Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max
Abstract
:1. Introduction
2. Results
2.1. Genome-Wide Characterization of Full-Length Transcripts in Soybean by Iso-Seq
2.2. Comprehensive Temporal Analysis of Alternative Splicing Dynamics during Nodule and Root Development
2.3. Differential Transcript Usage Evaluated by Isoform Expression Levels
2.4. Long Non-Coding RNA Identified from Iso-Seq Transcripts
3. Discussion
4. Materials and Methods
4.1. Materials and Growth Conditions
4.2. RNA Preparation
4.3. Library Preparation and Sequencing
4.4. RT-PCR for Validation
4.5. Pacbio Data Analysis
4.6. Integrative Analysis of Iso-Seq with Illumina Short Reads
4.7. Annotation of Pacbio Isoforms
4.8. LncRNAs Identification
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Library Size (kb) | SMRT Cells | Polymerase Reads | FLNC 1 | High Quality Isoforms |
---|---|---|---|---|
1–2 | 12 | 905,500 | 419,736 | 117,970 |
2–4 | 12 | 1,231,202 | 612,254 | 144,968 |
3–5 | 12 | 1,238,704 | 542,507 | 105,423 |
3.5–6 | 8 | 697,016 | 161,752 | 55,532 |
4–10 | 8 | 818,271 | 246,844 | 28,810 |
Total | 52 | 4,890,693 | 1,983,093 | 452,703 |
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Liu, J.; Chen, S.; Liu, M.; Chen, Y.; Fan, W.; Lee, S.; Xiao, H.; Kudrna, D.; Li, Z.; Chen, X.; et al. Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max. Int. J. Mol. Sci. 2022, 23, 7371. https://doi.org/10.3390/ijms23137371
Liu J, Chen S, Liu M, Chen Y, Fan W, Lee S, Xiao H, Kudrna D, Li Z, Chen X, et al. Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max. International Journal of Molecular Sciences. 2022; 23(13):7371. https://doi.org/10.3390/ijms23137371
Chicago/Turabian StyleLiu, Jing, Shengcai Chen, Min Liu, Yimian Chen, Wei Fan, Seunghee Lee, Han Xiao, Dave Kudrna, Zixin Li, Xu Chen, and et al. 2022. "Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max" International Journal of Molecular Sciences 23, no. 13: 7371. https://doi.org/10.3390/ijms23137371