, T.; Che, D.; Dong, J. Genome-Wide Identification and Analysis of the Aux/IAA Gene Family in Rosa hybrida—“The Fairy”: Evidence for the Role of RhIAA25 in Adventitious Root Development. Agronomy 2024, 14, 2005. https://doi.org/10.3390/agronomy14092005
Zhang W, Zhang Y, Huangfu M, Fan Y, Zhang J, Yang T, Che D, Dong J. Genome-Wide Identification and Analysis of the Aux/IAA Gene Family in Rosa hybrida—“The Fairy”: Evidence for the Role of RhIAA25 in Adventitious Root Development. Agronomy. 2024; 14(9):2005. https://doi.org/10.3390/agronomy14092005
Chicago/Turabian StyleZhang, Wuhua, Yifei Zhang, Minge Huangfu, Yingdong Fan, Jinzhu Zhang, Tao Yang, Daidi Che, and Jie Dong. 2024. "Genome-Wide Identification and Analysis of the Aux/IAA Gene Family in Rosa hybrida—“The Fairy”: Evidence for the Role of RhIAA25 in Adventitious Root Development" Agronomy 14, no. 9: 2005. https://doi.org/10.3390/agronomy14092005
APA StyleZhang, W., Zhang, Y., Huangfu, M., Fan, Y., Zhang, J., Yang, T., Che, D., & Dong, J. (2024). Genome-Wide Identification and Analysis of the Aux/IAA Gene Family in Rosa hybrida—“The Fairy”: Evidence for the Role of RhIAA25 in Adventitious Root Development. Agronomy, 14(9), 2005. https://doi.org/10.3390/agronomy14092005