{
  "abstract": "Introduction: Epimedium pubescens Maxim. (Berberidaceae) is a botanical source of Herba Epimedii and is rich in prenylated flavonoids such as icariin. Although a chromosome-level genome is available for E. pubescens , its genomic and transcriptomic resources are dispersed across public resource platforms. We developed EpuDB ( https://www.gzybioinformatics.cn/EpuDB/ ) to bring these resources together in a searchable and programmatically accessible database.\n\nMethods: EpuDB links 42,827 official gene loci to functional annotations, gene-family classifications, transcriptomic profiles, differential-expression results, co-expression networks and orthology-inferred candidate protein–protein interactions.\n\nResults: The database contains 1,991 transcription factors, 521 transcriptional regulators, 1,139 protein kinases, 505 cytochrome P450s and 1,106 ubiquitination-system components, together with 2,399 candidate protein–protein interaction pairs. Its transcriptome compendium includes 70 RNA-seq samples from six BioProjects and 58 within-project differential-expression contrasts, yielding 59,713 significant differentially expressed gene records. The historical and BioProject-adjusted co-expression networks contain 358,077 and 134,840 positive edges, respectively, and 73,411 and 171,368 negative edges, respectively. In an icariin-biosynthesis case study, three representative loci were prioritized: Ebr01G061770 and Ebr01G061810 as candidate O-methyltransferases, and Ebr05G059870 as a candidate R2R3-MYB transcriptional regulator associated with prenyltransferase genes.\n\nDiscussion: Collectively, the domain, expression and co-expression evidence for these loci provides a testable hypothesis for 4′-O-methylation and for transcriptional regulation, respectively. EpuDB provides a traceable starting point for gene discovery and hypothesis generation in E. pubescens .",
  "abstract_shown": true,
  "affiliations": [
    "Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 5,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Jiaotong Yang"
    },
    {
      "affs": [
        0
      ],
      "name": "Siran Wang"
    },
    {
      "affs": [
        0
      ],
      "name": "Mingxian Zhou"
    },
    {
      "affs": [
        0
      ],
      "name": "Yaxin Shuai"
    },
    {
      "affs": [
        0
      ],
      "name": "Qingwen Sun"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/20pegezmyvh55.bib",
  "cited_by": 0,
  "doi": "10.3389/fpls.2026.1967816",
  "fulltext_url": null,
  "id": "20pegezmyvh55",
  "issns": [
    "1664-462X"
  ],
  "landing_url": "https://www.frontiersin.org/articles/10.3389/fpls.2026.1967816/full",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7223827744",
  "pdf_url": "https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2026.1967816/pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-27",
  "publisher": "Frontiers Media SA",
  "ris": "https://research.draconitic.com/paper/20pegezmyvh55.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:25Z",
      "native_id": "10.3389/fpls.2026.1967816",
      "source": "crossref",
      "url": "https://www.frontiersin.org/articles/10.3389/fpls.2026.1967816/full"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens",
  "title_text": "EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:25Z",
  "url": "https://research.draconitic.com/paper/20pegezmyvh55",
  "venue": "Frontiers in Plant Science",
  "versions": []
}