Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis
Abstract
:1. Introduction
2. Results
2.1. Systemic Characterization of the Dof Gene Family in A. trifoliata
2.2. Classification of the Dof TFs in A. trifoliata
2.3. Gene Structure, Conserved Motifs and Phylogenetic Tree of AktDofs
2.4. Ka/Ks Value of Homologous AktDof Pairs
2.5. Interspecies Collinearity of AktDofs
2.6. Identification of Cis-Acting Elements of the AktDof Gene Family
2.7. Expression Profiles of AktDofs in A. trifoliata Tissues at Various Stages
2.8. Effects of Exogenous Hormones on the Expression of AktDofs
2.9. Differential Expression of AktDofs in Response to Photoperiod Treatments
3. Discussion
3.1. AktDof Gene Family Members May Have Evolutionarily Diverged
3.2. The functions of AktDofs Could Largely Differ
3.3. Some Putative Candidate Genes Are Involved in the Response to Photoperiod
4. Materials and Methods
4.1. Identification of Dof TFs in A. trifoliata
4.2. Sequence Characteristic Analysis, Phylogenetic Analyses, and Collinearity of AktDofs
4.3. Expression Analysis of AktDofs in Different Fruit Tissues and at Different Developmental Stages of A. trifoliata
4.4. Expression Patterns of AktDofs in Response to Different Hormone Treatments and Different Photoperiods
4.5. RNA Isolation and RT-qPCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Dof Genes | Gene Length (bp) | Number of Exons | Chromosome Location | Duplication Type | Putative Protein | ||||
---|---|---|---|---|---|---|---|---|---|
Length (AA) | PI | MW (kDa) | |||||||
AktDof1 | 607 | 2 | chr1 | 9908538 | 9909145 | Dispersed | 192 | 8.97 | 21.70 |
AktDof2 | 488 | 2 | chr1 | 24576861 | 24577349 | WGD or Segmental | 150 | 9.48 | 16.95 |
AktDof3 | 1355 | 1 | chr1 | 26704731 | 26706086 | WGD or Segmental | 273 | 8.59 | 31.04 |
AktDof4 | 966 | 1 | chr2 | 5412299 | 5413265 | WGD or Segmental | 194 | 8.94 | 21.30 |
AktDof5 | 1657 | 1 | chr2 | 5509001 | 5510658 | WGD or Segmental | 308 | 8.71 | 33.27 |
AktDof6 | 833 | 1 | chr2 | 5980914 | 5981747 | WGD or Segmental | 277 | 8.96 | 30.69 |
AktDof7 | 1438 | 1 | chr3 | 43888045 | 43889483 | WGD or Segmental | 317 | 9.03 | 34.91 |
AktDof8 | 3242 | 2 | chr3 | 44585557 | 44588799 | WGD or Segmental | 330 | 8.85 | 35.76 |
AktDof9 | 797 | 1 | chr3 | 52617421 | 52618218 | WGD or Segmental | 265 | 9.33 | 29.27 |
AktDof10 | 942 | 1 | chr4 | 1921930 | 1922872 | Dispersed | 273 | 4.73 | 30.57 |
AktDof11 | 782 | 1 | chr4 | 10404006 | 10404788 | WGD or Segmental | 260 | 6.81 | 28.96 |
AktDof12 | 1388 | 1 | chr4 | 10759535 | 10760923 | Dispersed | 308 | 9.11 | 32.57 |
AktDof13 | 1581 | 2 | chr4 | 10814000 | 10815581 | WGD or Segmental | 332 | 9.23 | 36.12 |
AktDof14 | 1913 | 2 | chr4 | 41906084 | 41907997 | WGD or Segmental | 313 | 9.14 | 34.43 |
AktDof15 | 2446 | 2 | chr5 | 3830380 | 3832826 | WGD or Segmental | 301 | 6.04 | 33.46 |
AktDof16 | 3272 | 2 | chr5 | 6188849 | 6192121 | WGD or Segmental | 469 | 6.65 | 51.93 |
AktDof17 | 1406 | 1 | chr5 | 8819151 | 8820557 | WGD or Segmental | 297 | 6.75 | 33.39 |
