Mung bean (Vigna radiata) is a globally important legume crop valued for its short growing cycle, nitrogen-fixing capacity and high nutritional value, particularly in developing countries. Here we report a comprehensive graph-based pan-genome assembled from 11 genetically diverse global accessions. The framework captures 75,268 gene families (50.86% core, 35.19% dispensable and 13.95% private) and 66,862 nonredundant structural variants. Integrating these structural variants and single nucleotide polymorphisms, genome-wide association studies across five environments identified candidate genes for 20 agronomic traits, underscoring the pivotal roles of these variants in driving mung bean domestication and improvement. Mechanistically, we demonstrate that a 68-bp promoter insertion in VrTIFY6B and a 136-bp promoter deletion in VrPGIP1 regulate flavonoid content and confer bruchid resistance, respectively. These genomic resources and actionable functional variants provide a powerful toolkit to accelerate mung bean improvement through marker-assisted breeding, genomic selection and genome editing to address global food security.

Hosts must distinguish mutualistic symbionts from antagonists while avoiding harmful immune overactivation, yet the mechanisms maintaining this balance remain unclear. This challenge is acute during biological invasions, where exposure to novel microbial communities can outpace host genetic adaptation. Dendroctonus valens (RTB) associates with its mutualistic fungus Leptographium procerum (Lp), forming an invasive beetle-fungus complex during attacks on Chinese pines. Lp fails to trigger antimicrobial peptide expression but induces the heat shock protein 83 (HSP83). The native antagonist Ophiostoma minus (Om) activates immunity through pattern recognition receptors, including PGRP-SA, PGRP-SC2, βGRP3, and βGRP5. HSP83 modulates these responses through two-tiered negative regulation. First, it associates with PGRP-SA, βGRP3, and βGRP5 to attenuate Om detection. Second, it interacts with NF-κB-like factor Dorsal to limit antimicrobial peptide production. This symbiont-induced regulation enables selective defense, supporting RTB survival during combined Lp and Om exposure while limiting excessive Toll-dependent PRR/AMP activation and easing immune-metabolic trade-offs. These findings define a symbiont-assisted, mutation-independent mechanism of host adjustment during biological invasions, in which microbial partners provide immediate immune benefits and influence host success in novel environments.

Pine wilt disease (PWD), caused by pine wood nematode (PWN, Bursaphelenchus xylophilus), severely threatens global pine forests. The Catharanthus roseus receptor-like kinase 1 L (CrRLK1L) family plays a critical role in plant defense against pathogen invasion. While recent studies have begun to elucidate the molecular mechanism of interaction between host trees and PWN, the function of CrRLK1L family members in gymnosperms remain poorly understood. Here, we analyzed the transcriptomic response of Pinus tabulaeformis to PWN infection and identified 58 CrRLK1L genes. Among them, PtTHESEUS1 (PtTHE1), a homolog of Arabidopsis THESEUS1, exhibited sustained transcriptional induction during PWN infection, as validated by RT-qPCR. Functional analyses showed that Arabidopsis theseus1 mutant was more susceptible to PWN, suggesting the involvement of PtTHE1 in host defense. The extracellular domain of PtTHE1 interact with BxEF1, a PWN secreted protein. BxEF1 was strongly expressed during early infection stage and predominantly localized in the dorsal gland of the PWN. Silencing of BxEF1 significantly impaired PWN feeding speed and reduced pathogenicity. In summary, BxEF1, a parasitism-promoting protein secreted by PWN, is perceived by PtTHE1, ultimately triggering host immunity. Our findings reveal a novel molecular mechanism of pine resistance to PWN and provide functional insights into CrRLK1L-mediated immunity in gymnosperms.

