Systematic Identification of Methyl Jasmonate-Responsive Long Noncoding RNAs and Their Nearby Coding Genes Unveils Their Potential Defence Roles in Tobacco BY-2 Cells
Abstract
:1. Introduction
2. Results
2.1. Reliable Mining for lncRNAs Indicates That Intergenic Transcripts Are the Most Prominent Group
2.2. The lncRNAs in BY-2 Cells Have Extreme Genus Specificity for Nicotiana
2.3. The Upregulated lncRNAs Constitute a Large Majority of the MeJA-Responsive lncRNAs
2.4. Potential Up- and Downregulated Target Genes of MeJA-Upregulated lncRNAs Are Responsible for Different Biological Functions and Metabolic Patterns
2.5. Response-Associated Target Genes of Some Conserved MeJA-Responsive lncRNAs Are Involved in Plant Defence and Stress Resistance
2.6. MeJA-Responsive Stress- or Defence-Related Cis-Regulatory Elements May Be Responsible for the Upregulation of lncRNAs and Be Involved in Plant Defence through Their Target Genes
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Growth Conditions
4.2. General RNA-Seq Read Mapping and Assembly
4.3. lncRNA Identification and Prediction
4.4. Differential Expression Analysis of MeJA-Responsive lncRNAs
4.5. Prediction of Cis-Regulating Target Genes of MeJA-Responsive lncRNAs
4.6. Expression Pattern Comparison of Cis-Regulated Target Genes with Their MeJA-Responsive lncRNAs
4.7. Gene Ontology and Pathway Enrichment Analysis
4.8. Cis-Regulatory Element Prediction in the Promoter Sequences
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Zheng, K.; Wang, Z.; Pang, L.; Song, Z.; Zhao, H.; Wang, Y.; Wang, B.; Han, S. Systematic Identification of Methyl Jasmonate-Responsive Long Noncoding RNAs and Their Nearby Coding Genes Unveils Their Potential Defence Roles in Tobacco BY-2 Cells. Int. J. Mol. Sci. 2022, 23, 15568. https://doi.org/10.3390/ijms232415568
Zheng K, Wang Z, Pang L, Song Z, Zhao H, Wang Y, Wang B, Han S. Systematic Identification of Methyl Jasmonate-Responsive Long Noncoding RNAs and Their Nearby Coding Genes Unveils Their Potential Defence Roles in Tobacco BY-2 Cells. International Journal of Molecular Sciences. 2022; 23(24):15568. https://doi.org/10.3390/ijms232415568
Chicago/Turabian StyleZheng, Kaifeng, Zitao Wang, Lu Pang, Zhongbang Song, Heping Zhao, Yingdian Wang, Bingwu Wang, and Shengcheng Han. 2022. "Systematic Identification of Methyl Jasmonate-Responsive Long Noncoding RNAs and Their Nearby Coding Genes Unveils Their Potential Defence Roles in Tobacco BY-2 Cells" International Journal of Molecular Sciences 23, no. 24: 15568. https://doi.org/10.3390/ijms232415568