EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens
- 1Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine
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.
Methods: 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.
Results: 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.
Discussion: 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 .
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BibTeX
@article{yang2026epudb,
title = {{EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens}},
author = {Jiaotong Yang and Siran Wang and Mingxian Zhou and Yaxin Shuai and Qingwen Sun},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1967816},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1967816/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens
AU - Jiaotong Yang
AU - Siran Wang
AU - Mingxian Zhou
AU - Yaxin Shuai
AU - Qingwen Sun
PY - 2026
DA - 2026/10/27
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1967816
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1967816/full
AB - 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. Methods: 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. Results: 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. Discussion: 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 .
SN - 1664-462X
ER -