The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba
Abstract
:1. Introduction
2. Results
2.1. Quality and Statistics of Whole Transcriptome Sequencing
2.2. Regulatory Networks of lncRNA-miRNA-mRNA
2.3. Regulatory Networks of circRNA–miRNA–mRNA
2.4. Identification and Characteristics of Candidate Genes
2.5. Identification of Allelic Variations
2.6. Phylogenetic Analysis of Cellulose Synthase and Cellulose Synthase-like Proteins
2.7. Differentially Expressed Genes in the Phenylpropane Pathway
3. Discussion
4. Materials and Methods
4.1. Plant Materials and RNA Sampling
4.2. Library Preparation and Sequencing
4.3. Quality Control
4.4. Read Mapping and Assembly
4.5. Identification of mRNAs, lncRNAs, circRNAs, and miRNAs
4.6. Quantification and Differential Expression Analysis
4.7. Construction of the Regulatory Network
4.8. Quantitative Real-Time PCR
4.9. Phylogenetic Analysis
4.10. SNP Analysis
4.11. Heatmap and Gene Analysis
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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SNP Type | Transition SNPs | Transversion SNPs | ||||
---|---|---|---|---|---|---|
C/T | A/G | A/T | A/C | G/T | G/C | |
Number of allelic sites | 26,704 | 26,579 | 9163 | 8453 | 8444 | 7579 |
Frequency (%) | 30.72 | 30.58 | 10.54 | 9.73 | 9.71 | 8.72 |
Total (percent of total) | 53,283 (61.30%) | 33,639 (38.70%) |
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Bai, Q.; Shi, L.; Li, K.; Xu, F.; Zhang, W. The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba. Int. J. Mol. Sci. 2024, 25, 2171. https://doi.org/10.3390/ijms25042171
Bai Q, Shi L, Li K, Xu F, Zhang W. The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba. International Journal of Molecular Sciences. 2024; 25(4):2171. https://doi.org/10.3390/ijms25042171
Chicago/Turabian StyleBai, Qingsong, Lingling Shi, Kejian Li, Fang Xu, and Weihua Zhang. 2024. "The Construction of lncRNA/circRNA–miRNA–mRNA Networks Reveals Functional Genes Related to Growth Traits in Schima superba" International Journal of Molecular Sciences 25, no. 4: 2171. https://doi.org/10.3390/ijms25042171