Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plants and Growth Conditions
2.2. RNA Isolation, Small RNA Library Construction. and Sequencing
2.3. Small RNA Sequencing Data Pre-Processing and microRNA Identification
2.4. Analysis of Virus-Derived siRNAs
2.5. Differential Expression Analysis of miRNAs
2.6. miRNA Target Prediction and Enrichment Analysis
2.7. Evaluation of the Expression of miRNAs and Their Potential Target Genes
2.8. Cleavage Sites Validation of Target Genes of miRNAs
3. Results
3.1. CaCV Symptom Development in Resistant Capsicum Plants at Elevated Temperatures
3.2. Small RNAs in CaCV-Infected and Virus-Free Capsicum Grown at Different Temperatures
3.3. Identification of Known and Novel miRNAs
3.4. Differentially Expressed miRNAs
3.5. Functional Analysis of Predicted Target Genes of DE miRNAs in Response to CaCV under Ambient and High-Temperature Conditions
3.6. Validation of the Expression Patterns of Selected miRNAs and Their Target Genes
3.7. Identification of miRNA-Mediated Cleavage of Target Genes
4. Discussion
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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miRNA ID | HV/AV_log2 (FC) | AV/AM_log2 (FC) | HV/HM_log2 (FC) | HM/AM_log2 (FC) |
---|---|---|---|---|
Can-miR408a-5p | 4.94651183 | 2.15675264 | ||
Can-miR408a-3p | 4.52786751 | −1.431929 | 1.87576962 | |
Can-miR398b-3p | 4.3647467 | −1.1693631 | 2.7875221 | |
Can-miR397-5p | 3.41052681 | −1.3643359 | 1.80648604 | |
Can-miR397-3p | 3.09698569 | −1.1034217 | 1.41436391 | |
Can-miRN492-5p | 2.4800554 | 2.07163552 | ||
Can-miR_N7b-3p | 2.22044295 | 1.95841442 | ||
Can-miR_N7c-3p | 2.22044295 | 1.95841442 | ||
Can-miR_N7d-3p | 2.16627692 | 1.84961374 | ||
Can-miR393-3p | 2.00053338 | |||
Can-miRN37-Novel-5p | 1.97325814 | 1.2736888 | ||
Can-miR_N2a-3p | 1.66675404 | |||
Can-miR172a-m1-3p | 1.62135413 | |||
Can-miR172d-3p | 1.61286777 | |||
Can-miR_N71a-5p | 1.60761055 | |||
Can-miR_N50a-5p | 1.51467255 | |||
Can-miR403-3p | 1.29105902 | 1.04987498 | ||
Can-miRN25-Novel-3p | 1.27226491 | 1.27136116 | ||
Can-miR160a-m1-5p | 1.25709852 | |||
Can-miRC13.1-m1-5p | 1.19626839 | |||
Can-miRC13.2-m1-5p | 1.19626839 | |||
Can-miR157c-5p | −1.0923326 | |||
Can-miR157b-5p | −1.1162378 | |||
Can-miR169h-3p | −1.1385036 | −1.8141374 | ||
Can-miR_N80a-3p | −1.4595388 | |||
Can-miR477a-5p | −1.6760649 | −3.4314472 | ||
Can-miR164b-5p | −1.7200209 | |||
Can-miR164c-5p | −1.7417164 | |||
Can-miR477b-5p | −1.7912909 | −2.9432463 | ||
Can-miRN482-5p | −1.8617146 | −2.2237655 | ||
Can-miR399a-Known-5p | −1.9889216 | −5.5813609 | ||
Can-miR399b-Known-5p | −1.9889216 | −5.5813609 | ||
Can-miR399c-Known-5p | −1.9889216 | −5.5813609 | ||
Can-miR399d-Known_1-5p | −1.9889216 | −5.5813609 | ||
Can-miR399d-Known-5p | −1.9889216 | −5.5813609 |
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Tsai, W.-A.; Brosnan, C.A.; Mitter, N.; Dietzgen, R.G. Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures. Pathogens 2024, 13, 745. https://doi.org/10.3390/pathogens13090745
Tsai W-A, Brosnan CA, Mitter N, Dietzgen RG. Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures. Pathogens. 2024; 13(9):745. https://doi.org/10.3390/pathogens13090745
Chicago/Turabian StyleTsai, Wei-An, Christopher A. Brosnan, Neena Mitter, and Ralf G. Dietzgen. 2024. "Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures" Pathogens 13, no. 9: 745. https://doi.org/10.3390/pathogens13090745