Transcriptomic Analysis Revealed Key Defense Genes and Signaling Pathways Mediated by the Arabidopsis thaliana Gene SAD2 in Response to Infection with Pseudomonas syringae pv. Tomato DC3000
Abstract
:1. Introduction
2. Results
2.1. SAD2 Expression Increased Resistance to Pst DC3000 Infection
2.2. RNA-Sequencing Library Construction, Sequencing, and Read Mapping
2.3. DEGs in Col-0, sad2-5, and OESAD2/Col-0 after Pst DC3000 Infection
2.4. Key DEGs Regulated by SAD2 and Involved in the Pst DC3000 Defense Response
2.5. GO Term and KEGG Pathway Enrichment among Pathogen-Induced DEGs
2.6. Identification of Transcription Factors (TFs) Involved in the Pathogen Response
2.7. Verification of RNA-Seq Results via RT-qPCR
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. Arabidopsis Inoculation with Pst DC3000 and Leaf Sample Collection
4.3. RNA Extraction, cDNA Library Construction, and Illumina Deep Sequencing
4.4. RNA-Sequencing Data Analysis
4.5. Gene Enrichment Analysis
4.6. Validation of RNA-Seq Data
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Samples | Replicate | Raw Reads | Raw Bases | Clean Reads | Clean Bases | Q20 (%) | Q30 (%) | GC (%) | Total_ Mapping (%) |
---|---|---|---|---|---|---|---|---|---|
Col-0_0d | 1 | 35,015,991 | 5.25 G | 34,168,202 | 5.13 G | 98.01 | 94.20 | 45.34 | 97.79 |
2 | 35,996,956 | 5.39 G | 34,874,632 | 5.23 G | 97.97 | 94.14 | 45.48 | 98.02 | |
3 | 39,606,195 | 5.94 G | 38,314,248 | 5.75 G | 98.06 | 94.37 | 45.27 | 97.93 | |
Col-0_1d | 1 | 39,189,239 | 5.87 G | 38,014,575 | 5.7 G | 98.07 | 94.38 | 44.98 | 97.98 |
2 | 38,505,552 | 5.77 G | 37,168,785 | 5.58 G | 98.07 | 94.35 | 45.05 | 98.05 | |
3 | 40,696,320 | 6.1 G | 39,371,453 | 5.91 G | 97.95 | 94.12 | 45.25 | 97.90 | |
Col-0_2d | 1 | 38,202,509 | 5.73 G | 37,115,329 | 5.57 G | 97.98 | 94.12 | 44.75 | 98.03 |
2 | 39,131,200 | 5.86 G | 37,617,017 | 5.64 G | 97.96 | 94.09 | 45.11 | 98.00 | |
3 | 42,585,194 | 6.38 G | 41,201,001 | 6.18 G | 97.98 | 94.17 | 45.11 | 97.06 | |
Col-0_3d | 1 | 38,249,317 | 5.73 G | 37,029,249 | 5.55 G | 98.09 | 94.41 | 44.87 | 98.04 |
2 | 35,949,275 | 5.39 G | 34,517,786 | 5.18 G | 98.02 | 94.22 | 45.01 | 97.92 | |
3 | 34,922,101 | 5.23 G | 33,703,571 | 5.06 G | 98.14 | 94.54 | 44.98 | 98.08 | |
sad2-5_0d | 1 | 37,867,490 | 5.68 G | 36,537,734 | 5.48 G | 98.11 | 94.48 | 45.32 | 97.33 |
2 | 40,558,326 | 6.08 G | 39,307,108 | 5.9 G | 98.08 | 94.43 | 45.26 | 97.29 | |
3 | 44,222,634 | 6.63 G | 42,603,821 | 6.39 G | 98.06 | 94.44 | 45.37 | 96.85 | |
sad2-5_1d | 1 | 38,518,272 | 5.77 G | 37,239,684 | 5.59 G | 98.11 | 94.48 | 45.13 | 97.60 |
2 | 39,760,691 | 5.96 G | 38,544,874 | 5.78 G | 97.98 | 94.12 | 45.05 | 97.60 | |
3 | 38,946,660 | 5.84 G | 37,622,323 | 5.64 G | 98.00 | 94.18 | 45.00 | 97.37 | |
