PeuDB: a comprehensive genomic and transcriptomic platform for gene function analysis in Peucedanum praeruptorum

Peucedanum praeruptorum Dunn (Qianhu) is a traditional Chinese medicinal herb widely used for treating respiratory and inflammatory ailments. Its roots are rich in pharmacologically active compounds, particularly coumarins and flavonoids, yet the genetic basis underlying the biosynthesis of these metabolites remains insufficiently characterized. The availability of high-quality genome assemblies and extensive transcriptomic data now enables systematic gene-function analysis in this species. Here, we present PeuDB, a comprehensive genomic and transcriptomic platform that integrates two independently annotated reference assemblies—the PP_2024v2 telomere-to-telomere assembly and the PP_2024v1 chromosome-level assembly—and expression profiles for 135 independent biological samples across nine BioProjects. Predicted genes were functionally annotated against NR, Swiss-Prot, TAIR10, TrEMBL, GO, KEGG, and Pfam. Six major gene-family categories were classified, comprising 5,981 transcription factors and transcriptional regulators, 2,916 protein kinases, 1,940 carbohydrate-active enzymes, 1,879 transporters, 3,112 ubiquitin-related proteins, and 594 cytochrome P450 genes. Following tissue-stratified batch correction, direct Pearson-correlation and mutual-rank filtering identified 427,999 positive co-expression relationships (255,633 for PP_2024v2 and 172,366 for PP_2024v1). In addition, strict reciprocal-best-hit projection of evidence-filtered Arabidopsis interaction data yielded 5,864 confidence-filtered interolog predictions (3,027 and 2,837, respectively). PeuDB also links 24,846 accepted cross-assembly gene pairs for identifier conversion. Built on a LAMP (Linux, Apache, Mysql, PHP) architecture, the platform provides a user-friendly interface for search, visualization, and analysis, including BLAST, JBrowse2, expression heatmaps, co-expression and predicted protein-interaction networks, enrichment and differential-expression analysis, primer design, ID conversion, and multiple-sequence alignment. Reproducible F6′H and WRKY case-study workflows demonstrate how these resources can support candidate prioritization while distinguishing computational hypotheses from experimental validation. PeuDB is freely accessible at https://www.gzybioinformatics.cn/PeuDB and provides a resource for investigating gene function and medicinal-compound biosynthesis in P. praeruptorum . PeuDB also provides a versioned, read-only REST API with OpenAPI/Swagger documentation. The API enables programmatic retrieval of assembly information, gene annotations and sequences, raw TPM profiles, cross-assembly mappings, co-expression relationships, and predicted protein interactions.