Transposable elements contribute to species diversification and adaptive evolution. However, it remains challenging to reconcile the impacts of TEs on microevolution (within species) and macroevolution (among species) given their huge pool and complex dynamics in genomes. Here, we generated the genome for the notorious worldwide migratory locust, Locusta migratoria, sampled from Qinghai-Tibet Plateau. Comparative genome analyses uncovered extensive TE-driven genome size variation, and lineage-specific expansion of TEs, particularly of the PiggyBac superfamily in the locust. Whole-genome resequencing of 153 locust individuals collected across an altitudinal gradient ranging from 2 to 4100 m clarified their distinct elevational genetic divergence, which is consistent across SNP and TE insertion polymorphisms analysis. A total of 11 869 TE insertions were found within selective sweeps, including at least 279 genes associated with altitude adaptation. TEs from five superfamilies, accounting for 55.68% of the candidate adaptive TEs, exhibited significant expansion in both microevolution and macroevolution. We validated that PiggyBac insertion into the PIEZO gene induced alternative splicing and enhanced flight performance under hypoxia through AMPK pathway. These data provide robust evidence that TEs are central drivers of genomic evolution across micro- and macroevolutionary scales, shaping genomic landscape and promoting adaptive change.

Avena fatua (weedy oat) is a globally pervasive weed, notorious for its adaptability to extreme environments and herbicide tolerance. Here, we present the 10.98-Gb hexaploid genome of A. fatua and a variation map from 768 wild and cultivated oats (A. fatua, A. sterilis and A. sativa), elucidating their genetic relationship and evolutionary history. Population genomic analyses reveal genetic connections between A. fatua and cultivated naked oats, and identify divergent regions between A. fatua and A. sativa enriched in genes associated with biotic and abiotic stresses. Among them, a herbicide-resistance locus is identified on chromosome 4D, with A. fatua accessions carrying a highly differentiated haplotype from cultivated oats. Multi-omics profiling and functional validation demonstrate that one expanded GST gene in this locus contributes significantly to oat herbicide resistance. Our study provides genomic resources for understanding A. fatua's broad adaptability to diverse environmental conditions, facilitating the development of climate-resilient oat varieties.

Woolly apple aphid (WAA), Eriosoma lanigerum (Hausmann), is a worldwide invasive pest that seriously damages apple trees in almost all apple-growing areas. Waxy secretion is characterised as an important weapon in increasing invasion and adaptation to a broad range of biological and abiotic factors. We used PacBio reads to produce a 357 Mb highquality chromosome-level assembly for the WAA genome. The N50 lengths of contigs and chromosomes were 4.0 Mb and 65.1 Mb, respectively. In total, 95 Mb (12.5%) repeat sequences and 15,906 gene models were identified in the genome. We identified 101 expanded and 33 exclusive orthologous groups in E. lanigerum, mainly functioning in cell growth and death, signal transduction, and carbohydrate and amino acid metabolism, which contribute to adaptation and metabolite synthesis. To uncover the molecular basis of wax synthase processes, related enzymes and transporters were identified through transcriptomes of five developmental stages and among three segments. Although wax synthase-related genes were not found in WAA genome and other related species, four genes were identified involved in fatty acid biosynthesis and metabolism, thereby producing and transporting the waxy secretion of WAA. These results indicated that different pathways might be employed by WAA in wax ester biosynthesis compared with other eukaryotic organisms. These findings collectively provide novel insight into the molecular mechanisms of the wax synthase processes of WAA.

Plants have coevolved with herbivorous insects for millions of years, resulting in variation in resistance both within and between species. Using a manipulative experiment combined with untargeted metabolomics, microbiome sequencing and transcriptomics approaches, we investigated the roles of plant metabolites and the microbiome in defence mechanisms in native resistant Manchurian ash (Fraxinus mandshurica) trees and non-native susceptible velvet ash (Fraxinus velutina) trees against the highly invasive emerald ash borer (EAB, Agrilus planipennis). Comparative transcriptomics and metabolomics analyses show that the phenylpropanoid pathway, which is enriched in differentially expressed genes and differentially abundant metabolites, may serve as a potential regulator of resistance. Additionally, the microbiome is distinctly shifted in two ash species. Indicator taxa analysis reveals that the distinct genera are dominant in the galleries of two ash species, for example, Pseudomonas in velvet, and Hafnia-Obesumbacterium in Manchurian. The strong correlation between indicator taxa and metabolites suggests that the chemical compounds might impact the microbial community in phloem directly or indirectly, or vice versa. This study significantly enhances our understanding of the variation in resistance between ash species and its contribution to the invasion success of EAB, providing valuable insights for the development of pest management strategies.

