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.

Phoebe zhennan, an endemic species of Lauraceae in China, is an ecologically and economically important timber tree that has undergone severe population decline and is considered endangered. Despite its importance and threatened status, the absence of haplotype‐resolved genomic resources has hindered detailed genetic and evolutionary studies. Here, we report the first haplotype‐resolved chromosome‐level genome of P. zhennan using ONT ultra‐long reads and Hi‐C technology. The assemblies for Haplotype A (HapA, 956.20 Mb) and Haplotype B (HapB, 910.89 Mb) were each anchored to 12 chromosomes, with scaffold N50 values of 86.27 Mb and 77.12 Mb, respectively. A total of 33 757 and 33 651 protein‐coding genes were identified for HapA and HapB, respectively, of which 95% were functionally annotated. Comparative analyses revealed extensive structural heterozygosity, including 112 inversions, 2371 translocations, 6 059 780 single‐nucleotide polymorphisms (SNPs), 345 228 insertions, and 348 584 deletions. This haplotype‐resolved assembly further elucidates the characteristics of chromosomal structural variation and provides an important genetic resource for future studies on the evolution, conservation, and functional biology of P. zhennan.

Magnoliaceae, a typical boreotropical relict lineage, shows striking species richness in tropical regions, making it an important model for testing the time-for-speciation and diversification rate hypotheses for present-day diversity patterns. Here, we reconstructed a time-calibrated phylogeny using plastomes from 123 species, representing Liriodendron and all 15 sections of Magnolia, and investigated its colonization and diversification history. Our results reveal that Magnoliaceae likely experienced peak extinction during the mid-Eocene, accompanied by a range contraction from high latitudes to the amphi-Pacific tropics, followed by the rise of tropical clades with rapid diversification. Phylogenetic generalized least squares analysis demonstrates that diversification rate explains clade-level diversity variation more strongly than time for speciation. Tropical regions, such as South America and Southeast Asia, with high Magnoliaceae diversity consistently show elevated diversification rates and shorter time for speciation. These results indicate that higher diversification rate, rather than longer time for speciation, explains the high diversity of Magnoliaceae in tropical clades and regions. Our findings not only shed light on the evolutionary history of Magnoliaceae but also provide important insights into the broader processes that shape tropical biodiversity.

Since the concept of the tree of life was introduced about 150 years ago, a considerable fraction of the scientific community has focused its efforts on its reconstruction, with remarkable progress during the last two decades with the advent of DNA sequences. However, the assemblage of a comprehensive and explorable tree of life has been a difficult task to achieve due to two main obstacles: i) information is scattered into several individual sources and ii) practical visualization tools for exploring large trees are needed. To overcome both challenges, we aimed to synthesize a family-level tree of life by compiling over 1400 published phylogenetic studies, choosing the source trees that represent the best phylogenetic hypotheses to date based on a set of objective criteria. Moreover, we dated the tree by employing over 550 secondary calibrations using publicly available sequences for more than 5000 taxa, and by incorporating age ranges from the fossil record for over 2800 taxa. Additionally, we developed a mobile app for smartphones to facilitate the visualization and exploration of the resulting tree. Interactive features include exploration by the zooming and panning gestures of touch screens, collapsing branches, visualizing specific clades as subtrees, a search engine, and a timescale to determine extinction and divergence dates, among others. Small illustrations of organisms are displayed at the terminals to better visualize the morphological diversity of life. Our assembled tree currently includes over 7000 families, and its content will be expanded through regular updates to cover all life on earth at family level.