Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet
Abstract
1. Introduction
2. Materials and Methods
2.1. Data Acquisition
2.2. Identification and Phylogenetic Analysis of SRS Family Members
2.3. Analysis of Promoter Sequences of SRS Family Members at the Pan-Genome Level
2.4. Motif and Conserved Domain Analysis
2.5. Collinearity and Selective Pressure Analysis
2.6. RNA-seq Data Mining
2.7. RT-qPCR Validation
2.8. Gene Co-Expression and Protein–Protein Interaction Networks
3. Results
3.1. Pan-Genome Distribution of the SiSRS Gene Family
3.2. Pan-Genome-Based Nomenclature for Gene Family Members
3.3. Pan-Genome-Based Promoter Analysis
3.4. Pan-Genome-Based Motif and Conserved Domain Analysis
3.5. SiSRS Family Members in xm and Yu1
3.6. SiSRS Promoter Architecture and Stress-Responsive Cis-Regulatory Element Profiling in xm and Yu1
3.7. Expression Profiling of xm_SiSRS Genes in Salt and Drought Stress
3.8. Gene Co-Expression Network and PPI Analysis
4. Discussion
4.1. Pan-Genome Analysis as a Paradigm Shift in Gene Family Annotation
4.2. Evolutionary Conservation and Functional Constraints of SiSRS Genes
4.3. xm_SiSRS5 Is the Important SiSRS Member
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Li, R.; Lei, C.; Zhang, Q.; Guo, X.; Cui, X.; Wang, X.; Li, X.; Gao, J. Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet. Plants 2025, 14, 1257. https://doi.org/10.3390/plants14081257
Li R, Lei C, Zhang Q, Guo X, Cui X, Wang X, Li X, Gao J. Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet. Plants. 2025; 14(8):1257. https://doi.org/10.3390/plants14081257
Chicago/Turabian StyleLi, Ruimiao, Cuiyun Lei, Qiang Zhang, Xiaomeng Guo, Xiting Cui, Xingchun Wang, Xukai Li, and Jianhua Gao. 2025. "Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet" Plants 14, no. 8: 1257. https://doi.org/10.3390/plants14081257
APA StyleLi, R., Lei, C., Zhang, Q., Guo, X., Cui, X., Wang, X., Li, X., & Gao, J. (2025). Pan-Genome-Based Characterization of the SRS Transcription Factor Family in Foxtail Millet. Plants, 14(8), 1257. https://doi.org/10.3390/plants14081257