Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops
Abstract
:1. Introduction
2. Results
2.1. Identification, Phylogenetic Analysis, and Classification in the Gramineae Crops
2.2. The Expansion and Evolutionary Pattern of the GeBP Genes
2.3. The Conserved Motif and Gene Structure Analysis
2.4. Expression Profiles of the GeBP Genes across Different Rice Tissues and Developmental Stages
2.5. Expression Profiles of the GeBP Genes in Rice under Various Hormonal Stresses
2.6. Expression Profiles of the GeBP Genes in Rice under Various Metal Ion Stresses
2.7. The Subcellular Localization of OsGeBP11 and OsGeBP12 in Rice
3. Materials and Methods
3.1. Plant Materials and Growth Conditions
3.2. Hormone and Metal Ion Stress Treatments
3.3. Genome-Wide Identification of the GeBP Genes in Gramineae Crops
3.4. Phylogenetic Relationship Analyses
3.5. Duplication Events, Orthologous Groups, Conserved Motifs, and Gene Structure Analyses
3.6. RNA Extraction, cDNA Synthesis, and Quantitative Real-Time PCR
3.7. Transient Expression of the Enhanced Green Fluorescent Protein (eGFP) Constructs in the Rice Protoplast
3.8. Statistical Analysis
4. Discussion
4.1. Characterization of the GeBP Genes in Gramineae Crops
4.2. Expression Profiles of the GeBP Genes in Gramineae Crops
5. Conclusion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
GeBP | GLABROUS1 enhancer-binding protein |
TF | Transcription factor |
GA | Gibberellin |
CK | Cytokinin |
cDNA | Complementary DNA |
NJ | Neighbor-joining |
Ka/Ks | nonsynonymous (Ka) /Synonymous (Ks) substitution |
qRT-PCR | Quantitative real-time PCR |
Bd | Brachypodium distachyon |
Hv | Hordeum vulgare |
Oi | Oryza. sativa ssp.indica |
Oj | Oryza. sativa ssp. japonica |
Or | Oryza rufipogon |
Sb | Sorghum bicolor |
Si | Setaria italica |
Ta | Triticum aestivum |
Zm | Zea mays |
WGD | Whole genome duplication |
MYA | Million years |
OGs | Orthologous groups |
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Seq_1 | Seq_2 | Ka | Ks | Ka/Ks | Duplication Type | Date (MYA) | Purifying Selection |
---|---|---|---|---|---|---|---|
BdGeBP10 | BdGeBP3 | 0.2840 | 0.5749 | 0.4940 | WGD or segmental duplication | 15.61 | YES |
BdGeBP12 | BdGeBP10 | 0.8732 | 1.1050 | 0.7902 | WGD or segmental duplication | 47.98 | YES |
BdGeBP12 | BdGeBP8 | 0.3481 | 0.7242 | 0.4807 | WGD or segmental duplication | 19.13 | YES |
BdGeBP2 | BdGeBP4 | 0.2667 | 0.5949 | 0.4483 | WGD or segmental duplication | 14.65 | YES |
OiGeBP7 | OiGeBP8 | 0.3827 | 0.7380 | 0.5185 | WGD or segmental duplication | 21.03 | YES |
OjGeBP4 | OjGeBP8 | 0.3516 | 0.5702 | 0.6166 | WGD or segmental duplication | 19.32 | YES |
OjGeBP6 | OjGeBP9 | 0.2728 | 0.5102 | 0.5346 | WGD or segmental duplication | 14.99 | YES |
OjGeBP10 | OjGeBP13 | 0.3549 | 0.6963 | 0.5097 | WGD or segmental duplication | 19.50 | YES |
