EpuDB: an integrated functional genomics database and REST API for Epimedium pubescens

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.

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.

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.

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.