Nature Plants

Introductory paragraphWheat provides about 20% of total dietary calories worldside1. Wheat diseases, including wheat stripe (yellow) rust, cause billions of dollars in losses each year2. Wheat stripe (yellow) rust is caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst) which is best controlled by fungicide application and disease resistant wheat cultivars3. To-date, there are over 80 catalogued and >10 cloned yellow rust resistance genes (Yr genes)4. Yet our knowledge of corresponding avirulence (Avr) genes lags far behind5-8. The absence of cloned Avrs reflects Psts complex genome and the lack of robust transformation and genetic systems3. Recent advances in generating high-quality genome assemblies and the development of wheat defense assays have addressed these challenges9-11. Here we clone AvrYr7 which is recognized by Yr712. We further identify six additional alleles of AvrYr7 that escape recognition due to non-synonymous genetic variations, transposable element activity, missense mutation, and expression polymorphism. These findings provide critical insights into virulence evolution in one of the worlds most important wheat pathogens.

Quantitative pollen viability analysis is a critical but labor-intensive step in plant reproductive biology. Existing deep-learning Segment Anything Models (SAM) fail to reliably segment viable pollen in Alexander-stained anthers. To address this, we fine-tuned an existing Cellpose-SAM model for pollen segmentation. We integrated it into PAT (Pollen Analysis Tool), a cross-platform desktop application. PAT features instance segmentation with interactive quality control, an in-app model retraining module, and publication-ready statistical outputs. We deployed PAT in an EMS suppressor screen of semi-sterile Arabidopsis smg7-6 mutants, enabling efficient candidate prioritization for whole genome sequencing and mapping candidate mutation. This screen led to the identification of a point mutation in CAP-D2 (capd2-2), a Condensin I subunit, that rescues the smg7-6 meiotic phenotype. Notably, mutation in a Condensin II subunits (CAP-D3 and CAP-H2) does not confer rescue. Further characterization suggests the capd2-2 allele is hypomorphic, showing no defects in vegetative growth, chromocenter compaction, or transposable element silencing. Collectively, we demonstrate that accessible AI tools have the potential to bridge gaps in plant phenotyping and accelerate the pace of biological discovery. HighlightWe combined AI-powered image analysis with an easy-to-use desktop app to automate plant pollen counting, then used it to identify a new genetic suppressor of meiotic defects.

Polyamines (PAs) are ubiquitous metabolites that, despite their simple structure, profoundly influence plant growth, development, and stress adaptation. Their cellular levels are largely determined by arginine decarboxylase (ADC), a key rate-limiting enzyme in their biosynthesis. We previously identified a [~]50 bp GC-rich sequence in the 5' untranslated region (UTR) of plant ADC genes, termed the ADC-box, that is conserved across land plants. Transient reporter assays in tomato, in which ADC upstream regions were decoupled from their native coding sequences and fused to reporter genes, suggested that this element represses translation. However, its function in the native genomic context and its impact on PA homeostasis remain unclear. Here, we combined CRISPR-Cas9 genome editing, metabolite profiling, enzymatic assays, and RNA structure probing to define ADC-box function in tomato and in the seedless land plant Marchantia polymorpha, which retains a conserved [~]20 bp core region. Mutation of the M. polymorpha ADC-box increased ADC activity and altered PA levels, indicating that the ADC-box functions as a conserved translational repressor. In tomato, disruption of the ADC-boxes in SlADC1 and SlADC2 increased ADC activity, demonstrating that the ADC-box acts as a translational repressor in its native context. These ehects were most pronounced under cold stress, when ADC transcript levels increase, suggesting that the ADC-box buhers stress-induced translation. Metabolically, ADC-box disruption led to agmatine accumulation and alterations in upstream intermediates, while downstream PA pools remained largely unchanged. SHAPE analysis revealed that the tomato ADC-box folds into a three-stem RNA structure, with a central stem representing the major inhibitory module. ADC-box mutants displayed altered plant-microbe interactions, with enhanced resistance to Pseudomonas syringae and Tobacco rattle virus, but increased susceptibility to Ralstonia solanacearum and Tomato yellow leaf curl virus. Together, these findings establish the ADC-box as an evolutionarily conserved cis-regulatory element that stabilizes PA homeostasis and modulates plant-microbe interactions.

C4 photosynthesis improves light, water and nitrogen-use efficiencies and can raise yield by 50% compared with the ancestral C3 pathway. Engineering C4 traits into C3 crops could substantially boost food production but requires coordinated modifications to leaf anatomy and cell-specific photosynthetic function. For example, C4 leaves contain more numerous, shorter bundle sheath cells that are photosynthetically active. In searching for transcriptional regulators of bundle sheath development in C3 rice, we unexpectedly found OSA3, a plasma membrane H+-ATPase that is expressed in bundle sheath cells as they elongate, and when knocked out reduces their length due to reduced apoplastic acidification. Bundle sheath cell number and chloroplast occupancy are increased. Thus, switching between C3 and C4 bundle sheath identity is controlled by acid growth, and OSA3 represents a simple tool for C4 engineering.

