PmiREN: Plant microRNA Encyclopedia

Overview

Welcome to PmiREN

PmiREN (Plant miRNA ENcyclopedia) is a comprehensive functional plant miRNA database. In current version, PmiREN contains 20388 miRNA loci (MIRs) belonging to 5757 families, 1365 clusters, 1668 syntenic blocks and 141327 predicted miRNA-target pairs in 88 species phylogenetically ranging from chlorophytes to angiosperms. In addition, 1537 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. PmiREN has many unique features such as annotating miRNAs with an uniform method, solid and extensive information on miRNA synteny, conservation, expression, references, and providing many convenient data accesses, powerful search and download engines. We believe PmiREN is a truly functional knowledgebase and will provide novel insights into plant miRNA research and benefit the whole research community.

The phylogenetic tree represents all plant species in PmiREN

The phylogenetic tree represents all plant species in PmiREN. They are 2 chlorophytes, 1 moss, 1 lycophyte, 2 gymnosperms, 1 basal angiosperm, 1 magnolia, 18 monocotyledons, and 62 eudicotyledons. For these species, complete or near complete genome sequences as well as deeply sequenced sRNA-Seq datasets were available. In addition, 116 PARE-Seq datasets from 21 species were used to validate predicted miRNA-target pairs.

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Examples of the expression patterns of miRNAs in Arabidopsis thaliana

Expression values (RPM) of all miRNAs in Arabidopsis thaliana were achieved from 39 sRNA-Seq datasets from different tissues including flower, inflorescence, leaf, root, seeding and silique. The log10 value of RPM mean of each miRNA in a specific tissue was employed to make the heat map analysis. The hierarchical clustering was generated by Pearson correlation coefficients of these values. Gradient colors from red to blue indicate the expression value from high to low.

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Examples of conservation analyses of miRNA families

The matrix consists of 88 plant species represented by a phylogenetic tree (rows) and 30 representative miRNA families (columns). A box is highlighted by blue if at least one member of a given miRNA family was annotated in PmiREN.

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Examples of syntenic miRNAs in Poaceae

Syntenic miRNA gene pairs of 3 species in grass family including Oryza sativa (rice), Brachypodium distachyon and Oryza nivara were displayed by Circos diagram. Grey lines indicate syntenic miRNAs between Oryza sativa and Oryza nivara. Blue lines indicate syntenic miRNAs between Oryza sativa and Brachypodium distachyon. Green lines indicate syntenic miRNAs between Oryza nivara and Brachypodium distachyon. Red lines indicate syntenic miRNAs within Oryza sativa.

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Examples of predicted miRNA target genes and their validations by PARE-Seq

Two examples including one conserved miRNA isoform (miR157a/b/c/d) and one non-conserved one (miRN011) from tomato (Solanum lycopersicum) were displayed. The complimentary between miRNAs and targets was predicted by both RNAhybrid and psRNATarget. Validations from two tissues (fruit and leaf) by PARE-Seq data were achieved by CleaveLand4.

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Comparison and analysis of miR156/157/529 superfamily in land plants

A possible evolutionary model for the dynamic divergence of miR156/157/529 superfamily in land plants. Weblogo on the left side shows the sequence similarity and difference of miR156, miR157 and miR529 while the cartoon on the right side presents their existence in different evolutionary branches.

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Summary of updated content in PmiREN version 2

PmiREN version 2 has been upgraded in four aspects, including user interface, tools, resource and community. The website has made six improvements in user interface, providing a more beautiful, convenient and safe interface. 11 data mining tools have been added to PmiREN, involving sequence, function and molecular experiment. Resource and community pages provide users with a platform for the latest research progress and communication.

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Summary of updated datasets in PmiREN version 2

On the basis of the previous 7 datasets in version 1, the website has added 33 new plant species. In the new version of PmiREN, 10 new datasets have been added, involving sequence analysis, function annotation, evolution and publication.

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Integrated TF-miRNA-target network

The integrated TF-miRNA-target network is retrieved from Gao et.al’s work. The network integrates MTIs (2,466), TMIs (2019), and TTIs (15,797), which consist of 2096 nodes (genes) and 20,282 directed edges (interactions). miRNA-target interactions (MTIs), TF-miRNA interactions (TMIs), and TF-target interactions (TTIs)

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