Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress
Abstract
:1. Introduction
2. Results
2.1. Identification and Phylogenetic Analysis of JmAP2/ERF Genes
2.2. Gene Structure and Conserved Motif Analysis of JmAP2/ERFs
2.3. Chromosome Distribution, Duplication Events and Synteny Analysis of JmAP2/ERFs
2.4. Analysis of Cis-Acting Elements in JmAP2/ERF Promoters
2.5. Interaction Network Analysis of JmAP2/ERF Proteins
2.6. Expression Profiles of JmAP2/ERF Genes under Cold Stress Using qRT-PCR
3. Discussion
3.1. Identification of the AP2/ERF Superfamily
3.2. The Characteristics Information of AP2/ERF Superfamily in J. mandshurica
3.3. Gene Duplication Events Are Vital Factors in the JmAP2/ERF Superfamily Evolution
3.4. Exploring AP2/ERF Genes Function and Expression Profile in J. mandshurica
4. Materials and Methods
4.1. Identification and Sequence Analysis of JmAP2/ERF Genes
4.2. Phylogenetic Analysis, Gene Structure Identification and Conserved Motif Distribution
4.3. Chromosomal Distribution, Gene Duplications, and Evolutionary Analysis
4.4. Cis-Acting Element Analysis
4.5. Prediction of the Protein Interaction Network
4.6. Plant Materials and Cold Stress Treatments
4.7. RNA Extraction and qRT-PCR Analysis
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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Classification | Domains | Group | Number of Genes |
---|---|---|---|
RAV subfamily | AP2-B3 | 6 | |
Soloist subfamily | AP2 | 4 | |
AP2 subfamily | AP2 | ANT | 3 |
AP2-AP2 | AP2 | 24 | |
Total JmAP2 genes | 27 | ||
DREB subfamily | AP2 | I | 10 |
AP2 | II | 11 | |
AP2 | III | 27 | |
AP2 | IV | 9 | |
Total JmDREB genes | 57 | ||
ERF subfamily | AP2 | V | 19 |
AP2 | VI | 8 | |
AP2 | VII | 5 | |
AP2 | VIII | 18 | |
AP2 | IX | 29 | |
AP2 | X | 8 | |
AP2 | VI-L | 3 | |
Total JmERF genes | 90 | ||
Total JmAP2/ERF genes | 184 |
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Zhao, M.; Li, Y.; Zhang, X.; You, X.; Yu, H.; Guo, R.; Zhao, X. Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress. Int. J. Mol. Sci. 2022, 23, 15225. https://doi.org/10.3390/ijms232315225
Zhao M, Li Y, Zhang X, You X, Yu H, Guo R, Zhao X. Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress. International Journal of Molecular Sciences. 2022; 23(23):15225. https://doi.org/10.3390/ijms232315225
Chicago/Turabian StyleZhao, Minghui, Yan Li, Xinxin Zhang, Xiangling You, Haiyang Yu, Ruixue Guo, and Xiyang Zhao. 2022. "Genome-Wide Identification of AP2/ERF Superfamily Genes in Juglans mandshurica and Expression Analysis under Cold Stress" International Journal of Molecular Sciences 23, no. 23: 15225. https://doi.org/10.3390/ijms232315225