Skip to content
DraconiticResearch
Search Sources API
206,690 studies31 sourcesUpdated 28 min ago
Peer-reviewedCC BY-NC 4.0Nucleic Acids Research

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

  • Chuan Zhang1,2
  • Jiawen Zhao1,2
  • Xingchen Yu1,2
  • Qi Wang1,2
  • Anyu Zhao1,2,3
  • Yanlin Ren1,2
  • Yixiang Yang1,2
  • Haikun Wei1,2
  • Yonghao Ma4
  • Ke-Wang Xu3
  • Lei Li5
  • Zhonglong Guo1,2,6
1 more authors
  • Xiaozeng Yang1,2,6
6 affiliations
  1. 1State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 ,
  2. 2Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 ,
  3. 3College of Life Sciences, Nanjing Forestry University , Nanjing 210037 ,
  4. 4Hangzhou Jinqun Technology Co., Ltd ., Hangzhou 311227 ,
  5. 5State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang , Weifang, Shandong 261325 ,
  6. 6China National Botanical Garden , Beijing 100093 ,
Open at sourcePDFDOICite

Abstract

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/.

Related

  1. Integrated microRNA and mRNA Profiling in the Corneal Endothelium of Fuchs Endothelial Corneal Dystrophy
    Dmitriy Ryazantsev, Elena Sharova, Denis Gudkov +5
    International Journal of Molecular SciencesPeer-reviewedCC BY 4.0General biochemistryCrossref
  2. An encyclopedia of human enhancer–gene regulatory interactions
    Andreas R. Gschwind, Kristy S. Mualim, Alireza Karbalayghareh +43
    NaturePeer-reviewedCC BYFull text152 citedMolecular biology & gene regulationOpenAlex
  3. An integrative multi-omics modeling framework for chemotherapy response prediction through microRNA–target regulatory signatures
    Briefings in bioinformaticsPeer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMC
  4. Mechanical Loading Reshapes Mesenchymal Stem/Stromal Cell-Derived Extracellular Vesicle microRNA Cargo Toward Predicted Immunomodulatory and EV Cargo-Trafficking Pathways: An In Vitro Mechanobiology Study
    Mahammad Gardashli, Elena Della Bella, Manuel Herzog +3
    BiomoleculesPeer-reviewedCC BYFull textGeneral biochemistryEurope PMC
  5. MicroRNA Responses Associated with Vector-Borne Diseases in Humans and Arthropod Vectors: A Systematic Review
    Tilini K. De Silva, John Stenos, Stephen R. Graves +5
    International journal of molecular sciencesPeer-reviewedCC BYFull textGeneral biochemistryEurope PMC

Cite

BibTeXRIS
BibTeX
@article{zhang2026pmiren30,
  title = {{PmiREN3.0: a multi-omics integrated and AI-assisted encyclopedia for plant microRNA research}},
  author = {Chuan Zhang and Jiawen Zhao and Xingchen Yu and Qi Wang and Anyu Zhao and Yanlin Ren and Yixiang Yang and Haikun Wei and Yonghao Ma and Ke-Wang Xu and Lei Li and Zhonglong Guo and Xiaozeng Yang},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = nov,
  doi = {10.1093/nar/gkag1133},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1133/9013738},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - PmiREN3.0: a multi-omics integrated and AI-assisted encyclopedia for plant microRNA research
AU  - Chuan Zhang
AU  - Jiawen Zhao
AU  - Xingchen Yu
AU  - Qi Wang
AU  - Anyu Zhao
AU  - Yanlin Ren
AU  - Yixiang Yang
AU  - Haikun Wei
AU  - Yonghao Ma
AU  - Ke-Wang Xu
AU  - Lei Li
AU  - Zhonglong Guo
AU  - Xiaozeng Yang
PY  - 2026
DA  - 2026/11/06
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1133
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1133/9013738
AB  - 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/.
SN  - 0305-1048
SN  - 1362-4962
ER  -