Genome-Wide Identification of the DGK Gene Family in Kiwifruit (Actinidia valvata Dunn) and an Expression Analysis of Their Responses to Waterlogging Stress
Abstract
:1. Introduction
2. Materials and Methods
2.1. Identification of DGK Genes in A. valvata
2.2. Physiochemical Properties, Protein Secondary Structure, and 3D Modeling of AvDGK Proteins
2.3. Phylogenetic Analyses and Multiple Sequence Alignment of AvDGK Proteins
2.4. Analysis of Gene Structures and Conserved Motifs
2.5. Chromosome Location, Gene Duplication, and a Collinearity Analysis of AvDGK Genes
2.6. Cis-Regulatory Element Prediction and an Analysis of Promoters
2.7. Gene Expression Analysis of AvDGKs
2.8. Plant Materials and Treatments
2.9. RNA Extraction and qRT-PCR Analysis
2.10. Statistical Analysis
3. Results
3.1. Genome-Wide Identification of DGK Genes in A. valvata
3.2. Phylogenetic Analysis and Multiple Sequence Alignment of DGK Genes
3.3. Functional Domain, Secondary Structure, and 3D Modeling of AvDGKs
3.4. Gene Structure, Domain, and Conserved Motif Analysis of AvDGKs
3.5. Synteny and Gene Duplication Analysis of AvDGKs
3.6. Analysis of Cis-Elements in the Promoters of AvDGK Genes
3.7. Expression Patterns of AvDGKs in Kiwifruit
3.8. RT-qPCR of AvDGKs under Waterlogging Stress at Different Times
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Gene Name | Gene ID | CDS Length (bp) | Number of Amino Acids (aa) | Molecular Weight (kDa) | pI | Subcellular Localization |
---|---|---|---|---|---|---|
AvDGK5a | Ava05g00367 | 2139 | 712 | 79.50 | 8.62 | Nucleus |
AvDGK5b | Avb05g00366 | 2139 | 712 | 79.31 | 8.74 | Nucleus |
AvDGK7a | Ava07g00406 | 2139 | 712 | 79.24 | 8.14 | Nucleus |
AvDGK7b | Avb07g00371 | 2139 | 712 | 79.39 | 8.14 | Nucleus |
AvDGK12a | Ava12g00623 | 1449 | 482 | 54.05 | 8.57 | Chloroplast. Cytoplasm. Nucleus |
AvDGK12b | Avb12g00588 | 1392 | 463 | 51.84 | 7.06 | Cytoplasm |
AvDGK13a | Ava13g01333 | 1419 | 472 | 53.55 | 9.16 | Chloroplast |
AvDGK13b | Avb13g01246 | 1419 | 472 | 53.28 | 8.68 | Chloroplast. Cytoplasm. Nucleus |
AvDGK16a | Ava16g01104 | 1446 | 481 | 53.40 | 6.84 | Chloroplast |
AvDGK16b | Avb16g01069 | 1437 | 478 | 53.14 | 6.87 | Chloroplast |
AvDGK17a | Ava17g00287 | 1473 | 490 | 54.90 | 6.39 | Chloroplast. Cytoplasm |
AvDGK17b | Avb17g00295 | 1473 | 490 | 54.95 | 6.31 | Cytoplasm. Nucleus |
AvDGK18a | Ava18g00909 | 1446 | 481 | 53.53 | 6.72 | Chloroplast |
AvDGK18b | Avb18g00884 | 1371 | 456 | 50.84 | 6.41 | Chloroplast |
AvDGK19a | Ava19g00482 | 2199 | 732 | 80.77 | 6.32 | Nucleus |
AvDGK19b | Avb19g00480 | 2205 | 734 | 81.06 | 6.50 | Nucleus |
AvDGK23a | Ava23g00486 | 2205 | 734 | 80.91 | 6.44 | Nucleus |
AvDGK23b | Avb23g00493 | 2205 | 734 | 80.83 | 6.41 | Nucleus |
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Zhang, M.; Liu, C.; Wang, F.; Liu, S.; Gao, J.; Li, J.; Mo, Q.; Ye, K.; Qi, B.; Gong, H. Genome-Wide Identification of the DGK Gene Family in Kiwifruit (Actinidia valvata Dunn) and an Expression Analysis of Their Responses to Waterlogging Stress. Horticulturae 2024, 10, 310. https://doi.org/10.3390/horticulturae10040310
Zhang M, Liu C, Wang F, Liu S, Gao J, Li J, Mo Q, Ye K, Qi B, Gong H. Genome-Wide Identification of the DGK Gene Family in Kiwifruit (Actinidia valvata Dunn) and an Expression Analysis of Their Responses to Waterlogging Stress. Horticulturae. 2024; 10(4):310. https://doi.org/10.3390/horticulturae10040310
Chicago/Turabian StyleZhang, Meijuan, Cuixia Liu, Faming Wang, Shibiao Liu, Jianyou Gao, Jiewei Li, Quanhui Mo, Kaiyu Ye, Beibei Qi, and Hongjuan Gong. 2024. "Genome-Wide Identification of the DGK Gene Family in Kiwifruit (Actinidia valvata Dunn) and an Expression Analysis of Their Responses to Waterlogging Stress" Horticulturae 10, no. 4: 310. https://doi.org/10.3390/horticulturae10040310
APA StyleZhang, M., Liu, C., Wang, F., Liu, S., Gao, J., Li, J., Mo, Q., Ye, K., Qi, B., & Gong, H. (2024). Genome-Wide Identification of the DGK Gene Family in Kiwifruit (Actinidia valvata Dunn) and an Expression Analysis of Their Responses to Waterlogging Stress. Horticulturae, 10(4), 310. https://doi.org/10.3390/horticulturae10040310