Abstract
Main conclusion
miRNA targets from Citrus sinensis are predicted and validated using degradome data. They show an up-regulation upon infection with CPsV, with a positive correlation between target expression and symptom severity.
Abstract
Sweet orange (Citrus sinensis) may suffer from disease symptoms induced by virus infections, thus resulting in drastic economic losses. Infection of sweet orange plants with two isolates of citrus psorosis virus (CPsV), expressing different symptomatologies, alters the accumulation of a set of endogenous microRNAs (miRNAs). Here, we predicted ten putative targets from four down-regulated miRNAs: three belonging to the CCAAT-binding transcription factor family (CBFAs); an Ethylene-responsive transcription factor (RAP2-7); an Integrase-type DNA-binding superfamily protein (AP2B); Transport inhibitor response 1 (TIR1); GRR1-like protein 1-related (GRR1); Argonaute 2-related (AGO2), Argonaute 7 (AGO7), and a long non-coding RNA (ncRNA). We validated six of them through analysis of leaf degradome data. Expressions of the validated targets increase in infected samples compared to healthy tissue, showing a more striking up-regulation those samples with higher symptom severity. This study contributes to the understanding of the miRNA-mediated regulation of important transcripts in Citrus sinensis through target validation and shed light in the manner a virus can alter host regulatory mechanisms leading to symptom expression.
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Abbreviations
- AGO2:
-
Argonaute 2-related
- AGO7:
-
Argonaute 7
- AP2B:
-
Integrase-type DNA-binding superfamily protein
- CBF:
-
CCAAT-binding transcription factor
- CPsV:
-
Citrus psorosis virus
- GRR1:
-
GRR1-like protein 1-related
- ncRNA:
-
Non-coding RNA
- RAP2-7:
-
Ethylene-responsive transcription factor
- Targets:
-
Targeting specific transcript RNAs
- TIR1:
-
Transport inhibitor response 1
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Acknowledgements
We thank Dr. Carmen Hernández Fort and Dr. Eduardo J. Peña for critical reading of the manuscript. We also thank Romina N. Ramos for help with statistical analysis and A.E. Claudio A. Gómez (Laboratorio de Protección Vegetal y Biotecnología, EEA-Concordia, INTA) for providing Citrus sinensis plants.
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Fig. S1 Target plot (t-plot) of validated miRNAs targets in Citrus sinensis. The abundance of each signature is plotted as a function of its position in the transcript. Slicing site (red dot) coincides with a high stack of reads (PDF 476 kb)
425_2019_3294_MOESM2_ESM.tif
Table S1 Oligonucleotides used for primers. All sequences ID were taken from http://citrus.hzau.edu.cn. The respective annealing temperatures used in qPCR analysis are indicated. Primer efficiency (E) was calculated as: 10(-1/slope). Slope shows the correlation between the number of copies and the Ct mean for each pair of primers. The % Efficiency = (E – 1) × 100% (TIFF 167115 kb)
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Marmisolle, F.E., Arizmendi, A., Ribone, A. et al. Up-regulation of microRNA targets correlates with symptom severity in Citrus sinensis plants infected with two different isolates of citrus psorosis virus. Planta 251, 7 (2020). https://doi.org/10.1007/s00425-019-03294-0
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DOI: https://doi.org/10.1007/s00425-019-03294-0