Land plants underpin civilization and planetary health, yet their genomic diversity remains largely uncharted. Current resources are unstandardized and scarce, lacking reference genomes for 95% of genera, 70% of families, and 51% of orders, impeding evolutionary and functional insight. We thus propose the PLANeT initiative, an international effort to generate high-quality, standardized genomes across the plant tree of life. Integrating artificial intelligence (AI) with genomics, we will decode conserved principles to advance fundamental plant biology, biodiversity conservation, crop improvement, and natural product discovery. Engaging around 100 labs to train 1,000 scientists, we will tackle pivotal questions for a sustainable future.

Peanut (Arachis hypogaea L.) is a globally significant leguminous oil crop. Here we present telomere-to-telomere genome assemblies for two diploid and four tetraploid peanut varieties, resulting in high-quality reference genomes, showing that the complex activities of transposable elements, chromosomal rearrangements and centromere expansions within subgenomes collectively contribute to the asymmetrical evolution of the tetraploid genome, and unique structural variants in the four tetraploid peanut varieties provide clear evidence of domestication. Population analyses of 521 peanut accessions revealed asymmetric selection events between subgenomes during breeding, and genome-wide association studies identified candidate genes linked to oil content, seed size and weight, kernel dehydration rate, and arachidic acid content. In addition, transcriptomic and metabolomic analyses revealed enhanced activity in lipidomic and anthocyanin biosynthetic pathways during seed development. These comprehensive findings provide insights into genome organization, evolutionary dynamics and phenotypic differentiation across peanut varieties that could inform future peanut breeding and improvement strategies.

Climate change demands accelerated plant adaptation and de novo domestication. Yet current enviromics focuses disproportionately on external environments, neglecting internal dynamics-gene expression, metabolic flux, and signal transduction-within predictive envirotyping frameworks. This gap constrains plant-environment adaptation research and crop improvement. Integrating multi-scale envirotyping with plant-environment interaction networks could catalyze a paradigm shift from empirical selection to mechanism-informed design breeding. Four challenges remain: (1) constructing adaptive multi-dimensional networks, (2) engineering transgenerational epigenetic reprogramming, (3) scaling domestication pipelines, and (4) predicting adaptive trajectories. Future efforts should converge on five domains: high-throughput microprobe envirotyping arrays, spatiotemporally resolved multi-omics, decoding epigenetic memory carriers, artificial intelligence (AI)-guided genome design, and phenotype prediction models. Ultimately, advancing from multi-omics dissection and mechanistic interpretation to targeted de novo design will enable the precise engineering of crop adaptive responses to environmental change.

Butternut squash (Cucurbita moschata) is an economically important crop; however, its genetic improvement has been hindered by the lack of high-resolution genomic resources and limited germplasm availability. In this study, we present a gap-free, telomere-to-telomere (T2T) genome assembly of C. moschata PKUMo, generated using high-accuracy Oxford Nanopore reads. The final assembly spans 314.34 Mb and is organized into 20 pseudomolecules, each represented by a single contig. Our analysis revealed that 40.58% of the genome consists of transposable elements, which have undergone significant expansion over the past 0.27 million years. Comparative genomic analysis with Cucurbita maxima (HZAU) identified substantial structural differences, including 27.20 Mb of inversions and 9.50 Mb of translocations, mainly affecting pericentromeric regions. We further investigated the evolution of centromeric regions in C. moschata and revealed distinct centromeric structures between PKUMo and HZAU. Notably, PKUMo centromeres exhibit increased transposon activity, particularly involving LTR retrotransposons. To facilitate functional genomics, we optimized an EMS-based pollen mutagenesis protocol, generating a mutant library comprising 60,000 M1 seeds and 800 M2 families, with 15.5% showing visible phenotypic variation. This library provides a valuable resource for dissecting agronomic traits and supports forward genetic approaches for identifying key genes in C. moschata. Using this T2T genome assembly, we successfully identified the causal genes Cmos16G0077000 linked to a yellow-leaf phenotype and Cmos14G0126400 associated with a miniature squash (mSq) phenotype. Overall, the PKUMo T2T genome assembly, together with the extensive mutant library, provides a robust foundation for exploring agronomic traits and accelerating genetic improvement in Cucurbita breeding programs.

