{
  "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/.",
  "abstract_shown": true,
  "affiliations": [
    "State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 ,",
    "Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences , Beijing 100093 ,",
    "College of Life Sciences, Nanjing Forestry University , Nanjing 210037 ,",
    "Hangzhou Jinqun Technology Co., Ltd ., Hangzhou 311227 ,",
    "State Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang , Weifang, Shandong 261325 ,",
    "China National Botanical Garden , Beijing 100093 ,"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 13,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Chuan Zhang"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Jiawen Zhao",
      "orcid": "0009-0002-4129-8571"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Xingchen Yu"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Qi Wang"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Anyu Zhao"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Yanlin Ren"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Yixiang Yang"
    },
    {
      "affs": [
        0,
        1
      ],
      "name": "Haikun Wei"
    },
    {
      "affs": [
        3
      ],
      "name": "Yonghao Ma"
    },
    {
      "affs": [
        2
      ],
      "name": "Ke-Wang Xu"
    },
    {
      "affs": [
        4
      ],
      "name": "Lei Li",
      "orcid": "0000-0001-8304-1286"
    },
    {
      "affs": [
        0,
        1,
        5
      ],
      "name": "Zhonglong Guo"
    },
    {
      "affs": [
        0,
        1,
        5
      ],
      "name": "Xiaozeng Yang",
      "orcid": "0000-0002-8529-0371"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/bwcj4zs77v3pq.bib",
  "cited_by": 0,
  "doi": "10.1093/nar/gkag1133",
  "fulltext_url": null,
  "id": "bwcj4zs77v3pq",
  "issns": [
    "0305-1048",
    "1362-4962"
  ],
  "landing_url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1133/9013738",
  "language": null,
  "licence": "CC-BY-NC-4.0",
  "licence_label": "CC BY-NC 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [],
  "openalex": null,
  "pdf_url": "https://academic.oup.com/nar/advance-article-pdf/doi/10.1093/nar/gkag1133/73148357/gkag1133.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-06",
  "publisher": "Oxford University Press (OUP)",
  "ris": "https://research.draconitic.com/paper/bwcj4zs77v3pq.ris",
  "sources": [
    {
      "first_seen": "2026-11-06T12:21:08Z",
      "native_id": "10.1093/nar/gkag1133",
      "source": "crossref",
      "url": "https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1133/9013738"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "issn:0305-1048",
      "subfield": "molecular-biology"
    }
  ],
  "title": "PmiREN3.0: a multi-omics integrated and AI-assisted encyclopedia for plant microRNA research",
  "title_text": "PmiREN3.0: a multi-omics integrated and AI-assisted encyclopedia for plant microRNA research",
  "type": "peer-reviewed",
  "updated_at": "2026-11-08T00:22:15Z",
  "url": "https://research.draconitic.com/paper/bwcj4zs77v3pq",
  "venue": "Nucleic Acids Research",
  "versions": []
}