Transposon-Associated Small RNAs Involved in Plant Defense in Poplar
Abstract
1. Introduction
2. Materials and Methods
2.1. Plant Material and Fungal Treatments
2.2. Library Preparation and NGS Sequencing
2.3. sRNAome and mRNA Analysis
2.4. Effector Prediction
2.5. Target Prediction
2.6. Locations of miRNAs in the P. trichocarpa Genome
2.7. TE Annotation
2.8. Pseudogene Annotation
3. Results
3.1. Poplar sRNAs Expressed During a Rust Fungus Infection
3.2. Pseudogenes and Transposons Act as Catalysts for the Formation of siRNA Clusters
3.3. Infection Stage-Specific Differences in the siRNAs Primarily Originate from the Transposon Regions
3.4. Populus siRNAs Mediate Plant–Pathogen Interactions, as Revealed Using a Shotgun Strategy
3.5. The Populus-Specific miRNAs Are More Involved in the Regulation of the Disease-Resistance (DR) Genes
3.6. Populus-Specific miR6579 and miR6590 Target Numerous NB-LRR Genes
4. Discussion
4.1. Transposons and Posttranscriptional Regulation
4.2. Cross-Kingdom RNAi and sRNAs Mediate Plant–Pathogen Interactions
4.3. Disease Resistance Associated with Populus-Specific miRNAs
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Position | a Expected (SD) | Observed | Z Score b | p-Value |
---|---|---|---|---|
Pseudogene | 475.80 (6.16) | 625 | 24.22 | 1.39 × 10−127 |
Up | 3192.40 (23.28) | 2973 | −9.42 | 2.26 × 10−21 |
Down | 3078.80 (33.52) | 2586 | −14.7 | 3.22 × 10−49 |
5′ UTR | 450.60 (20.88) | 330 | −5.78 | 3.74 × 10−9 |
3′ UTR | 570.60 (9.28) | 395 | −18.92 | 3.90 × 10−80 |
Intron | 2923.40 (27.52) | 982 | −70.55 | 0.00 |
Transposon | 4271.00 (39.6) | 8159 | 98.18 | 0.00 |
Intergenic | 4731.40 (59.68) | 4703 | −0.47 | 0.32 |
No. of Conserved miRNA a | No. of Populus-miRNAs | Conserved miRNAs Targeting Disease Resistance Genes b | Populus-Specific miRNA Targeting Disease Resistance Genes c | Adjusted p-Value d |
---|---|---|---|---|
30 | 181 | 7 | 120 | 0.009 |
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Long, C.; Du, Y.; Guan, Y.; Liu, S.; Xie, J. Transposon-Associated Small RNAs Involved in Plant Defense in Poplar. Plants 2025, 14, 1265. https://doi.org/10.3390/plants14081265
Long C, Du Y, Guan Y, Liu S, Xie J. Transposon-Associated Small RNAs Involved in Plant Defense in Poplar. Plants. 2025; 14(8):1265. https://doi.org/10.3390/plants14081265
Chicago/Turabian StyleLong, Cui, Yuxin Du, Yumeng Guan, Sijia Liu, and Jianbo Xie. 2025. "Transposon-Associated Small RNAs Involved in Plant Defense in Poplar" Plants 14, no. 8: 1265. https://doi.org/10.3390/plants14081265
APA StyleLong, C., Du, Y., Guan, Y., Liu, S., & Xie, J. (2025). Transposon-Associated Small RNAs Involved in Plant Defense in Poplar. Plants, 14(8), 1265. https://doi.org/10.3390/plants14081265