Jul 2026· Journal of Systematics and Evolution· 0 citations· 37 references
TL;DR
To improve cross‐species comparability, standardized annotations for 27 high‐quality genomes are generated with a unified pipeline, thereby minimizing annotation biases that often hinder comparative analyses across data sets produced by different studies.
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.
Derris trifoliata
Lour. is a common mangrove‐associated legume important for coastal ecosystem stability and serves as a natural source of rotenoids. However, the lack of high‐quality reference genomes has hindered the investigation of its evolutionary history and key functional traits. Here, we present a high‐quality, chromosome‐level genome assembly for
D. trifoliata
, representing the first reported genome resource for rotenoid‐producing legumes. The assembled genome spans 811 Mb across 11 chromosomes, with a BUSCO completeness of 98.3% and all telomeres and centromeres identified. Evolutionary analysis revealed two rounds of whole‐genome duplication event shared with Papilionoideae. The more recent event, along with lineage‐specific tandem and proximal duplications, drove the expansion of genes involved in stress responses and secondary metabolism, facilitating adaptation to extreme intertidal environments. Metabolomic profiling identified four major rotenoids predominantly accumulated in roots, which likely provide effective chemical defense against the belowground stress in mangrove habitats. By integrating transcriptomic and metabolomic data, we reconstructed the rotenone biosynthesis pathway and identified candidate enzymes and transcription factors. Notably, the potential tandem expansion and functional evolution of the key biosynthesis genes
2ODD
s offer clues to the evolution of specialized biosynthesis pathways. This high‐quality genome, combined with multi‐omics analyses, provides insight into the environmental adaptation and specialized metabolism of
D. trifoliata
, establishing a valuable foundation for broader evolutionary research and future biotechnological applications of rotenoid‐producing legumes.
Yutian Lei, Hui Feng, Minghui Yin et al.· Journal of Systematics and E...· 0 citations
Wild perennial plants can be domesticated to make agriculture more diverse and resilient, but many have large genomes that have been recalcitrant to analysis. Here, we report phased genome assemblies for Silphium integrifolium Michx. and S. perfoliatum L., two species native to North America under domestication, and demonstrate the utility of trio-binning for genome assembly using an interspecific hybrid. These genomes have chromosomes reaching 1.8 Gb and a helical structure preserved during interphase with a loop circumference of 43 Mb. A genome-informed low coverage and target sequencing strategy enables the refinement of the genus phylogeny, reveals the spatial distribution and structure of natural populations, and identifies 81 loci associated with environmental and domestication traits. Variants in a MATE transporter, α/β hydrolase, and ortholog of Arabidopsis ACT Domain Repeat (ACR4) protein explain significant variance in floral architecture. These advances in genome assembly and genotyping could expand the range of candidates for de novo crop domestication. Silphium species native to North American prairies show strong drought tolerance. This study presents a haplotype-phased genome of a hybrid between S. integrifolium (oilseed crop) and S. perfoliatum (biomass/fiber crop), identifying loci linked to environmental adaptation and domestication.
Renan Souza, J. Clevenger, Jerry W. Jenkins et al.· Nature Communications· 0 citations
Abstract Callery pear (Pyrus calleryana) is a deciduous species native to East Asia with notable ornamental and ecological value, but the genomic resources for this species remain limited. Here, we report the first haplotype‐resolved, chromosome‐scale genome of P. calleryana. The final genome assembly comprises two phased haplotypes measuring 506.97 and 504.62 Mb. These haplotypes contain 41,234 and 41,329 predicted protein‐coding genes, respectively, with more than 97% of the genes receiving functional annotations. Comparative genomic analyses further identified 680 species‐specific orthogroups enriched in hormone signaling, metabolic processes, and stress‐responsive pathways, among which several LIK1‐like genes may contribute to environmental adaptation. This high‐quality genome assembly offers an essential foundation for subsequent studies on the ecological adaptability, invasiveness, and functional genomics of P. calleryana.
Xiaogang Dai, Xiaoyue Yang, Changci Jiang et al.· The Plant Genome· 0 citations
This high-quality, chromosome-level reference genome provides a foundational resource for understanding the population genetic structure, adaptive evolution and speciation mechanisms of C. appendiculata, thereby offering valuable insights into its evolutionary history and conservation.
Yongchao Tang, B. Xiao, Ruimin Yu et al.· Scientific Data· 0 citations
An integrated analysis of the F. mandshurica mitochondrial genome is presented, revealing its unique structural and evolutionary characteristics and enrich the mitochondrial genome resources for Oleaceae species and highlight the potential of mitochondrial genes to elucidate plant evolutionary history.
Dongmei Wang, Xinrui Wang, Hong-Da Song et al.· BMC Plant Biology· 0 citations
Texas wintergrass is a cool-season perennial bunchgrass native to North America with ecological and agronomic importance as a winter forage species, yet genomic resources for this species remain limited. Here, we present the first de novo genome assembly of N. leucotricha generated using PacBio HiFi sequencing. Assembly with hifiasm produced a 959.92 Mb genome with 8X coverage, comprising 2,394 contigs with an N50 of 530.6 kb. Assembly completeness was high, with 99.6% of Benchmarking Universal Single-Copy Orthologs (BUSCOs) identified, although a substantial proportion were duplicated. Genome size estimates based on flow cytometry and k-mer analysis, together with assembly metrics, indicate a repeat-rich and structurally complex genome. Repeat annotation revealed that 64.42% of the genome consists of repetitive elements, predominantly long terminal repeat (LTR) retrotransposons, including Ty1/Copia, and Gypsy/DIRS1. Gene prediction using the homology-based pipeline GeMoMa identified 54,132 high-confidence genes, of which 53,868 were functionally annotated and 26,346 were assigned to KEGG pathways. Mining for genome-wide simple sequence repeats (SSRs) identified over 38,000 markers, with a validated subset demonstrating use for genetic diversity analysis. Reference-guided alignment and scaffolding using Brachypodium distachyon and Oryza sativa provided comparative frameworks for evaluating conserved sequence relationships between Texas wintergrass and representative grass genomes. Our results establish a genomic resource for Texas wintergrass, supporting future studies in comparative genomics and molecular breeding.
Christian J Stephens, N. J. Turner, P. Mangat et al.· G3· 0 citations