Polygonaceae, with ecological versatility and global distribution, is an ideal system for investigating plant adaptation. However, the genomic mechanisms underlying its karyotype evolution and environmental resilience remain unclear. We herein present chromosome-level genomes of 11 species from 10 Polygonaceae genera. Our analyses reveal that Gypsy retrotransposons are key drivers of genome size variations in Polygonaceae. We reconstructed a Polygonaceae ancestral karyotype comprising 28 proto-chromosomes and elucidated evolutionary trajectories via extensive chromosomal rearrangements. Furthermore, we constructed a cross-genus super pan-genome for Polygonaceae, identifying 80,055 gene families, of which 9,845 (12.30%) are core gene families. Private genes are found to contribute significantly to interspecific differences in adaptability. Notably, gene copy number variations are identified as a critical factor influencing adaptations to diverse niches involving species-specific increases in metabolic pathways. This study provides a genomic framework for Polygonaceae karyotype plasticity and adaptive innovation, offering insights into plant evolution under environmental challenges.

Common oat, belonging to the genus Avena with 30 recognized species, is a nutritionally important cereal crop and high-quality forage worldwide. Here, we construct a genus-level super-pangenome of Avena comprising 35 high-quality genomes from 14 cultivated oat accessions and 21 wild species. The fully resolved phylogenomic analysis unveils the origin and evolutionary scenario of Avena species, and the super-pangenome analysis identifies 26.62% and 59.93% specific genes and haplotypes in wild species. We delineate the landscape of structural variations (SVs) and the transcriptome profile based 1,401 RNA-sequencing (RNA-seq) samples from diverse abiotic stress treatments in oat. We highlight the crucial role of SVs in modulating gene expression and shaping adaptation to diverse stresses. Further combining SV-based genome-wide association studies (GWASs), we characterize 13 candidate genes associated with drought resistance such as AsARF7, validated by transgenic oat lines. Our study provides unprecedented genomic resources to facilitate genomic, evolution and molecular breeding research in oat.

Common oat, one of the most important crops worldwide, comprises hulled and hulless types with substantial agronomic differences. However, their evolutionary history and the genomic basis of phenotypic variations remain unclear. Herein, we report a 10.83 Gb high-quality genome (contig N50 of 104.56 Mb) for hulless oat Pinyan6 and construct the structural variation (SV) landscape between hulled and hulless oats. Population genetic analysis of 431 global oat accessions (21 wild, 246 hulled, and 164 hulless) reveals their evolutionary history and genetic divergence. Integrating the SV data, we demonstrate the potential impact of SVs on population divergence and phenotypic variation between hulled and hulless oats. An SV-based genome-wide association study further identifies a highly differentiated locus and the AsMC1 gene, a candidate linked to differences in lemma lignin content between hulled and hulless oats. Our Pinyan6 genome and rich genetic variations provide important resources for functional genomics and molecular breeding of oat.

Reynoutria multiflora is a widely used medicinal plant in China. Its medicinal compounds are mainly stilbenes and anthraquinones which possess important pharmacological activities in anti-aging, anti-inflammatory and anti-oxidation, but their biosynthetic pathways are still largely unresolved. Here, we reported a near-complete genome assembly of R. multiflora consisting of 1.39 Gb with a contig N50 of 122.91 Mb and only one gap left. Genome evolution analysis revealed that two recent bursts of long terminal repeats (LTRs) contributed significantly to the increased genome size of R. multiflora, and numerous large chromosome rearrangements were observed between R. multiflora and Fagopyrum tataricum genomes. Comparative genomics analysis revealed that a recent whole-genome duplication specific to Polygonaceae led to a significant expansion of gene families associated with disease tolerance and the biosynthesis of stilbenes and anthraquinones in R. multiflora. Combining transcriptomic and metabolomic analyses, we elucidated the molecular mechanisms underlying the dynamic changes in content of medicinal ingredients in R. multiflora roots across different growth years. Additionally, we identified several putative key genes responsible for anthraquinone and stilbene biosynthesis. We identified a stilbene synthase gene PM0G05131 highly expressed in roost, which may exhibit an important role in the accumulation of stilbenes in R. multiflora. These genomic data will expedite the discovery of anthraquinone and stilbenes biosynthesis pathways in medicinal plants.

