Collections for walnut family: scientists propose "evolution-guided" databases (WalDB) for walnut family (Juglandaceae)

BEIJING — As genomic technologies advance, the walnut family (Juglandaceae)—encompassing ecologically and economically vital woody plants like walnuts, pecans, and wingnuts—has emerged as a premier model for studying plant evolution. However, fragmented genomic resources and inconsistent analytical standards have long hindered researchers from piecing together the complete evolutionary puzzle of this critical lineage.

In a major advancement for phylogenomics published in Journal of Systematics and Evolution (JSE), researchers from the Beijing Normal University (BNU) walnut team present WalDB (Walnut Family Database), the most comprehensive clade-wide multi-omics platform specifically developed for Juglandaceae.

"The walnut family holds a treasure trove of evolutionary stories, from ancient hybridization events to diverse phenotypes—such as the red stigmas in walnuts we previously reported, and divergent heterodichogamy-determining sites across genera that have attracted widespread interest," says Prof. Bo-Wen Zhang, a researcher at BNU. "But to accurately trace these mechanisms across the entire family, we needed a reliable, unified genomic foundation. WalDB provides that critical infrastructure."

Beyond Cultivars: Comprehensive Coverage and Unified Standards

For years, researchers studying woody plant evolution have faced a significant bottleneck. While domestic and international teams have made exciting discoveries regarding the environmental adaptation and network-like evolution of the walnut family, the underlying genomic data has remained highly scattered. Furthermore, most existing databases focus heavily on collecting datasets for cultivated specimens and germplasm resources, often overlooking the immense biodiversity and conservation value of wild woody trees. This lack of comprehensive coverage has hindered our ability to explore the evolutionary history of the entire clade.

WalDB directly addresses this challenge by integrating an unprecedented volume of data: 79 nuclear genome assemblies spanning all nine genera, 170 chloroplast genomes, 22 mitochondrial assemblies, alongside population-level variant datasets (SNPs and SVs) and transcriptomes from 19 studies.

Crucially, to facilitate reliable cross-species phylogenomics, the BNU team applied a rigorous, unified ab initio annotation pipeline to 27 representative high-quality genomes. This standardization effectively minimizes historical analytical biases, providing researchers with a highly comparable baseline for studying whole-genome duplication events and functional divergences.

An Interactive Hub for Evolutionary Discovery

Beyond acting as a massive data repository, WalDB is engineered as a highly interactive virtual laboratory. The platform is equipped with robust modules and built-in bioinformatics tools designed to lower the barrier to complex genomic exploration.

Researchers and students alike can utilize the platform to:

Identify Orthologs: Trace the evolutionary lineage of specific genes of interest across the family.

Visualize Synteny: Intuitively map chromosome rearrangements and structural conservation between species.

Analyze Expression: Leverage transcriptomic data for rapid gene co-expression and functional enrichment analyses.

Calculate Evolutionary Rates: Easily assess genomic distances using built-in Ka/Ks calculation tools.

Moving from Data to Discovery

The integration of such vast, standardized multi-omics data with accessible analytical tools marks a pivotal step forward for plant biology.

"We designed this platform to be scalable and highly accessible," the research team notes. "Whether a researcher is investigating the genetic basis of a tree's resistance to drought, or exploring deep phylogenetic diversification, WalDB empowers them to quickly test hypotheses and uncover new insights."

The study concludes that clade-specific, standardized platforms like WalDB are essential for the future of evolutionary biology, ensuring that the study of woody plants transitions from navigating fragmented data to accelerating true evidence-based discovery.

(Note: The database can be accessed at https://cmb.bnu.edu.cn/WalDB/)

 

Original Source:

Liu ZZ et al. 2026. WalDB: An evolutionary multi‐omics database for the walnut family (Juglandaceae). Journal of Systematics and Evolution. https://doi.org/10.1111/jse.70095

Keywords: database, evolutionary genomics, multi‐omics, plant systematics

Author’s Institution:

The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Beijing Normal University (BNU), is one of the leading institutions specializing ecology and evolutionary research in China.

About JSE:

Journal of Systematics and Evolution (JSE) is a peer-reviewed, bi-monthly international English-language journal dedicated to the understanding of biodiversity and evolution. Papers in any of the following and related fields will be considered: systematics and biodiversity conservation, paleobiology and biogeography, adaptation, speciation and domestication, evolutionary genomics and Evo-Devo, theory and methods in evolutionary biology.

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