OrGeBP6 | OrGeBP9 | 0.2853 | 0.6970 | 0.4093 | WGD or segmental duplication | 15.67 | YES |
OrGeBP4 | OrGeBP8 | 0.3498 | 0.5667 | 0.6172 | WGD or segmental duplication | 19.22 | YES |
OrGeBP10 | OrGeBP13 | 0.3429 | 0.7032 | 0.4876 | WGD or segmental duplication | 18.84 | YES |
SbGeBP17 | SbGeBP10 | 0.4878 | 1.0186 | 0.4789 | WGD or segmental duplication | 26.80 | YES |
SbGeBP4 | SbGeBP6 | 0.3067 | 0.8060 | 0.3806 | WGD or segmental duplication | 16.85 | YES |
SbGeBP5 | SbGeBP16 | 0.3966 | 0.8534 | 0.4647 | WGD or segmental duplication | 21.79 | YES |
SbGeBP8 | SbGeBP9 | 0.0045 | 0.0359 | 0.1244 | WGD or segmental duplication | 0.25 | YES |
SiGeBP10 | SiGeBP4 | 0.4122 | 0.6411 | 0.6430 | WGD or segmental duplication | 22.65 | YES |
SiGeBP12 | SiGeBP7 | 0.4039 | 0.7101 | 0.5687 | WGD or segmental duplication | 22.19 | YES |
TaGeBP10 | TaGeBP11 | 0.0035 | 0.0843 | 0.0410 | WGD or segmental duplication | 0.19 | YES |
TaGeBP1 | TaGeBP2 | 0.0739 | 0.1727 | 0.4280 | WGD or segmental duplication | 4.06 | YES |
TaGeBP1 | TaGeBP3 | 0.0758 | 0.1790 | 0.4233 | WGD or segmental duplication | 4.16 | YES |
TaGeBP2 | TaGeBP3 | 0.0107 | 0.0813 | 0.1319 | WGD or segmental duplication | 0.59 | YES |
TaGeBP4 | TaGeBP5 | 0.0993 | 0.1508 | 0.6587 | WGD or segmental duplication | 5.46 | YES |
ZmGeBP10 | ZmGeBP6 | 0.0599 | 0.2385 | 0.2510 | WGD or segmental duplication | 3.29 | YES |
ZmGeBP11 | ZmGeBP16 | 0.3334 | 0.6935 | 0.4808 | WGD or segmental duplication | 18.32 | YES |
ZmGeBP11 | ZmGeBP8 | 0.3210 | 0.8094 | 0.3966 | WGD or segmental duplication | 17.64 | YES |
ZmGeBP12 | ZmGeBP3 | 0.0340 | 0.1367 | 0.2487 | WGD or segmental duplication | 1.87 | YES |
ZmGeBP18 | ZmGeBP11 | 0.0306 | 0.1401 | 0.2183 | WGD or segmental duplication | 1.68 | YES |
ZmGeBP1 | ZmGeBP9 | 0.0418 | 0.1690 | 0.2474 | WGD or segmental duplication | 2.30 | YES |
ZmGeBP8 | ZmGeBP16 | 0.0377 | 0.1678 | 0.2248 | WGD or segmental duplication | 2.07 | YES |
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Huang, J.; Zhang, Q.; He, Y.; Liu, W.; Xu, Y.; Liu, K.; Xian, F.; Li, J.; Hu, J. Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops. Int. J. Mol. Sci. 2021, 22, 8758. https://doi.org/10.3390/ijms22168758
Huang J, Zhang Q, He Y, Liu W, Xu Y, Liu K, Xian F, Li J, Hu J. Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops. International Journal of Molecular Sciences. 2021; 22(16):8758. https://doi.org/10.3390/ijms22168758
Chicago/Turabian StyleHuang, Jishuai, Qiannan Zhang, Yurong He, Wei Liu, Yanghong Xu, Kejia Liu, Fengjun Xian, Junde Li, and Jun Hu. 2021. "Genome-Wide Identification, Expansion Mechanism and Expression Profiling Analysis of GLABROUS1 Enhancer-Binding Protein (GeBP) Gene Family in Gramineae Crops" International Journal of Molecular Sciences 22, no. 16: 8758. https://doi.org/10.3390/ijms22168758