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MicroRNAs in plant-parasitic nematodes: what are they and why should we care?

Dave T. Ste-Croix

Dave T. Ste-Croix

Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development CentreSaint-Jean-sur-Richelieu, Canada
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Ste-Croix, Dave T.
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Benjamin Mimee

Benjamin Mimee

Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu Research and Development CentreSaint-Jean-sur-Richelieu, Canada
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Mimee, Benjamin
  
24. Sept. 2025
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Artikel-Kategorie: Review
Online veröffentlicht: 24. Sept. 2025
Eingereicht: 17. Juni 2025
DOI: https://doi.org/10.2478/jofnem-2025-0041
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© 2025 Dave T. Ste-Croix et al., published by Sciendo
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Figure 1:

Canonical miRNA biogenesis pathways in animals and plants. miRNA synthesis begins with the transcription of pri-miRNAs, which are then cleaved into pre-miRNAs by different enzymes. These precursors are subsequently processed into mature miRNAs—within the nucleus in plants, but in the cytoplasm in animals. The resulting miRNA duplexes are then loaded onto different AGO proteins, with distinct AGO associations in plants versus animals. AGO, argonaute; miRNAs, microRNAs; pre-miRNAs, precursor miRNAs; pri-miRNAs, primary miRNAs.
Canonical miRNA biogenesis pathways in animals and plants. miRNA synthesis begins with the transcription of pri-miRNAs, which are then cleaved into pre-miRNAs by different enzymes. These precursors are subsequently processed into mature miRNAs—within the nucleus in plants, but in the cytoplasm in animals. The resulting miRNA duplexes are then loaded onto different AGO proteins, with distinct AGO associations in plants versus animals. AGO, argonaute; miRNAs, microRNAs; pre-miRNAs, precursor miRNAs; pri-miRNAs, primary miRNAs.

Tools and databases commonly used in the study of non-model organisms’ miRNAs_

Tool Description Access link Reference
DATABASES
miRBase The primary repository for miRNA sequences and annotation. https://www.mirbase.org/ Kozomara et al. (2019)
MirGeneDB High-confidence, manually curated miRNA gene database. https://mirgenedb.org/ Clarke et al. (2025)
Rfam Database of ncRNA families from a wide array of species. https://rfam.org Kalvari et al. (2021)
TargetWormScan Searchable database of predicted regulatory targets of worm miRNAs. https://www.targetscan.org/worm_52/ Lewis et al. (2005)
PmiREN Comprehensive plant repository of plant miRNAs. https://pmiren.com/ Guo et al. (2020)
ncPlantDB Database specialized in ncRNAs in plants. https://bis.zju.edu.cn/ncPlantDB/index/ Liu et al. (2025)
ExoCarta Database containing information on exosomal proteins and RNAs including miRNAs. http://exocarta.org/index.html Keerthikumar et al. (2016)
miRTarBase Comprehensive collection of validated miRNA-mRNA targets. https://mirtarbase.cuhk.edu.cn/~miRTarBase/miRTarBase_2025/php/index.php Cui et al. (2025)
miRecords Resource for animal miRNA-target interactions including C.elegans. http://c1.accurascience.com/miRecords/ Xiao et al. (2009)
PREDICTION TOOLS
MirDeep2 Most widely used tool for both known and novel miRNA prediction in animals and plants. https://github.com/rajewsky-lab/mirdeep2 Friedländer et al. (2012)
miRanalyzer Tool for the detection of known, and prediction of new miRNAs, in high-throughput sequencing experiments. http://bioinfo2.ugr.es/miRanalyzer/ Hackenberg et al. (2011)
miRPlant miRNA predictor utilizing plant-specific parameters (e.g., handling of diverse hairpin lengths and sequences). https://sourceforge.net/projects/mirplant/ An et al. (2014)
sRNAbench Part of the sRNAToolKit suite for miRNA discovery and quantification using sRNASeq data. http://bioinfo5.ugr.es/srnatoolbox/ Aparicio-Puerta et al. (2022)
ShortStack Highly accurate, plant-optimized, and supports multi-mapping small RNAs. https://github.com/MikeAxtell/ShortStac Axtell (2013)
miRPara Predicted miRNA precursors based on structural and sequence features. https://github.com/weasteam/miRPara Wu et al. (2011)
RNAFold Comprehensive collection of tools for folding, design and analysis of RNA sequences. http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi Gruber et al. (2008)
TARGET PREDICTION
miRanda An miRNA target scanner that aims to predict mRNA targets for miRNAs using dynamic-programming alignment and thermodynamics. https://github.com/hacktrackgnulinux/miranda Betel et al. (2010)
RNAHybrid Tool for finding the minimum free energy hybridization of a long and a short RNA. https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid Krüger and Rehmsmeier (2006)
psRNATarget Specifically developed to identify target transcripts of plant regulatory sRNAs. https://www.zhaolab.org/psRNATarget/ Dai and Zhao (2011)
p-TarPMir Deep learning model adapted for plant miRNA target prediction. https://ptarpmir.cu-bic.ca Ajila et al. (2023b)
miTAR Animal trained hybrid deep learning approach to predict miRNA targets. https://github.com/tjgu/miTAR Gu et al. (2021)

Distinguishing characteristics inherent to miRNA and siRNA_

Feature miRNA siRNA
Origin Endogenous Endogenous and exogenous
Structure Hairpin precursor Long dsRNA
Processing enzymes Dicer1 or DCL1 (in nucleus, mostly) Dicer2 or DCL4 (also DCL2, DCL3 depending on siRNA class)
Target complementarity Partial (often with central mismatches) or near perfect Usually perfect or near-perfect
Function Post-transcriptional gene regulation (mRNA degradation or translational inhibition) Gene silencing, antiviral defense, transposon suppression, RdDM
Target specificity Often targets multiple genes in the same family Highly specific to one or few targets
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