Genome-Wide Identification and Expression Profiling of SlGeBP Gene Family in Response to Hormone and Abiotic Stresses in Solanum lycopersicum L.
Abstract
1. Introduction
2. Results
2.1. Identification and Physical and Chemical Parameters of SlGeBP Gene Family in Tomato
2.2. Chromosome Distribution and Multiple Sequence Alignment Analysis of SlGeBP Genes
2.3. Spatial Structure and Phylogenetic Analysis of SlGeBP Genes
2.4. Gene Structure, Conserved Motif, and Collinearity Analysis of SlGeBP Genes
2.5. Analysis of the cis-Acting Regulatory Elements in the SlGeBP Gene Promoters
2.6. Tissue-Specific Expression Profiles Analysis of SlGeBPs
2.7. Expression Profiles of SlGeBP Genes in Response to Plant Hormones
2.8. Expression Profiles of SlGeBP Genes in Response to Stresses
2.9. Prediction of the Protein–Protein Interaction with SlGeBP Proteins
2.10. The Interaction Between and Subcellular Localization of SlGeBP1 and SlGeBP5
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Identification of SlGeBP in Tomato
4.3. Physicochemical Characterization and Multiple Sequence Alignment of SlGeBP Proteins
4.4. Three-Dimensional Structure, Secondary Structure, and Subcellular Localization Prediction
4.5. Phylogenetic Analysis
4.6. Gene Structure, Conserved Motifs, and Collinearity Analysis of SlGeBP Proteins
4.7. cis-Acting Element Analysis
4.8. Hormone and Stress Treatments
4.9. RNA Extraction and qRT-PCR
4.10. Predicting the Interactors with SlGeBP Proteins
4.11. Subcellular Localization of SlGeBP1 and SlGeBP5
4.12. Yeast Two-Hybrid Assay (Y2H)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
bZIP | Basic region leucine zipper |
CD-Search | Conserved domain search |
DPA | Day post anthesis |
DUF573 | Domain of Unknown Function 573 |
GeBP | The GLABROUS1 enhancer-binding protein |
GPL | GeBP-like |
HHM | Hidden Markov model |
MV | Methyl viologen |
NCBI | National Center for Biotechnology Information |
NJ | Neighbor joining method |
NLS | Nuclear localization signal |
PaxDb | Protein Abundance Database |
PEPPI | Pipeline for the Extraction of Predicted Protein-protein Interactions |
pLDDT | Per-residue model confidence score |
PPI | protein-protein interaction |
qRT-PCR | Quantitative real-time polymerase chain reaction |
RRs | response regulators |
TAIR | The Arabidopsis Information Resource |
TF | Transcription factor |
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Gene Name | Gene Accession | Genomic Locus | Exon | AA | MW(Da) | pI | Strand | A.I | GRAVY | Best Hit in Arabidopsis |
---|---|---|---|---|---|---|---|---|---|---|
SlGeBP1 | Solyc01g097890 | ch01:88581415..88583129 | 1 | 454 | 48,609.88 | 5.83 | - | 73.60 | −0.371 | AT3G04930.2 |
SlGeBP2 | Solyc02g005290 | ch02:7633701..7645348 | 8 | 519 | 57,645.42 | 9.45 | - | 85.08 | −0.491 | AT1G61730.1 |
SlGeBP3 | Solyc02g014740 | ch02:18023947..18024618 | 1 | 224 | 26,187.87 | 9.24 | + | 69.46 | −1.073 | AT4G00390.1 |
SlGeBP4 | Solyc02g014750 | ch02:18044460..18044933 | 1 | 158 | 18,184.97 | 8.66 | + | 71.97 | −0.617 | AT4G00390.1 |
SlGeBP5 | Solyc02g083750 | ch02:47039175..47040441 | 1 | 422 | 46,853.96 | 4.71 | - | 71.28 | −0.687 | AT5G28040.1 |
SlGeBP6 | Solyc05g051330 | ch05:61607815..61608822 | 1 | 336 | 37,761.07 | 5.00 | - | 72.96 | −0.692 | AT5G28040.1 |
SlGeBP7 | Solyc07g052760 | ch07:61209111..61210259 | 1 | 383 | 42,923.35 | 6.42 | + | 59.48 | −1.000 | AT4G00390.1 |
SlGeBP8 | Solyc07g052830 | ch07:61287331..61288758 | 2 | 321 | 35,723.94 | 5.12 | + | 65.88 | −0.909 | AT4G00390.1 |
SlGeBP9 | Solyc07g052900 | ch07:61314239..61315432 | 1 | 398 | 44,075.41 | 5.80 | + | 64.13 | −0.972 | AT4G00390.1 |
SlGeBP10 | Solyc07g063840 | ch07:66179566..66180037 | 1 | 157 | 18,606.58 | 5.20 | + | 58.14 | −1.295 | AT2G25650.1 |
SlGeBP11 | Solyc07g064000 | ch07:66308723..66309386 | 1 | 221 | 25,221.15 | 4.26 | - | 63.82 | −1.167 | AT2G25650.1 |
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Cao, H.; Wang, D.; Li, X.; Zhang, Y.; Su, D.; Lu, W.; Xu, K.; Li, Z. Genome-Wide Identification and Expression Profiling of SlGeBP Gene Family in Response to Hormone and Abiotic Stresses in Solanum lycopersicum L. Int. J. Mol. Sci. 2025, 26, 6008. https://doi.org/10.3390/ijms26136008
Cao H, Wang D, Li X, Zhang Y, Su D, Lu W, Xu K, Li Z. Genome-Wide Identification and Expression Profiling of SlGeBP Gene Family in Response to Hormone and Abiotic Stresses in Solanum lycopersicum L. International Journal of Molecular Sciences. 2025; 26(13):6008. https://doi.org/10.3390/ijms26136008
Chicago/Turabian StyleCao, Haohao, Danfeng Wang, Xiaoli Li, Yi Zhang, Deding Su, Wang Lu, Kedong Xu, and Zhengguo Li. 2025. "Genome-Wide Identification and Expression Profiling of SlGeBP Gene Family in Response to Hormone and Abiotic Stresses in Solanum lycopersicum L." International Journal of Molecular Sciences 26, no. 13: 6008. https://doi.org/10.3390/ijms26136008
APA StyleCao, H., Wang, D., Li, X., Zhang, Y., Su, D., Lu, W., Xu, K., & Li, Z. (2025). Genome-Wide Identification and Expression Profiling of SlGeBP Gene Family in Response to Hormone and Abiotic Stresses in Solanum lycopersicum L. International Journal of Molecular Sciences, 26(13), 6008. https://doi.org/10.3390/ijms26136008