The Japanese sawyer beetle, Monochamus alternatus, is not only one of the most important wood boring pest itself, but also a major vector of the invasive pinewood nematode (PWN), which is the causal agent of the devastative pine wilt disease (PWD) and threats the global pine forest. Here, we present a near-complete genome of M. alternatus at the chromosome level. The assembled genome was 792.05 Mb with contig N50 length of 55.99 Mb, which is the largest N50 size among the sequenced Coleoptera insects currently. 99.57% of sequence was anchored onto ten pseudochromosomes (one X-chromosome and nine autosomes), and the final genome harbored only 13 gaps. BUSCO evaluation revealed the presence of 99.0% of complete core genes. Thus, our genome assembly represented the highest-contiguity genome assembly as well as high completeness in insects so far. We identified 20,471 protein-coding genes, of which 20,070 (98.04%) were functionally annotated. The genome assembly of M. alternatus provides a valuable resource for exploring the evolution of the symbiosis between PWN and the vector insects.

Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.

Okra (Abelmoschus esculentus) is an important vegetable crop with high nutritional value. However, the mechanism underlying its high nutrient content remains poorly understood. Here, we present a chromosome-scale genome of okra with a size of 1.19 Gb. Comparative genomics analysis revealed the phylogenetic status of A. esculentus, as well as whole-genome duplication (WGD) events that have occurred widely across the Malvaceae species. We found that okra has experienced three additional WGDs compared with the diploid cotton Gossypium raimondii, resulting in a large chromosome number (2n = 130). After three WGDs, okra has undergone extensive genomic deletions and retained substantial numbers of genes related to secondary metabolite biosynthesis and environmental adaptation, resulting in significant differences between okra and G. raimondii in the gene families related to cellulose synthesis. Combining transcriptomic and metabolomic analysis, we revealed the relationship between gene expression and metabolite content change across different okra developmental stages. Furthermore, the sinapic acid/S-lignin biosynthesis-related gene families have experienced remarkable expansion in okra, and the expression of key enzymes involved in the sinapic acid/S-lignin biosynthesis pathway vary greatly across developmental periods, which partially explains the differences in metabolite content across the different stages. Our study gains insights into the comprehensive evolutionary history of Malvaceae species and the genetic basis that underlies the nutrient content changes in okra, which will facilitate the functional study and genetic improvement of okra varieties.

Peptidoglycan recognition proteins (PGRPs) are a class of molecules that play a critical role in insect immunity. Understanding the function of PGRPs is important to improve the efficiency of microbial insecticides. In this study, we investigated the role of PGRP‐LB (a long type PGRP) in insect immunity against viruses using Spodoptera exigua and Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV) as an insect–virus model. We cloned and identified a PGRP‐LB gene from S. exigua ; the gene consisted of 7 exons that encoded a polypeptide of 234 amino acids with a signal peptide and a typical amidase domain. Expression analysis revealed that the abundance of SePGRP‐LB transcripts in the fat body was greater than in other tissues. Overexpression of SePGRP‐LB resulted in a significant decrease of 49% in the rate of SeMNPV‐infected cells. In addition, the multiplication of SeMNPV was significantly decreased: a decrease of 79% in the production of occlusion‐derived virion (ODV), and a maximum decrease of 50% in the production of budded virion (BV). In contrast, silencing of SePGRP‐LB expression by RNA interference resulted in a significant 1.65‐fold increase in the rate of SeMNPV‐infected cells, a significant 0.54‐fold increase in ODV production, a maximum 1.57‐fold increase in BV production, and the larval survival dropped to 21%. Our findings show that SePGRP‐LB has an antiviral function against SeMNPV, and therefore this gene may provide a target for lepidopteran pest control using virus insecticides.

Serine protease inhibitors (serpins) appear to be ubiquitous in almost all living organisms, with a conserved structure and varying functions. Serpins can modulate immune responses by negatively regulating serine protease activities strictly and precisely. The codling moth, Cydia pomonella (L.), a major invasive pest in China, can cause serious economic losses. However, knowledge of serpin genes in this insect remain largely unknown. In this study, we performed a systematic analysis of the serpin genes in C. pomonella, obtaining 26 serpins from the C. pomonella genome. Subsequently, their sequence features, evolutionary relationship, and expression pattern were characterized. Comparative analysis revealed the evolution of a number of serpin genes in Lepidoptera. Importantly, the evolutionary relationship and putative roles of serpin genes in C. pomonella were revealed. Additionally, selective pressure analysis found amino acid sites with strong evidence of positive selection. Interestingly, the serpin1 gene possessed at least six splicing isoforms with distinct reactive-center loops, and these isoforms were experimentally validated. Furthermore, we observed a subclade expansion of serpins, and these genes showed high expression in multiple tissues, suggesting their important roles in C. pomonella. Overall, this study will enrich our knowledge of the immunity of C. pomonella and help to elucidate the role of serpins in the immune response.