Tetraploid wheat (Triticum turgidum L., BBAA), a key pasta crop, serves as an untapped genetic resource with rich genomic diversity for hexaploid bread wheat improvement. Here we de novo assembled 12 genomes spanning all 10 recognized tetraploid wheat (genome BBAA) subspecies, and a graph-based pangenome was constructed. Chromosome rearrangements drove subgenome asymmetry and shaped genomic divergence, with an average of 0.25 million structural variations per accession, predominantly attributable to transposon activity. Using 736 globally distributed tetraploid wheat accessions, we identified locally adapted subgroups with untapped breeding potential and discovered a novel retrotransposon‑induced loss‑of‑function Btr1-A allele responsible for convergent adaptation of non-brittle rachis. Genome-wide association studies identified 287 loci associated with 32 traits. A homeodomain-leucine zipper transcription factor HAT14-B that enhances both spikelet number and grain size was identified. This subspecies-wide pangenome enriches Triticeae AB subgenome resources and facilitates the discovery and application of agronomically important genetic variations.

Aptamers are single-stranded DNA or RNA molecules that specifically bind to a wide range of target molecules with high affinity, making them powerful tools for synthetic biology. Traditional aptamer selection via Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is labor-intensive and prone to nonspecific binding. To address these issues, we developed the Bead-based One-Step aptamer Selection (BOSS) method. As proof of concept, we used this method to target Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (AtCOP1), a conserved E3 ubiquitin ligase central to photomorphogenesis. We expressed the N-terminal RING (Really Interesting New Gene) domain of AtCOP1, immobilized it on Ni-NTA beads, and incubated the beads with a random ssDNA library. After washing the beads with washing buffer and replacing the buffer five times, followed by high-throughput sequencing, we identified the high-affinity aptamer Lib1-9, with a Kd of 11.14 nM for AtCOP1-RING. Lib1-9 demonstrated species specificity, showing strong binding to AtCOP1, but not to other COP1 homologs. Truncation analysis revealed that the core variable region (△LR) of Lib1-9 retained near-full binding affinity (Kd = 1.679 nM) to AtCOP1, which is comparable to the values observed for thrombin-binding aptamers. When we delivered Cy5-labeled aptamers into the hypocotyl cells of transgenic YFP-NLS-AtCOP1/cop1-4 A. thaliana plants, both Cy5-Lib1-9 and Cy5-Lib2-11 colocalized with YFP-COP1. The BOSS method is an efficient platform for plant aptamer development, enabling the rapid generation of tools for synthetic biology applications such as COP1 biosensing and optogenetic control.

The spatial organization of essential, nonessential, and toxic metal(loid) elements (MEs) within plant cells underpins physiological function. Yet, comprehensive subcellular imaging of the full ME spectrum remains challenging due to trade-offs among spatial resolution, elemental coverage, and structural correlation. Here, we present an integrated scanning electron microscopy-focused ion beam-time-of-flight-secondary ion mass spectrometry platform that overcomes these limitations by achieving nanoscale coregistration of ultrastructure with ME distribution. Applying this high-fidelity workflow to Arabidopsis, soybean, and wheat, we constructed single-cell metallome maps revealing an evolutionarily conserved subcellular architecture: chloroplasts enrich essential MEs (e.g., magnesium, iron, copper), whereas vacuoles compartmentalize nonessential [e.g., lanthanum (La)] and toxic MEs [e.g., cadmium (Cd), lead, arsenic]. We demonstrate that while this architecture remains stable under homeostasis, it undergoes dynamic, stimulus-specific, and dose-dependent remodeling under stress. Low-dose La(III) enhances pairwise and higher-order colocalizations of essential MEs within chloroplasts, correlating with improved photosynthetic efficiency and growth. High-dose La(III) induces nonphysiological La-ME associations and, critically, drives aberrant Cd(II) accumulation in chloroplasts-revealing a cross-toxicity mechanism wherein La(III) disrupts native sequestration barriers. In contrast, although high-dose Cd(II) is largely excluded from chloroplasts, it triggers a widespread redistribution of essential MEs, progressively eroding spatial organization. Thus, while both ions inhibit growth, they perturb metallomic networks via distinct mechanisms: La(III)-mediated disruption of sequestration vs. Cd(II)-induced systemic compartmental collapse. Our findings establish that subcellular ME networks are dynamically regulated and orchestrate physiological outcomes.

