Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea
Abstract
:1. Introduction
2. Results
2.1. Impact of Cold on the Epicuticular Wax Structure on Leaves of T. salsuginea
2.2. Impact of Cold Treatment on Cuticular Wax of T. salsuginea
2.3. Impact of Cold Treatment on Cutin Monomers of T. salsuginea
2.4. Impact of Cold Stress on Total Fatty Acids in T. salsuginea
2.5. Transcriptome Sequencing and Reads Mapping
2.6. Functional Annotation and Classification of the Differentially Expressed Genes (DEGs)
2.7. Impact of Cold on Cuticle-Associated Gene Expression
3. Discussion
4. Materials and Methods
4.1. Plant Growth Condition and Low-Temperature Treatment
4.2. Scanning Electron Microscopy
4.3. Analysis of Surface Cuticular Wax Composition
4.4. Analysis of Cutin Monomer Composition
4.5. Determination of Total Fatty Acid Profiles
4.6. RNA Extraction, Library Preparation, and Transcriptome Sequencing
4.7. Reads Mapping and Gene Quantification
4.8. qRT-PCR
4.9. Statistical Analyses
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
BSTFA | N,O-bis(trimethylsilyl)trifluoroacetamide |
DEG | Differential expressed gene |
FID | Flame ionization detector |
FPKM | Fragment per kilobase of exon model per million mapped reads |
GC | Gas chromatography |
GO | Gene ontology |
KEGG | Kyoto encyclopedia of genes and genomes |
qRT-PCR | Quantitative reverse transcription RT-PCR |
SEM | Scanning electron microscopy |
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Sample Name | CK_1 | CK_2 | CK_3 | 4 °C_1 | 4 °C_2 | 4 °C_3 |
---|---|---|---|---|---|---|
Raw Data Size (bp) | 1,197,620,550 | 1,162,182,850 | 1,199,812,800 | 1,140,096,000 | 1,178,295,300 | 1,188,882,800 |
Raw Reads Number | 23,952,411 | 23,243,657 | 23,996,256 | 22,801,920 | 23,565,906 | 23,777,656 |
Clean Data Size (bp) | 1,195,529,000 | 1,159,996,950 | 1,197,116,750 | 1,137,586,350 | 1,176,087,850 | 1,186,401,500 |
Clean Reads Number | 23,910,580 | 23,199,939 | 23,942,335 | 22,751,727 | 23,521,757 | 23,728,030 |
Clean Data Rate (%) | 99.82 | 99.81 | 99.77 | 99.77 | 99.81 | 99.79 |
Clean Reads Q20 (%) | 96.80 | 96.20 | 96.70 | 96.00 | 95.70 | 96.50 |
Total Mapped Reads (%) (reference genome/gene) | 97.12/89.86 | 96.89/89.85 | 97.32/90.35 | 96.90/90.73 | 96.87/90.59 | 97.17/90.96 |
Unique Match (%) (reference genome/gene) | 79.91/75.68 | 77.53/75.42 | 79.88/75.52 | 78.31/78.78 | 79.52/78.56 | 80.76/78.71 |
Multiposition Match (%) (reference genome/gene) | 17.21/14.19 | 19.36/14.43 | 17.44/14.84 | 18.59/11.95 | 17.35/12.03 | 16.41/12.24 |
Total Unmapped Reads (%) (reference genome/gene) | 2.88/10.14 | 3.11/10.15 | 2.68/9.65 | 3.10/9.27 | 3.14/9.41 | 2.83/9.04 |
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Share and Cite
He, J.; Tang, S.; Yang, D.; Chen, Y.; Ling, L.; Zou, Y.; Zhou, M.; Xu, X. Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea. Int. J. Mol. Sci. 2019, 20, 4519. https://doi.org/10.3390/ijms20184519
He J, Tang S, Yang D, Chen Y, Ling L, Zou Y, Zhou M, Xu X. Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea. International Journal of Molecular Sciences. 2019; 20(18):4519. https://doi.org/10.3390/ijms20184519
Chicago/Turabian StyleHe, Junqing, Shuai Tang, Di Yang, Yue Chen, Ludi Ling, Yanli Zou, Minqi Zhou, and Xiaojing Xu. 2019. "Chemical and Transcriptomic Analysis of Cuticle Lipids under Cold Stress in Thellungiella salsuginea" International Journal of Molecular Sciences 20, no. 18: 4519. https://doi.org/10.3390/ijms20184519