PmiREN: Plant microRNA Encyclopedia

Overview

Welcome to PmiREN2.0

PmiREN (Plant miRNA ENcyclopedia) is a comprehensive functional plant miRNA database. In version 2.0, it contains 38,186 miRNA loci (MIR) belonging to 7,838 families, 1,668 syntenic blocks and 141,327 predicted miRNA-target pairs in 179 species phylogenetically ranging from chlorophytes to angiosperms. In addition, 2,331 deeply sequenced small RNA libraries were used in quantification of miRNA expression patterns, and 116 PARE-Seq libraries were employed to validate predicted miRNA-target pairs. Compared to version 1.0, PmiREN2.0 not only retains its full functions, but also adds 11 new tools for in-depth data mining and experimental practice, promoting the transition from data collection to fully functional knowledgebase. Furthermore, PmiREN forum was established for sharing resources and new discoveries, research communication and announcement release. We believe the PmiREN2.0 will consistently provide novel insights into miRNA research.

The phylogenetic tree represents all plant species in PmiREN2.0

<p>The phylogenetic tree represents all plant species in PmiREN2.0. They are 2 chlorophytes, 1 moss, 27 ferns and lycophytes, 2 gymnosperms, 1 basal angiosperm, 1 magnolia, 24 monocotyledons, and 121 eudicotyledons. For most of these species, complete or near complete genome sequences as well as deeply sequenced sRNA-Seq datasets are available.</p>

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Summary of content and features of PmiREN2.0

PmiREN2.0 has been upgraded in such aspects as more user-friendly and easy-to-navigate interfaces, new tools for mining miRNA functions and assisting design of molecular and genetic experiments, rich resources for miRNA research and an online forum for the plant miRNA research community.

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Integrated TF-miRNA-target network

An example of integrated TF-miRNA-target regulatory network, which is centered on Ath-miR408. The processing protocol was followed Gao et.al’s work (Gao et al., 2021, GPB).

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Phylogenetic analysis of miRNA families

The phylogenetic analysis of specific miRNA family was performed in all available plants of PmiREN2.0. Sequences were aligned using MAFFT (Katoh et al., 2019), and the phylogenetic trees were constructed using IQ-Tree with parameters ‘-m MFP -bb 1000 -bnni’ (Nguyen LT et al., 2015).

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Annotation of target genes by KEGG and InterProScan

For an individual target gene, KEGG and InterProScan were used to find the pathways it involved and annotate its functions with default parameters, respectively. By clicking on shortcut button, users can retrieve detailed annotation information linked to the related resource.

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Predicted motifs by PlantCare and PlantRegMap

To explore the upstream regulatory elements of miRNAs, PmiREN2.0 provides two tools, PlantCare and PlantRegMap, for the retrieval of TF binding motifs of miRNA promoters. In PmiREN2.0, there are 1,056,363 and 12,099,859 records of the motifs, respectively, by these two tools, when scanning 3,000 bp promoter candidates of miRNAs. The above is an example of Atr-MIR156a.

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Example of miRNA polymorphisms

Precursors of miRNAs are divided into five compartments based on current annotations, including 5’ arm, 3’ arm, mature, star and internal loop regions. Vcftools and in-house perl scripts were used to detect miRNA polymorphisms in the five regions. This figure exhibits 19 SNPs in the precursor of Osa-MIR395a.

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Three tools assisting design of molecular and genetic experiments

PmiREN2.0 provides three online tools to assist molecular and genetic experiments. ‘OE-miRNA’ is used to design primers for the experiments of overexpressing miRNAs. ‘AmiRNA’ could help silence miRNAs by constructing artificial miRNAs. ‘STTM’ is an effective tool for miRNA repression by designing a short tandem target mimic.

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