PmiREN3.0: a multi-omics integrated and AI-assisted encyclopedia for plant microRNA research

MicroRNAs (miRNAs) are key post-transcriptional regulators in gene regulatory networks (GRNs). Comprehensive research on miRNAs increasingly requires the integration of large and heterogeneous datasets, together with more efficient approaches to knowledge exploration. Here, we present PmiREN3.0, a major update of the Plant MicroRNA Encyclopedia. Compared with PmiREN2.0, species/subspecies coverage increased from 179 to 340, adding 22 orders, 51 families, and 108 genera. Using the same standardized workflow and annotation criteria as previous releases, high-confidence miRNAs were identified from 5319 small RNA sequencing (sRNA-seq) datasets, with miRNA loci increasing from 39 751 to 87 667 and miRNA families from 7838 to 18 389. Resources and tools from previous releases were extensively updated, while six new modules were added for primary transcripts, DNA methylation, RNA modifications, stress-responsive expression, metabolic pathways, and core GRNs. PmiREN3.0 also introduces miRai+, a knowledge service powered by artificial intelligence (AI) that combines a language model fine-tuned on miRNA knowledge with retrieval augmented generation. Evaluation yielded scores of 0.910 for answer relevance, 0.965 for faithfulness, and 0.906 for factual correctness. Together, PmiREN3.0 provides an expanded plant miRNA dataset and an integrated platform combining multi-omics data and AI-assisted knowledge services for plant miRNA research. PmiREN3.0 is available at https://pmiren.com/.