AktDof18 | 2109 | 2 | chr6 | 5604374 | 5606483 | WGD or Segmental | 287 | 7.11 | 32.07 |
AktDof19 | 2072 | 2 | chr6 | 6865819 | 6867891 | WGD or Segmental | 343 | 9.05 | 36.62 |
AktDof20 | 3579 | 2 | chr6 | 28715562 | 28719141 | WGD or Segmental | 489 | 5.98 | 53.72 |
AktDof21 | 2446 | 2 | chr7 | 28997114 | 28999560 | WGD or Segmental | 306 | 6.26 | 34.39 |
AktDof22 | 3358 | 3 | chr7 | 31830746 | 31834104 | WGD or Segmental | 522 | 8.56 | 57.10 |
AktDof23 | 1312 | 1 | chr7 | 33314300 | 33315612 | WGD or Segmental | 245 | 6.43 | 27.86 |
AktDof24 | 2102 | 3 | chr8 | 698486 | 700588 | WGD or Segmental | 318 | 8.92 | 34.53 |
AktDof25 | 1987 | 2 | chr8 | 2192672 | 2194659 | WGD or Segmental | 284 | 7.59 | 31.81 |
AktDof26 | 3551 | 2 | chr9 | 22881329 | 22884880 | WGD or Segmental | 489 | 6.19 | 54.40 |
AktDof27 | 2558 | 2 | chr10 | 31290225 | 31292783 | WGD or Segmental | 285 | 8.49 | 31.33 |
AktDof28 | 2380 | 2 | chr11 | 10569833 | 10572213 | WGD or Segmental | 286 | 8.12 | 31.21 |
AktDof29 | 2587 | 3 | chr11 | 47368316 | 47370903 | WGD or Segmental | 287 | 8.76 | 31.85 |
AktDof30 | 878 | 1 | chr11 | 47801725 | 47802603 | WGD or Segmental | 292 | 9.21 | 33.24 |
AktDof31 | 1676 | 1 | chr12 | 3108299 | 3109975 | Dispersed | 213 | 8.46 | 23.45 |
AktDof32 | 1976 | 2 | chr12 | 36036738 | 36038714 | WGD or Segmental | 261 | 9 | 28.81 |
AktDof33 | 1834 | 1 | chr13 | 6715548 | 6717382 | Tandem | 285 | 9.07 | 31.45 |
AktDof34 | 2870 | 2 | chr13 | 6735523 | 6738393 | WGD or Segmental | 308 | 8.65 | 34.15 |
AktDof35 | 639 | 1 | chr13 | 9523741 | 9524380 | WGD or Segmental | 151 | 9.4 | 16.85 |
AktDof36 | 926 | 1 | chr14 | 2280296 | 2281222 | Dispersed | 308 | 5.37 | 34.71 |
AktDof37 | 1590 | 2 | chr14 | 3970765 | 3972355 | WGD or Segmental | 323 | 9.11 | 34.40 |
AktDof38 | 12,257 | 3 | chr14 | 35699953 | 35712210 | WGD or Segmental | 480 | 5.32 | 52.39 |
AktDof39 | 1982 | 2 | chr15 | 24196450 | 24198432 | WGD or Segmental | 307 | 8.03 | 34.09 |
AktDof40 | 1598 | 1 | Contig00776 | 28846 | 30444 | Dispersed | 202 | 9.36 | 22.67 |
AktDof41 | 608 | 1 | Contig01043 | 19276 | 19884 | Dispersed | 202 | 9.36 | 22.67 |
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Zhang, Q.; Zhong, S.; Dong, Q.; Yang, H.; Yang, H.; Tan, F.; Chen, C.; Ren, T.; Shen, J.; Cao, G.; et al. Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis. Int. J. Mol. Sci. 2023, 24, 4973. https://doi.org/10.3390/ijms24054973
Zhang Q, Zhong S, Dong Q, Yang H, Yang H, Tan F, Chen C, Ren T, Shen J, Cao G, et al. Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis. International Journal of Molecular Sciences. 2023; 24(5):4973. https://doi.org/10.3390/ijms24054973
Chicago/Turabian StyleZhang, Qiuyi, Shengfu Zhong, Qing Dong, Hao Yang, Huai Yang, Feiquan Tan, Chen Chen, Tianheng Ren, Jinliang Shen, Guoxing Cao, and et al. 2023. "Identification of Photoperiod- and Phytohormone-Responsive DNA-Binding One Zinc Finger (Dof) Transcription Factors in Akebia trifoliata via Genome-Wide Expression Analysis" International Journal of Molecular Sciences 24, no. 5: 4973. https://doi.org/10.3390/ijms24054973