sad2-5_2d | 1 | 35,927,275 | 5.38 G | 34,755,848 | 5.21 G | 98.16 | 94.58 | 44.97 | 97.56 |
2 | 38,878,184 | 5.83 G | 37,212,316 | 5.58 G | 97.73 | 93.36 | 45.23 | 97.34 | |
3 | 36,917,936 | 5.53 G | 35,742,305 | 5.36 G | 97.99 | 94.20 | 45.10 | 97.27 | |
sad2-5_3d | 1 | 34,058,842 | 5.1 G | 32,974,801 | 4.95 G | 98.07 | 94.38 | 45.16 | 97.47 |
2 | 38,813,455 | 5.82 G | 37,614,495 | 5.64 G | 98.12 | 94.45 | 44.95 | 97.34 | |
3 | 41,067,633 | 6.16 G | 40,173,877 | 6.03 G | 97.79 | 93.66 | 45.37 | 96.55 | |
OESAD2_0d | 1 | 33,942,065 | 5.09 G | 33,246,869 | 4.99 G | 98.03 | 94.25 | 45.89 | 98.06 |
2 | 30,279,425 | 4.54 G | 29,684,633 | 4.45 G | 98.09 | 94.36 | 45.80 | 98.17 | |
3 | 39,884,234 | 5.98 G | 38,968,579 | 5.85 G | 98.10 | 94.43 | 46.15 | 98.11 | |
OESAD2_1d | 1 | 38,695,180 | 5.8 G | 37,829,383 | 5.67 G | 97.83 | 93.78 | 45.30 | 97.81 |
2 | 41,162,035 | 6.17 G | 40,342,339 | 6.05 G | 98.03 | 94.23 | 45.24 | 98.05 | |
3 | 27,256,874 | 4.08 G | 26,714,782 | 4.01 G | 97.90 | 93.90 | 45.18 | 98.00 | |
OESAD2_2d | 1 | 32,949,733 | 4.94 G | 32,275,938 | 4.84 G | 97.91 | 93.95 | 45.19 | 97.85 |
2 | 41,170,080 | 6.17 G | 40,515,870 | 6.08 G | 98.05 | 94.28 | 45.34 | 97.57 | |
3 | 35,475,771 | 5.32 G | 34,878,026 | 5.23 G | 98.12 | 94.42 | 45.18 | 98.03 | |
OESAD2_3d | 1 | 39,301,446 | 5.89 G | 38,509,059 | 5.78 G | 97.87 | 93.82 | 45.15 | 96.70 |
2 | 40,545,374 | 6.08 G | 39,523,760 | 5.93 G | 97.97 | 94.14 | 45.36 | 97.15 | |
3 | 40,018,743 | 6 G | 39,135,547 | 5.87 G | 98.01 | 94.19 | 45.34 | 97.86 |
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Li, S.; Shi, T.; Lyu, M.; Wang, R.; Xu, A.; Chen, L.; Luo, R.; Sun, Y.; Guo, X.; Liu, J.; et al. Transcriptomic Analysis Revealed Key Defense Genes and Signaling Pathways Mediated by the Arabidopsis thaliana Gene SAD2 in Response to Infection with Pseudomonas syringae pv. Tomato DC3000. Int. J. Mol. Sci. 2023, 24, 4229. https://doi.org/10.3390/ijms24044229
Li S, Shi T, Lyu M, Wang R, Xu A, Chen L, Luo R, Sun Y, Guo X, Liu J, et al. Transcriptomic Analysis Revealed Key Defense Genes and Signaling Pathways Mediated by the Arabidopsis thaliana Gene SAD2 in Response to Infection with Pseudomonas syringae pv. Tomato DC3000. International Journal of Molecular Sciences. 2023; 24(4):4229. https://doi.org/10.3390/ijms24044229
Chicago/Turabian StyleLi, Sha, Tiantian Shi, Mingjie Lyu, Rui Wang, Andi Xu, Luoying Chen, Rong Luo, Yinglu Sun, Xiaoying Guo, Jun Liu, and et al. 2023. "Transcriptomic Analysis Revealed Key Defense Genes and Signaling Pathways Mediated by the Arabidopsis thaliana Gene SAD2 in Response to Infection with Pseudomonas syringae pv. Tomato DC3000" International Journal of Molecular Sciences 24, no. 4: 4229. https://doi.org/10.3390/ijms24044229