Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (Coptis trifolia)
Abstract
1. Introduction
2. Results
2.1. Transcriptome Assembly
2.2. Transcriptome Analysis Using RNA-Seq Data
2.3. Identification of Full-Length Transcripts Involved in BIA Biosynthesis
2.4. qRT-PCR Validation of RNA-Seq Results for 15 BIA Biosynthetic Genes
2.5. Untargeted and Targeted Metabolite Profiling
3. Discussion
3.1. High-Quality Coptis trifolia Transcriptome Assembly via Integrated ONT and Illumina Sequencing
3.2. Differential Gene Expression Between Leaves and Roots
3.3. Accumulation of BIA and Their Biosynthetic Genes in C. trifolia
4. Materials and Methods
4.1. Plant Materials
4.2. RNA Extraction, Library Construction, and RNA-Sequencing
4.3. Analysis of RNA-Seq Data
4.4. Identification of Genes Involved in BIA Biosynthesis
4.5. Validation of RNA-Seq Results Using qRT-PCR
4.6. Metabolite Profiling
4.6.1. Targeted Analysis of Six BIA-Related Metabolites
4.6.2. Untargeted Metabolomics
4.6.3. Quality Control and Method Validation
4.6.4. Data Processing, Compound Detection, Grouping, Alignment, and Background Subtraction
4.6.5. Metabolite Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Koh, Y.-S.; Zhu, F.; Hwang, Y.; Yoo, M.-J. Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (Coptis trifolia). Int. J. Mol. Sci. 2025, 26, 9704. https://doi.org/10.3390/ijms26199704
Koh Y-S, Zhu F, Hwang Y, Yoo M-J. Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (Coptis trifolia). International Journal of Molecular Sciences. 2025; 26(19):9704. https://doi.org/10.3390/ijms26199704
Chicago/Turabian StyleKoh, Yoo-Shin, Fanchao Zhu, Yoojeong Hwang, and Mi-Jeong Yoo. 2025. "Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (Coptis trifolia)" International Journal of Molecular Sciences 26, no. 19: 9704. https://doi.org/10.3390/ijms26199704
APA StyleKoh, Y.-S., Zhu, F., Hwang, Y., & Yoo, M.-J. (2025). Transcriptomic and Metabolomic Insights into Benzylisoquinoline Alkaloid Biosynthesis in Goldthread (Coptis trifolia). International Journal of Molecular Sciences, 26(19), 9704. https://doi.org/10.3390/ijms26199704