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Research article - Peer-reviewed, 2023

Occurrence of RNA post-transcriptional modifications in plant viruses and viroids and their correlation with structural and functional features

Marquez-Molins, Joan; Juarez-Gonzalez, Vasti Thamara; Gomez, Gustavo; Pallas, Vicente; Martinez, German


Post-transcriptional modifications of RNA bases are widespread across all the tree of life and have been linked to RNA maturation, stability, and molecular interactions. RNA modifications have been extensively described in endogenous eukaryotic mRNAs, however, little is known about the presence of RNA modifications in plant viral and subviral RNAs. Here, we used a computational approach to infer RNA modifications in plant-pathogenic viruses and viroids using high-throughput annotation of modified ribonucleotides (HAMR), a software that predicts modified ribonucleotides using high-throughput RNA sequencing data. We analyzed datasets from representative members of different plant viruses and viroids and compared them to plant-endogenous mRNAs. Our approach was able to predict potential RNA chemical modifications (RCMs) in all analyzed pathogens. We found that both DNA and RNA viruses presented a wide range of RCM proportions while viroids had lowest values. Furthermore, we found that for viruses with segmented genomes, some genomic RNAs had a higher proportion of RCM. Interestingly, nuclear-replicating viroids showed most of the predicted modifications located in the pathogenesis region, pointing towards a possible functional role of RCMs in their infectious cycle. Thus, our results strongly suggest that plant viral and subviral RNAs might contain a variety of previously unreported RNA modifications, thus opening a new perspective in the multifaceted process of plant-pathogen interactions.


RNA; Pathogens; Immune response; Defense; RNA modifications; Epitranscriptomics; Viruses; Viroids; m1A

Published in

Virus Research
2023, volume: 323, article number: 198958
Publisher: ELSEVIER

Authors' information

Marquez-Molins, Joan
University of Valencia
Marquez-Molins, Joan
Universitat Politecnica de Valencia
Swedish University of Agricultural Sciences, Department of Plant Biology
Gomez, Gustavo
University of Valencia
Pallas, Vicente
CSIC-UPV - Instituto de Biologia Molecular y Celular de Plantas (IBMCP)
Martinez Arias, German (Martinez-Arias, Germán)
Swedish University of Agricultural Sciences, Department of Plant Biology

Associated SLU-program

SLU Network Plant Protection

UKÄ Subject classification

Bioinformatics and Systems Biology

Publication Identifiers


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