Plant de novo regeneration, unlike regeneration in most animal systems, relies on callus formation and re-establishment of stem cell niches (SCNs) rather than on pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain unknown. In this sduty, we used super-resolution multimodal spatial transcriptomics to profile approximately 1.2 million cells during tomato shoot regeneration from wounding to organogenesis. This spatiotemporal atlas resolved vascular-associated callus initiation, epidermal and pluripotent cell-state transitions, and the organization of Wuschel-expressing cells during niche formation. High-resolution spatial imaging identified a previously unrecognized ovoid-structured SCN composed of a peripheral signaling layer, an intermediate plastic compartment, and a central quiescent core. Within this architecture, EPFL8b is enriched in the signaling layer, whereas its receptors, ER and ERL1, are mainly localized to the plastic compartment. Genetic, peptide treatment, protein interaction, and spatial transcriptomic analyses showed that EPFL8b-mediated signaling contributes to SCN organization and shoot regeneration. Together, these findings expand traditional gene-centric paradigms, highlighting structural organization as a fundamental principle in regeneration and providing a high-resolution framework for studying SCN formation.

Transcriptional gene silencing (TGS) is critical in maintaining genome integrity in plants, during which DNA methylation plays a fundamental role. The establishment and maintenance of DNA methylation are well characterized, while the downstream events mediating transcriptional repression remain poorly understood. In this study, we performed a forward genetic screen for suppressors of hdp1-induced report gene silencing to identify components involved in TGS downstream of DNA methylation and identified Pre-mRNA processing factor 8 (PRP8), a well-known component of the spliceosome complex. Through comprehensive genetic analysis coupled with RNA sequencing and whole-genome bisulfite sequencing, we demonstrated that PRP8-mediated TGS of the transgenes along with a subset of endogenous genes and transposable elements in a DNA methylation-independent manner. Through high-throughput chromosome conformation capture (Hi-C) analysis, we demonstrated that PRP8 is required for maintaining pericentromeric heterochromatin interactions and higher-order chromatin organization. Further genetic analysis revealed that PRP8 acts synergistically with Arabidopsis MICRORCHIDIA (MORC) protein MORC6, HISTONE DEACETYLASE 6 (HDA6), MORPHEUS MOLECULE 1 (MOM1), and NUCLEAR RNA POLYMERASE D1B (NRPE1), suggesting its involvement in a previously uncharacterized TGS pathway. In summary, our findings establish PRP8 as a dual-function factor involved in both splicing and DNA methylation-independent TGS.

Plant de novo regeneration, a capacity absent in animals, relies on stem-cell-niche formation rather than pre-existing reservoirs. Growth hormones such as auxin and cytokinin, together with numerous genetic regulators, participate in regeneration, but the architectural principles coordinating extensive cellular reprogramming at the individual-cell scale remain elusive. Using super-resolution multimodal spatial transcriptomics to 1.16 million cells, we tracked tomato regeneration across temporal intervals from wounding to organogenesis. Datasets are available at http://www.single-cell-spatial.com .

Soybean (Glycine max), a photoperiod-sensitive legume critical for global protein and oil supply, relies on precise flowering-time regulation to achieve latitudinal adaptation. LATE ELONGATED HYPOCOTYL homologs (GmLHYs) promote flowering by repressing the floral inhibitor E1; however, the mechanisms that activate GmLHYs remain unclear. Although COMPASS (Complex of Proteins Associated with Set1) and COMPASS-like complexes catalyze histone H3 lysine 4 (H3K4) methylation, their functions have diverged considerably across species and remain largely uncharacterized in legumes. Here, we show that GmASH2R1 and GmASH2R2 form a COMPASS-like complex with GmRBL and GmWDR5a proteins that catalyzes genome-wide H3K4 mono-, di-, and trimethylation, revealing roles distinct from those of their counterparts in Arabidopsis thaliana. This complex directly activates GmLHY expression by promoting H3K4me3 deposition at GmLHY promoters, thereby accelerating flowering. Moreover, we uncover a tunable "Yin-Yang" module in which Nuclear Factor Y (NF-Y) subunits GmNF-YC4a and GmNF-YC4b interact with GmASH2R proteins but act as transcriptional repressors. These NF-YC proteins compete for CCAAT-box binding at GmLHY promoters, thereby antagonizing GmASH2R-mediated activation and fine-tuning flowering time. Population analyses suggest that the GmASH2R1/2-GmNF-YC4a/b module may have been subject to antagonistic selection during domestication and that specific allelic combinations could contribute to flowering-time plasticity, consistent with adaptive diversification across latitudinal gradients. Our findings establish the COMPASS-like complex as a central activator of flowering in soybean and reveal an epigenetic-transcriptional mechanism that fine-tunes flowering time to support environmental adaptation.

