P-TarPmiR accurately predicts plant-specific miRNA targets

Abstract

AbstractmicroRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been developed in plant species, but they often fail to discover new miRNA targets with non-canonical miRNA–mRNA binding. Here, the recently published TarDB database of plant miRNA–mRNA data is leveraged to retrain the TarPmiR miRNA target predictor for application on plant species. Rigorous experiment design across four plant test species demonstrates that animal-trained predictors fail to sustain performance on plant species, and that the use of plant-specific training data improves accuracy depending on the quantity of plant training data used. Surprisingly, our results indicate that the complete exclusion of animal training data leads to the most accurate plant-specific miRNA target predictor indicating that animal-based data may detract from miRNA target prediction in plants. Our final plant-specific miRNA prediction method, dubbed P-TarPmiR, is freely available for use at http://ptarpmir.cu-bic.ca. The final P-TarPmiR method is used to predict targets for all miRNA within the soybean genome. Those ranked predictions, together with GO term enrichment, are shared with the research community.

Catalase (CAT) Gene Family in Oil Palm (Elaeis guineensis Jacq.): Genome-Wide Identification, Analysis, and Expression Profile in Response to Abiotic Stress

“…Research on miRNAs in woody plants primarily focuses on their role in regulating biological activities like plant growth, development, signal transduction, stress response, and secondary metabolite generation. [40,41]. There have been reports on the relationship between miRNA and target genes in wheat [25] and cotton [30].…”

Characterization of microRNAs in the cyst nematode Heterodera glycines identifies possible candidates involved in cross-kingdom interactions with its host Glycine max

“…To predict the interaction between SCN miRNA and soybean mRNAs (Interspecies interactions), the plant-specific predictor P-TarPmiR was used [ 43 ]. Briefly, mature miRNA sequences were inputted alongside full soybean gene sequences, and interactions were predicted using the P-TarPmiR model trained on plant data.…”

Species-specific microRNA discovery and target prediction in the soybean cyst nematode

“…Similarly, a classifier utilizing the same prediction architecture as TarPMir was trained on data derived from TarDB 85 , a database of intraspecies plant miRNA:mRNA interactions. The Plant TarPMir classifier (P-TarPMir) 86 was applied to predict interactions between the high-confidence SCN mature miRNA and soybean mRNA. CE-TarPMir was applied to the high-confidence candidate mature SCN miRNA and all available SCN mRNA.…”