Characterization of the Expansin Gene Promoters in Populus trichocarpa
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials and Treatments
2.2. Expression Analysis of Expansin Genes
2.3. Expansin Gene and Promoter Sequences
2.4. Phylogenetic Analysis
2.5. Sequence Characterization of the Expansin Gene Promoters
2.6. Association Analysis between Expansin Gene Expression and Promoter Elements
3. Results
3.1. Expression Pattern of the Expansin Genes in Populus tomentosa under Stress Treatments
3.2. Base Usage Flanking the Start Codon
3.3. Base Usage in the Conserved Elements of Promoters
3.4. Sequence Similarity of the Promoters
3.5. Regulatory Elements in Poplar Expansin Gene Promoters
3.6. Promoter Components in Response to Plant Tissues and Growth Conditions
4. Discussion
4.1. Phylogeny of Promoters and Coding Sequences
4.2. Promoter Characteristics in Association with Gene Expression
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Location | A | C | G | T |
---|---|---|---|---|
−20 | 36.11% | 16.67% | 11.11% | 36.11% |
−19 | 27.78% | 16.67% | 25.00% | 30.56% |
−18 | 30.56% | 2.78% | 16.67% | 50.00% |
−17 | 44.44% | 5.56% | 16.67% | 33.33% |
−16 | 38.89% | 22.22% | 16.67% | 22.22% |
−15 | 33.33% | 16.67% | 8.33% | 41.67% |
−14 | 19.44% | 33.33% | 19.44% | 27.78% |
−13 | 27.78% | 22.22% | 22.22% | 27.78% |
−12 | 16.67% | 22.22% | 0.00% | 61.11% |
−11 | 25.00% | 25.00% | 16.67% | 33.33% |
−10 | 27.78% | 22.22% | 22.22% | 27.78% |
−9 | 25.00% | 5.56% | 25.00% | 44.44% |
−8 | 25.00% | 19.44% | 27.78% | 27.78% |
−7 | 44.44% | 19.44% | 22.22% | 13.89% |
−6 | 33.33% | 22.22% | 16.67% | 27.78% |
−5 | 50.00% | 13.89% | 16.67% | 19.44% |
−4 | 25.00% | 25.00% | 27.78% | 22.22% |
−3 | 50.00% | 2.78% | 33.33% | 13.89% |
−2 | 38.89% | 25.00% | 5.56% | 30.56% |
−1 | 75.00% | 11.11% | 8.33% | 5.56% |
+1 | 100.00% | 0.00% | 0.00% | 0.00% |
+2 | 0.00% | 0.00% | 0.00% | 100.00% |
+3 | 0.00% | 0.00% | 100.00% | 0.00% |
+4 | 16.67% | 13.89% | 66.67% | 2.78% |
+5 | 11.11% | 58.33% | 16.67% | 13.89% |
+6 | 44.44% | 5.56% | 8.33% | 41.67% |
Gene | Gene # | TSS | 5′ UTR Length (bp) | Gene | Gene # | TSS | 5′ UTR Length (bp) |
---|---|---|---|---|---|---|---|
PtrEXLA1 | Potri.004G181700 | C | 77 | PtrEXPA13 | Potri.016G135200 | A | 85 |
PtrEXLA2 | Potri.007G083400 | C | 88 | PtrEXPA14 | Potri.006G108000 | C | 120 |
PtrEXLB1 | Potri.003G083200 | C | 120 | PtrEXPA15 | Potri.010G202500 | C | 65 |
PtrEXLB2 | Potri.001G151500 | A | 76 | PtrEXPA16 | Potri.006G086100 | C | 61 |
PtrEXLB3 | Potri.001G147200 | A | 56 | PtrEXPA17 | Potri.002G017900 | A | 659 |
PtrEXLB4 | Potri.003G087000 | A | 55 | PtrEXPA18 | Potri.005G244100 | A | 58 |
PtrEXPA1 | Potri.001G240900 | C | 368 | PtrEXPA19 | Potri.002G184700 | T | 888 |
PtrEXPA2 | Potri.013G154700 | A | 91 | PtrEXPA20 | Potri.001G401700 | T | 633 |
PtrEXPA3 | Potri.010G167200 | A | 168 | PtrEXPA21 | Potri.009G169500 | A | 356 |
PtrEXPA4 | Potri.008G088300 | A | 117 | PtrEXPA22 | Potri.004G208300 | T | 713 |
PtrEXPA5 | Potri.009G031800 | C | 596 | PtrEXPA23 | Potri.017G140000 | A | 195 |
PtrEXPA6 | Potri.004G123200 | C | 199 | PtrEXPA24 | Potri.001G112866 | A | 320 |
PtrEXPA7 | Potri.008G057100 | A | 595 | PtrEXPA25 | Potri.016G097500 | A | 90 |
PtrEXPA8 | Potri.004G080200 | A | 573 | PtrEXPA26 | Potri.016G098700 | G | 96 |
PtrEXPA9 | Potri.017G085300 | C | 185 | PtrEXPA27 | Potri.017G092700 | A | 88 |
PtrEXPA10 | Potri.001G001100 | A | 230 | PtrEXPB1 | Potri.014G066300 | A | 68 |
PtrEXPA11 | Potri.013G060800 | C | 162 | PtrEXPB2 | Potri.019G101900 | A | 207 |
PtrEXPA12 | Potri.019G057500 | A | 72 | PtrEXPB3 | Potri.013G134300 | A | 205 |
Subfamily | EXPA | EXPB | EXLA | EXLB |
---|---|---|---|---|
EXPA | 23.20–39.00(30.87) | |||
47.60–94.30(59.05) | ||||
EXPB | 26.00–38.50(32.47) | 32.80–42.60(36.47) | ||
35.60–43.20(39.92) | 48.40–92.20(63.10) | |||
EXLA | 26.10–39.20(31.90) | 32.10–34.90(33.03) | 55.00(55.00) | |
35.80–42.60(38.42) | 45.00–46.80(45.82) | 89.50(89.50) | ||
EXLB | 24.50–36.00(30.20) | 29.10–33.60(31.58) | 29.40–33.50(31.00) | 27.50–35.10(31.82) |
33.10–42.60(37.90) | 41.40–46.50(44.01) | 49.80–53.40(51.31) | 52.40–89.70(68.93) |
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Zhang, J.; Li, X.; Wang, L.; Gong, L.; Li, M.; Xu, J. Characterization of the Expansin Gene Promoters in Populus trichocarpa. Forests 2024, 15, 1485. https://doi.org/10.3390/f15091485
Zhang J, Li X, Wang L, Gong L, Li M, Xu J. Characterization of the Expansin Gene Promoters in Populus trichocarpa. Forests. 2024; 15(9):1485. https://doi.org/10.3390/f15091485
Chicago/Turabian StyleZhang, Junkang, Xiaoyu Li, Lei Wang, Longfeng Gong, Mengtian Li, and Jichen Xu. 2024. "Characterization of the Expansin Gene Promoters in Populus trichocarpa" Forests 15, no. 9: 1485. https://doi.org/10.3390/f15091485