The phytochrome B (phyB)-transcription factor signaling module plays a critical role in regulating photomorphogenesis. In this study, TCP21, a member of the Class I TCP transcription factor family, was identified as a direct interacting partner of phyB. TCP21 negatively regulates photomorphogenesis through downregulating HY5 expression and repressing the transcriptional activity of HY5. Moreover, phyB physically interacts with TCP21 and inhibits its transcriptional activity. Notably, phyB outcompetes HY5 for binding to TCP21, thereby attenuating the interaction between TCP21 and HY5 and alleviating TCP21-mediated repression of HY5 DNA-binding ability. Collectively, these findings establish TCP21 as a key component within the phyB-HY5 signaling module, contributing to plant adaptation to dynamic light environments.

The recognition of plant-derived immunogenic peptides, known as phytocytokines (PCKs), by cell surface receptors triggers immune signaling pathways that bolster basal plant defense against pathogens. However, little is known about the molecular mechanisms that underlie PCK-mediated immune regulation in wheat. In this study, we identified a wheat PCK, delta-like PCK (DEP), that robustly activates immune responses and confers multi-pathogen resistance. DEP is perceived by the leucine-rich repeat (LRR) receptor kinases (RKs) DEP RECEPTOR 1 (DEPR1) and SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE 2 (SERK2) and triggers DEPR1- and SERK2-dependent immune signaling. Cryogenic electron microscopy structural analysis revealed that DEP2 binds to the extracellular LRR domain of DEPR1 and recruits SERK2 through a disulfide-bond-stabilized loop to promote DEPR1-SERK2 heterodimerization. Furthermore, we showed that the DEP2-DEPR1-SERK2 module confers wheat resistance to Xanthomonas translucens, Fusarium graminearum, and Fusarium pseudograminearum. We also demonstrated that this module enhances wheat resistance to X. translucens by antagonizing abscisic acid signaling. Collectively, our study reveals a novel PCK-mediated immune signaling pathway and suggests a promising strategy for engineering multi-pathogen resistance in wheat.

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), a repressor of seedling photomorphogenesis, is tightly controlled by light. In Arabidopsis, COP1 primarily acts as a part of large E3 ligase complexes and targets key light-signaling factors for ubiquitination and degradation. Upon light perception, the action of COP1 is precisely modulated by active photoreceptors. During seedling development, light plays a predominant role in modulating seedling morphogenesis, including inhibition of hypocotyl elongation, cotyledon opening and expansion, and chloroplast development. These visible morphological changes evidently result from networks of molecular action. In this review, we summarize current knowledge about the molecular role of COP1 in mediating light-controlled seedling development.

Auxin is a core phytohormone regulating plant elongation growth. While auxin typically promotes hypocotyl elongation, excessive amounts of auxin inhibit elongation. Moreover, auxin usually promotes light-grown, but inhibits dark-grown hypocotyl elongation. How dosage and light condition change the plant's response to auxin, also known as auxin's biphasic effect or dual effect, has long been mysterious. Auxin induces cell expansion primarily through apoplastic acidification and the subsequent 'acid growth' mechanism. Here we show that this pathway operates for both stimulatory and inhibitory auxin doses and under both dark and light conditions. Regardless of the dosage, more auxin induces more transcripts of SAURs (Small Auxin-Up RNAs), leading to a stronger activation of plasma membrane H+-ATPases (AHAs) and progressive acidification of the apoplast in hypocotyl epidermis. Apoplastic acidification promotes growth but only above a certain pH threshold, below which excessive acidification inhibits elongation. Auxin overdosage-triggered hypocotyl inhibition can be alleviated by suppressing the AHA activity or raising the apoplastic pH. Light-grown hypocotyls exhibit a higher apoplastic pH, which impedes cell elongation and counteracts auxin-induced over-acidification. Auxin and light antagonistically regulate the SAUR-PP2C.D-AHA pathway in the hypocotyl and influence plant elongation growth. Our findings suggest that the biphasic effect of auxin results from the biphasic response of hypocotyl cells to decreasing apoplastic pH.

