Genome-Wide Identification and Expression Analysis of Tomato ADK Gene Family during Development and Stress
Abstract
:1. Introduction
2. Results
2.1. Identification of the ADK Family in Tomato
2.2. Phylogenetic Analysis and Multiple Sequence Alignment of SlADK Genes
2.3. Motif Analysis
2.4. Gene Structure and Chromosomal Location Analysis of SlADKs
2.5. Cis-Regulatory Elements in SlADK Promoters
2.6. Synteny Analysis of SlADK Genes
2.7. Expression Pattern Analysis of SlADKs
2.8. Expression Characteristics of SlADKs under Diverse Abiotic Stresses
2.9. Expression Profiles of SlADKs in Response to Diverse Hormone Treatments
2.10. SlADK Expression Patterns under Stress Based on RNA-Seq Data
2.11. Coexpression and Correlation Network Analysis
2.12. Functional Analysis of SlADK10 Silencing in Tomato under Drought Stress
3. Discussion
4. Methods
4.1. Plant Materials and Growth Conditions
4.2. Identification of Tomato ADK Genes
4.3. Characteristics, Phylogenetic Relationships, and Sequence Analysis of ADK Proteins
4.4. Gene Structure, Chromosome Location, and CREs of SlADK Genes
4.5. Synteny Analysis of SlADK Genes
4.6. Expression Data Mining of Tomato SlADK Genes
4.7. Hormone and Abiotic Stress Treatments
4.8. RNA Isolation and Quantitative Real-Time PCR Analysis
4.9. Virus-Induced Gene Silencing
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Name | Gene ID | Chr | Genomic Location | Strand | ORF | Exon | AA | MW (kDa) | PI |
---|---|---|---|---|---|---|---|---|---|
SlADK1 | Solyc01g088480.2.1 | 1 | 83267069–83271080 | – | 630 | 10 | 209 | 22872.10 | 5.76 |
SlADK2 | Solyc02g093990.2.1 | 2 | 54662319–54663928 | – | 780 | 4 | 259 | 29003.16 | 6.45 |
SlADK3 | Solyc03g005050.2.1 | 3 | 44287–46883 | + | 852 | 4 | 283 | 31654.06 | 6.46 |
SlADK4 | Solyc03g083610.2.1 | 3 | 53563661–53567185 | + | 714 | 10 | 237 | 26768.76 | 8.83 |
SlADK5 | Solyc03g111200.2.1 | 3 | 61838312–61842194 | – | 735 | 6 | 244 | 26669.91 | 8.57 |
SlADK6 | Solyc04g049690.2.1 | 4 | 43054097–43062321 | – | 810 | 4 | 269 | 30011.55 | 6.90 |
SlADK7 | Solyc05g014980.2.1 | 5 | 9188640–9193694 | – | 729 | 6 | 242 | 26541.56 | 7.01 |
SlADK8 | Solyc06g065270.2.1 | 6 | 40705359–40709638 | – | 861 | 7 | 286 | 31970.68 | 6.96 |
SlADK9 | Solyc08g077300.2.1 | 8 | 61201659–61206762 | – | 651 | 8 | 216 | 24411.10 | 7.63 |
SlADK10 | Solyc09g007180.2.1 | 9 | 801969–804985 | – | 846 | 4 | 281 | 30520.98 | 6.36 |
SlADK11 | Solyc12g010380.2.1 | 12 | 3429721–3438938 | – | 1989 | 19 | 662 | 74110.62 | 6.67 |
Predicted Subcellular Localization | |||||
---|---|---|---|---|---|
Locus Name | Name | Wolf PSort | Predotar | TargetP | CELLO |
Solyc01g088480 | SlADK1 | cyto: 13 | none | other | cyto(2.70) |
Solyc02g093990 | SlADK2 | mito: 6 | mitochondria | mitochondrial transfer peptide | mito(1.76)/cyto(1.28) |
Solyc03g005050 | SlADK3 | mito: 8 | mitochondria | mitochondrial transfer peptide | cyto(1.49)/nucl(1.46)/mito(1.15) |
Solyc03g083610 | SlADK4 | mito: 7.5 | mitochondria | mitochondrial transfer peptide | cyto(2.93) |
Solyc03g111200 | SlADK5 | cyto: 8 | none | other | cyto(1.83)/mito(1.70) |
Solyc04g049690 | SlADK6 | mito: 10 | mitochondria | mitochondrial transfer peptide | mito(1.81)/nucl(1.52) |
Solyc05g014980 | SlADK7 | cyto: 6 | none | other | mito(1.83)/cyto(1.51) |
Solyc06g065270 | SlADK8 | chlo: 14 | plastid | chloroplast transfer peptide | chlo(2.32) |
Solyc08g077300 | SlADK9 | cyto: 9 | none | other | nucl(2.74) |
Solyc09g007180 | SlADK10 | chlo: 11 | mitochondria | mitochondrial transfer peptide | chlo(3.70) |
Solyc12g010380 | SlADK11 | chlo: 11 | plastid | chloroplast transfer peptide | chlo(3.42) |
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Yang, L.; Cao, H.; Zhang, X.; Gui, L.; Chen, Q.; Qian, G.; Xiao, J.; Li, Z. Genome-Wide Identification and Expression Analysis of Tomato ADK Gene Family during Development and Stress. Int. J. Mol. Sci. 2021, 22, 7708. https://doi.org/10.3390/ijms22147708
Yang L, Cao H, Zhang X, Gui L, Chen Q, Qian G, Xiao J, Li Z. Genome-Wide Identification and Expression Analysis of Tomato ADK Gene Family during Development and Stress. International Journal of Molecular Sciences. 2021; 22(14):7708. https://doi.org/10.3390/ijms22147708
Chicago/Turabian StyleYang, Lu, Haohao Cao, Xiaoping Zhang, Liangxian Gui, Qiang Chen, Gui Qian, Jiaxin Xiao, and Zhengguo Li. 2021. "Genome-Wide Identification and Expression Analysis of Tomato ADK Gene Family during Development and Stress" International Journal of Molecular Sciences 22, no. 14: 7708. https://doi.org/10.3390/ijms22147708