PmiREN

PmiREN provides an encyclopedia of plant microRNAs for identification, annotation, and target evidence across diverse plant species.

Key Features:

• High-Confidence Entries: PmiREN contains 16,422 high-confidence novel miRNA loci across 88 plant species and 3,966 entries retrieved from miRBase, produced by uniform processing of sequenced small RNA libraries using miRDeep-P2.
• Uniform Annotation Standards: PmiREN applies newly updated criteria for plant miRNA identification to ensure consistent annotations across species.
• Comprehensive Annotations: Each miRNA entry includes precursor sequence, precursor secondary structure, expression patterns, clusters and synteny within the genome, potential targets supported by Parallel Analysis of RNA Ends (PARE) sequencing, and literature references.
• Advanced Search Capabilities: The database provides eight built-in search engines for querying entries using various parameters.

Scientific Applications:

• Gene Regulation Studies: Use miRNA expression patterns and PARE-supported targets to investigate post-transcriptional regulation.
• Evolutionary Research: Conduct comparative analyses of miRNA conservation and divergence across multiple plant species.
• Functional Genomics: Identify novel miRNA loci and explore their potential functional roles within plant genomes.
• Data-Driven Research: Leverage comprehensive annotations and search engines for large-scale analyses of plant miRNA biology.

Methodology:

Sequenced small RNA libraries were uniformly processed using miRDeep-P2; entries include records retrieved from miRBase; updated criteria for plant miRNA identification were applied; potential targets were identified with Parallel Analysis of RNA Ends (PARE) sequencing.