Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato
Abstract
:1. Introduction
2. Results
2.1. Characterization of Alternative Splicing Events in Tomato Seedlings Growing in Two Distinct Environments
2.2. Transcriptional Response to Environmental Changes
2.3. Identification of Environment-Regulated Genes in Tomato
2.4. Response of Alternative Splicing to Environments
3. Discussion
3.1. Genotype-Dependent AS Regulation by Distinct Environments
3.2. Transcriptome Dynamics in Response to Environmental Fluctuations
4. Materials and Methods
4.1. Plant Growth Conditions
4.2. RNA Sequencing, Read Mapping and Transcript Assembly
4.3. Identification of AS Events
4.4. Gene Ontology Enrichment Analysis of Differentially Expressed Genes and Isoforms
4.5. Validation of Isoform Expression by RT-PCR and Quantitative RT-PCR (qRT-PCR)
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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ITAG2.4 ID | Fold Changes (log2) | Description | ||
---|---|---|---|---|
LA1589 | LA1781 | LA2706 | ||
Solyc11g068430 | −2.95 | −2.74 | −1.03 | Ferredoxin |
Solyc06g069730 | −1.30 | −3.34 | −1.28 | Chlorophyll a–b binding protein 4, chloroplastic |
Solyc05g056050 | −1.22 | −2.34 | −1.43 | Chlorophyll a–b binding protein |
Solyc08g006930 | −1.16 | −1.52 | −1.09 | Photosystem I reaction center subunit X psaK |
Solyc12g006140 | −1.14 | −3.16 | −1.48 | Chlorophyll a–b binding protein 37 |
Solyc02g077240 | −5.43 | −3.96 | −2.01 | Pyruvate decarboxylase |
Solyc10g076510 | −3.88 | −2.02 | −1.04 | Pyruvate decarboxylase |
Solyc06g048410 | −1.76 | −2.15 | −1.05 | Superoxide dismutase |
Solyc03g120990 | −1.24 | −2.50 | −2.12 | Malic enzyme; Malic enzyme, NAD-binding |
Solyc01g095140 | −2.80 | −2.34 | −1.04 | Late embryogenesis abundant protein; response to light |
Solyc10g047530 | −1.29 | −2.80 | −1.28 | Phototropic-responsive NPH3 family protein |
Solyc01g109700 | 1.00 | 1.31 | 1.01 | Transcription factor; Helix-loop-helix DNA-binding |
Solyc06g007180 | 1.78 | 4.10 | 3.72 | Asparagine synthase (Glutamine-hydrolyzing) |
Solyc05g008240 | infinite * | infinite | infinite | myb3 like; similar to R2R3-myb anthocyanin repressor |
Functional Category | S. Pimpinellifolium | S. Lycopersicum | |
---|---|---|---|
LA1589 | LA1781 | LA2706 | |
DNA modification | 2 (4.5) * | 2 (2.8) | 3 (2.3) |
RNA metabolism | 3 (6.8) | 8 (11.3) | 14 (10.9) |
Protein biosynthesis and modification | 10 (22.7) | 11 (15.5) | 14 (10.9) |
Response to stresses | 6 (13.6) | 7 (9.9) | 8 (6.2) |
Growth and development | 5 (11.4) | 5 (7.0) | 18 (14.0) |
Photosynthesis and light signaling | - | 4 (5.6) | 5 (3.9) |
miscellaneous | 3 (6.8) | 8 (11.3) | 14 (10.9) |
Unknown | 44 (34.1) | 26 (36.6) | 53 (41.1) |
Total | 44 (100) | 71 (100) | 129 (100) |
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Wang, G.; Weng, L.; Li, M.; Xiao, H. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato. Int. J. Mol. Sci. 2017, 18, 475. https://doi.org/10.3390/ijms18030475
Wang G, Weng L, Li M, Xiao H. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato. International Journal of Molecular Sciences. 2017; 18(3):475. https://doi.org/10.3390/ijms18030475
Chicago/Turabian StyleWang, Guixiang, Lin Weng, Meng Li, and Han Xiao. 2017. "Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato" International Journal of Molecular Sciences 18, no. 3: 475. https://doi.org/10.3390/ijms18030475