Rheum officinale, a member of the Polygonaceae family, is an important medicinal plant that is widely used in traditional Chinese medicine. Here, we report a 7.68-Gb chromosome-scale assembly of R. officinale with a contig N50 of 3.47 Mb, which was clustered into 44 chromosomes across four homologous groups. Comparative genomics analysis revealed that transposable elements have made a significant contribution to its genome evolution, gene copy number variation, and gene regulation and expression, particularly of genes involved in metabolite biosynthesis, stress resistance, and root development. We placed the recent autotetraploidization of R. officinale at ∼0.58 mya and analyzed the genomic features of its homologous chromosomes. Although no dominant monoploid genomes were observed at the overall expression level, numerous allele-differentially-expressed genes were identified, mainly with different transposable element insertions in their regulatory regions, suggesting that they functionally diverged after polyploidization. Combining genomics, transcriptomics, and metabolomics, we explored the contributions of gene family amplification and tetraploidization to the abundant anthraquinone production of R. officinale, as well as gene expression patterns and differences in anthraquinone content among tissues. Our report offers unprecedented genomic resources for fundamental research on the autopolyploid herb R. officinale and guidance for polyploid breeding of herbs.

Common buckwheat (Fagopyrum esculentum) and Tartary buckwheat (Fagopyrum tataricum), the two most widely cultivated buckwheat species, differ greatly in flavonoid content and reproductive mode. Here, we report the first high-quality and chromosome-level genome assembly of common buckwheat with 1.2 Gb. Comparative genomic analysis revealed that common buckwheat underwent a burst of long terminal repeat retrotransposons insertion accompanied by numerous large chromosome rearrangements after divergence from Tartary buckwheat. Moreover, multiple gene families involved in stress tolerance and flavonoid biosynthesis such as multidrug and toxic compound extrusion (MATE) and chalcone synthase (CHS) underwent significant expansion in buckwheat, especially in common buckwheat. Integrated multi-omics analysis identified high expression of catechin biosynthesis-related genes in flower and seed in common buckwheat and high expression of rutin biosynthesis-related genes in seed in Tartary buckwheat as being important for the differences in flavonoid type and content between these buckwheat species. We also identified a candidate key rutin-degrading enzyme gene (Ft8.2377) that was highly expressed in Tartary buckwheat seed. In addition, we identified a haplotype-resolved candidate locus containing many genes reportedly associated with the development of flower and pollen, which was potentially related to self-incompatibility in common buckwheat. Our study provides important resources facilitating future functional genomics-related research of flavonoid biosynthesis and self-incompatibility in buckwheat.

Background: The beet armyworm Spodoptera exigua is a polyphagous caterpillar that causes serious damage to many species of crops and vegetables. To gain insight into how this polyphagous insect differs from less harmful oligophagous species, we generated a chromosome-level assembly and compared it to closely related species with the same or different feeding habits.Results: Based on Illumina and Pacific Biosciences data and Hi-C technology, 425.6 Mb of genome sequences were anchored and oriented into 31 linkage groups, with an N50 length of 14.8 Mb. A total of 24,649 gene models were predicted, of which 97.4% were identified in the genome assembly. Chemosensory genes are vital for locating food: of the four main families, odorant-binding proteins, chemosensory proteins and olfactory receptors showed little difference, whereas gustatory receptors are greatly expanded in S. exigua. Examination of other polyphagous insects confirmed this difference from oligophagous congeners and further identified the bitter receptor subfamily as being particularly affected.Conclusion: Our high-quality genome sequence for beet armyworm identified a key expansion of the bitter gustatory receptor subfamily in this and other pests that differs crucially from more benign relatives and offers insight into the biology and possible future means of control for these economically important insects.

Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies.