Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions
Abstract
:1. Introduction
2. Results
2.1. Morphological Changes and Ethylene Measurement in “Nannongxuefeng” and “Qinglu” Following Waterlogging Stress
2.2. Transcriptome Sequencing and Read Assembly
2.3. Gene Annotation and Functional Classification
2.4. Identification of Transcription Factors (TFs) Involved in Waterlogging and Recovery in the Two Cultivars
2.5. Hormone Response and Biosynthesis
2.6. Other DEGs Involved in Waterlogging and Recovery in the Two Cultivars
2.7. Differential Transcription of Other Novel Genes Under the Waterlogging and Recovery Conditions
2.8. Verification of RNA-seq Data by Quantitative Real-Time PCR (qRT-PCR)
3. Discussion
3.1. Ethylene Results in Phenotypical Differences Between “Nannongxuefeng” and “Qinglu” after Waterlogging
3.2. Changes in the Expression of Transcription Factors under the Waterlogging and Reoxygenation Conditions
3.3. Waterlogging and Recovery Lead to Changes in Hormonal Responses and Biosynthesis-Related DEGs
3.4. ROS Signaling Pathway, Anaerobic Respiration and Carbohydrate Metabolism
3.5. Other Genes Involved in Waterlogging and Reoxygenation
4. Material and Methods
4.1. Plant Materials
4.2. Waterlogging Treatments
4.3. Ethylene Measurements
4.4. RNA Extraction, cDNA Library Construction and Sequencing
4.5. Transcriptome Data Processing and de novo Assembly
4.6. qRT-PCR Validation and Analysis
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Treatment | Ethylene Production (pl·fw−1·h−1) | |||||
---|---|---|---|---|---|---|
Time (Hours) | ||||||
0 h | 3 h | 6 h | 12 h | 24 h | 12 h + 2 h | |
”Qinglu” | ||||||
Control | 1.49 ± 0.22 a | 1.28 ± 0.12 c | 1.74 ± 0.36 c | 1.14 ± 0.05 c | 1.48 ± 0.45 c | 1.43 ± 0.08 b |
Waterlogging | 1.49 ± 0.22 a | 2.56 ± 0.10 b | 2.75 ± 0.11 b | 2.3 ± 0.18 b | 4.53 ± 0.23 b | 1.90 ± 0.57 b |
Waterlogging + ACC | 1.49 ± 0.22 a | 27.67 ± 2.86 a | 39.30 ± 2.39 a | 23.16 ± 1.57 a | 73.78 ± 1.72 a | 55.89 ± 3.38 a |
Waterlogging + AVG | 1.49 ± 0.22 a | 0.46 ± 0.02 d | 0.37 ± 0.01 d | 0.31 ± 0.02 d | 1.24 ± 0.15 c | 0.88 ± 0.05 c |
“Nannongxuefeng” | ||||||
Control | 2.35 ± 0.32 a | 2.19 ± 0.19 b | 3.33 ± 0.60 c | 2.48 ± 0.31 b | 2.40 ± 0.17 d | 2.19 ± 0.12 c |
Waterlogging | 2.35 ± 0.32 a | 2.93 ± 0.04 b | 4.35 ± 0.26 b | 3.03 ± 0.45 b | 17.03 ± 2.37 b | 5.98 ± 0.28 b |
Waterlogging + ACC | 2.35 ± 0.32 a | 42.93 ± 0.59 a | 51.85 ± 4.43 a | 32.83 ± 4.94 a | 74.22 ± 0.93 a | 62.58 ± 4.24 a |
Waterlogging + AVG | 2.35 ± 0.32 a | 0.79 ± 0.07 c | 1.24 ± 0.14 d | 0.54 ± 0.07 c | 3.61 ± 0.61 c | 1.17 ± 0.07 d |
Sample | Total Raw Reads (Mb) | Total Clean Reads (Mb) | Total Clean Bases (Gb) | Clean Reads Q20 (%) | Clean Reads Q30 (%) | Clean Reads Ratio (%) |
---|---|---|---|---|---|---|
Q 0 h | 67.41 | 67.01 | 6.70 | 97.31 | 93.36 | 99.41 |
QCK 12 h | 68.13 | 65.06 | 6.51 | 97.55 | 94.19 | 95.48 |
QW 12 h | 65.86 | 65.43 | 6.54 | 98.02 | 95.02 | 99.34 |
QCK 12 h + 2 h | 65.86 | 65.43 | 6.54 | 97.68 | 94.25 | 99.35 |
QW 12 h + 2 h | 67.39 | 65.97 | 6.60 | 97.67 | 94.14 | 97.9 |
X 0 h | 65.86 | 65.48 | 6.55 | 97.88 | 94.72 | 99.42 |
XCK 12 h | 65.86 | 65.48 | 6.55 | 97.93 | 94.84 | 99.42 |
XW 12 h | 65.86 | 65.02 | 6.50 | 98.09 | 95.17 | 98.72 |
XCK 12 h + 2 h | 65.86 | 65.52 | 6.55 | 98.06 | 95.1 | 99.48 |
XW 12 h + 2 h | 68.13 | 67.03 | 6.70 | 97.69 | 94.18 | 98.38 |
Sample | Total Number | Total Length | Mean Length | N50 | N70 | N90 | GC (%) |
---|---|---|---|---|---|---|---|
Q 0 h | 154,416 | 91,195,520 | 590 | 924 | 490 | 239 | 40.91 |
QCK 12 h | 76,075 | 39,322,976 | 516 | 738 | 389 | 220 | 41.74 |
QW 12 h | 134,241 | 81,313,892 | 605 | 950 | 511 | 246 | 39.97 |
QCK 12 h + 2 h | 149,040 | 90,100,401 | 604 | 956 | 511 | 244 | 40.36 |
QW 12 h + 2 h | 70,777 | 31,838,872 | 449 | 567 | 327 | 209 | 42.13 |
X 0 h | 149,070 | 91,615,155 | 614 | 983 | 522 | 245 | 40.02 |
XCK 12 h | 151,868 | 94,221,259 | 620 | 1002 | 530 | 247 | 39.96 |
XW 12 h | 148,994 | 87,558,806 | 587 | 898 | 489 | 241 | 40.18 |
XCK 12 h + 2 h | 147,947 | 89,776,249 | 606 | 955 | 517 | 246 | 40.21 |
XW 12 h + 2 h | 50,049 | 21,171,969 | 423 | 510 | 320 | 209 | 42.44 |
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Zhao, N.; Li, C.; Yan, Y.; Cao, W.; Song, A.; Wang, H.; Chen, S.; Jiang, J.; Chen, F. Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions. Int. J. Mol. Sci. 2018, 19, 1455. https://doi.org/10.3390/ijms19051455
Zhao N, Li C, Yan Y, Cao W, Song A, Wang H, Chen S, Jiang J, Chen F. Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions. International Journal of Molecular Sciences. 2018; 19(5):1455. https://doi.org/10.3390/ijms19051455
Chicago/Turabian StyleZhao, Nan, Chuanwei Li, Yajun Yan, Wen Cao, Aiping Song, Haibin Wang, Sumei Chen, Jiafu Jiang, and Fadi Chen. 2018. "Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions" International Journal of Molecular Sciences 19, no. 5: 1455. https://doi.org/10.3390/ijms19051455