WalDB: An evolutionary multi‐omics database for the walnut family (Juglandaceae)

Abstract Juglandaceae (the walnut family) comprises nine genera with deep evolutionary history and substantial ecological and economic importance; yet, available genomic resources remain fragmented, taxonomically incomplete, and inconsistently annotated. Here, we present Walnut Family DB (WalDB; https://cmb.bnu.edu.cn/WalDB/ ), a clade‐wide multi‐omics database specifically developed for evolutionary and comparative genomic research in Juglandaceae. WalDB integrates 79 nuclear genome assemblies, 170 chloroplast genomes, 22 mitochondrial assemblies, population‐level variant data sets (SNP and SV VCF files from 10 projects), and transcriptomic resources from six projects and 19 studies. Organized into six interactive modules, the platform enables family‐wide exploration of genome structure, gene evolution, and functional divergence. Importantly, to improve cross‐species comparability, we generated standardized ab initio annotations for 27 high‐quality genomes with a unified pipeline, thereby minimizing annotation biases that often hinder comparative analyses across data sets produced by different studies. Integrated tools further support ortholog identification, synteny visualization, co‐expression and enrichment analyses, and Ka/Ks‐based genomic distances' calculation. By combining broad taxonomic coverage with standardized annotation and evolutionary analysis tools, WalDB provides a comprehensive and scalable resource for investigating genome evolution, adaptation, and phylogenetic diversification in Juglandaceae.