Leaf rust is a devastating disease of wheat. Growing rust-resistant wheat varieties is the best strategy to mitigate this threat. Here, we generate a 10.51-gigabase chromosome-scale assembly of the durum wheat landrace PI 192051. Using mutagenesis and transcriptome sequencing, we identify the leaf rust resistance gene Lr.ace-4A within a recombination-sparse region of PI 192051 and demonstrate that Lr.ace-4A is identical to the previously designated Lr30 gene in hexaploid wheat. Lr.ace-4A/Lr30 encodes a non-canonical coiled-coil nucleotide-binding leucine-rich repeat receptor, featuring tandem nucleotide-binding domains. This gene is both necessary and sufficient to confer resistance to leaf rust, as demonstrated by CRISPR/Cas9-induced mutations and transgenic complementation. Lr.ace-4A provides near-immunity resistance in durum wheat, though its effectiveness is diminished in hexaploid wheat. Two amino acid polymorphisms differentiate the resistant and susceptible Lr.ace-4A haplotypes, with transgenic plants carrying either susceptible variant showing susceptibility. The cloning of Lr.ace-4A will accelerate its deployment in wheat breeding programs.

In plants, microRNAs (miRNAs) participate in complex gene regulatory networks together with the transcription factors (TFs) in response to biotic and abiotic stresses. To date, analyses of miRNAs-induced transcriptome remodeling are at the whole plant or tissue levels. Here, Arabidopsis's ABA-induced single-cell RNA-seq (scRNA-seq) is performed at different stages of time points-early, middle, and late. Single-cell level primary miRNAs (pri-miRNAs) atlas supported the rapid, dynamic, and cell-type specific miRNA responses under ABA treatment. MiRNAs respond rapidly and prior to target gene expression dynamics, and these rapid response miRNAs are highly cell-type specific, especially in mesophyll and vascular cells. MiRNA-TF-mRNA regulation modules are identified by identifying miRNA-contained feed-forward loops (M-FFLs) in the regulatory network, and regulatory networks with M-FFLs have higher co-expression and clustering coefficient (CC) values than those without M-FFLs, suggesting the hub role of miRNAs in regulatory networks. The cell-type-specific M-FFLs are regulated by these hub miRNAs rather than TFs through sc-RNA-seq network analysis. MiR858a-FBH3-MYB module inhibited the expression of MYB63 and MYB20, which related to the formation of plant secondary wall and the production of lignin, through M-FFL specifically in vascular. These results can provide prominent insights into miRNAs' dynamic and cell-type-specific roles in plant development and stress responses.

Soybean is a critical source of protein and vegetable oil worldwide. Expanding its cultivation into salinity lands represents a promising strategy for increasing production; however, soil salinity severely limits soybean growth by disrupting physiological and metabolic homeostasis. Although beneficial endophytes can enhance plant stress adaptation, the molecular mechanisms by which they reprogram host responses under salinity remain poorly understood. In this study, we isolated Pseudomonas sp. 77S3 from salt-tolerant wild soybean and demonstrated its exceptional ability to significantly improve growth and salt tolerance in cultivated soybean under salt stress, using both fresh and fermented formulations. Integrated transcriptomic and metabolomic analyses revealed that 77S3 inoculation systemically reprograms gene expression and metabolic networks in soybean roots. Key to this reprogramming was the enhancement of nitrogen metabolism, orchestrated largely by the nitrate transporter NRT1.5, which facilitated nitrogen reallocation under stress. Functional studies using nrt1.5 knockdown lines confirmed that NRT1.5 is essential for 77S3-mediated improvements in salt tolerance, ion homeostasis, root architecture remodelling, and carbon-nitrogen rebalancing. Additionally, 77S3 increased antioxidant capacity, modulated phytohormone signalling, particularly in auxin and ethylene pathways, and improved phosphorus and potassium solubilisation. These multi-level adaptations collectively enhance salinity resilience in soybean. Our findings provide novel insights into the mechanistic basis of endophyte-induced salt tolerance and support the use of Pseudomonas sp. 77S3 as a sustainable bioinoculant for soybean production in saline agriculture.

Dear Editor, Cucumber,Cucumis sativus,is a major vegetable crop globally.In addition to being consumed fresh or sliced,pickling cucumber rep-resents a key cultivated type,widely grown in open fields across regions including the Americas,Europe,and Asia(Shetty and Wehner,2002).Pickling cucumbers are characterized by numerous lateral branches,firm fruit,and notable acidity.The genome of American pickling cucumber,Gy14 v.2,has been assembled and released with an assembly size of 258.62 Mb,which is significantly lower than the estimated size of 350 Mb(Cavagnaro et al.,2010).