Belowground plant trait research has predominantly focused on trade-offs in fine root traits via the root economics space. Yet, this fine root framework captures only a fraction of the functional strategies plants employ beneath the soil surface. Here, we broaden the perspective on belowground plant functioning by integrating traits related to root system extent, clonality and bud banks, using data from the new UNDERPLOT database. This integration links measurable traits to key belowground functions: resource acquisition, spatial exploration, and persistence. Our analysis shows that the fine root economics space explains less than 5% of the variation in traits related to root system extent, clonality, and bud banks. Instead, an expanded trait analysis reveals three significant dimensions, explaining 62% of total trait variation. The third dimension, represents an independent, persistence-related gradient, not captured by existing root economics frameworks. We propose that understanding belowground plant strategies requires embracing additional functional gradients. The strategy of persistence, in particular, varies significantly across growth forms and is a critical dimension of plant response to resource limitation and stress, becoming increasingly important as global change shifts disturbance regimes.

Arbuscular mycorrhizal (AM) symbiosis is conserved across land plants and is the default nutrient uptake strategy in nature. Within roots, AM colonisation is tightly patterned and dynamically tuned by nutritional cues. Multiple genetic modules contribute to this regulation, including the phosphate starvation response, DWARF14-LIKE (D14L) karrikin signalling, and the common symbiosis signalling pathway (CSSP). Transcriptional overlap among these has led to the hypothesis that phosphate starvation and D14L signalling act upstream of the CSSP. Here, we examined the epistatic relationship between D14L and CSSP in rice. Overexpression of an autoactive gain-of-function CCaMK (gofCCaMKox) restored AM colonisation and symbiosis marker gene expression in d14l mutants to wild-type levels or above, whereas overexpression of wild-type CCaMK did not, confirming that CSSP operates downstream of D14L signalling. However, gofCCaMKox did not rescue the d14l mesocotyl elongation phenotype, supporting a bifurcation of D14L into developmental and symbiotic outputs. Unexpectedly, gofCCaMKox also expanded fungal access to normally restrictive tissue domains (the meristematic zone and endodermis) assigning a role for CCaMK activation in defining root zone and cell-type competence for AM colonisation. Despite restored colonisation, introduction of gofCCaMKox into d14l produced arbuscules, which however were less developed and had increased hyphal septation, revealing a CCaMK-independent role for D14L in intraradical colonisation and arbuscule development. Transcriptome profiling resolved AM-relevant genes into modules controlled by CCaMK activation alone, in combination with D14L, or requiring additional colonisation-associated cues, and further suggested CCaMK primarily acts through AP2 transcription factors. Together, these findings reinforce CCaMK as a master regulator of AM symbiosis at the genetic, transcriptomic and anatomical levels while uncovering CCaMK-independent functions of D14L in arbuscule development.

Gibberellins (GAs) influence cell division and elongation, profoundly shaping plant architecture and yield. GA perception occurs when bioactive GAs bind the receptor GID1, promoting DELLA degradation and activating transcriptional programs. While GA signaling in the root endodermis is essential for promoting root elongation, functions of other layers in spatial control of GA responses have not been explored. Here, we developed a synthetic GA (sGA) that does not bind endogenous GID1, together with a modified GID1 (mGID1) engineered to selectively recognize sGA, enabling cell-specific activation of GA signaling in vivo. Using this system in Arabidopsis, we demonstrate that coordinated action of GA signaling in the endodermis, epidermis, and other layers is required for full root elongation. Moreover, cell type-specific expression of GA biosynthetic enzymes indicates the existence of intercellular GA transport. The sGA-mGID1 system provides a versatile platform for spatially precise reprogramming of hormone signaling, enabling synthetic control of developmental processes such as root-shoot growth balance, thereby advancing applications in plant synthetic biology and sustainable crop improvement.

Microtubule dynamics underpin cell division, movement, and growth in eukaryotic organisms. KATANIN p60 is a microtubule-severing protein that promotes proper cell elongation and division. In plants, division positioning is initiated in late G2 via the formation of a microtubule structure called the preprophase band (PPB). Maize p60 mutants have defects in microtubule severing and form abnormal PPBs in symmetrically dividing cells, including both incompletely assembled and misoriented PPBs. Here, we show that an asymmetric division required to generate stomatal complexes in maize p60 mutants have normally positioned but often incompletely formed PPBs. Incompletely formed PPBs lead to misoriented divisions and nuclear positioning defects in p60 mutants.

Senescence enables plants to remobilize and recycle nutrients from aging organs to support growth, reproduction, and survival. In annual crops like maize, nitrogen remobilization from leaves to grain is incomplete, with 30-50% of nitrogen stranded in aboveground tissues and subject to environmental loss. Mitigating nitrogen loss in annual crops could be achieved by leveraging the physiological strategies of perennial grasses, which remobilize nitrogen and other nutrients into underground organs at the end of the growing season, thereby preventing environmental leakage. To uncover the molecular basis of perennial nitrogen recycling to underground organs, we built a transcriptomic atlas from field-grown plants, comprising 2,685 RNA-seq libraries from 14 grass species within the Panicoideae (Poaceae), utilizing maize and sorghum as annual references for comparative analyses. The atlas spans leaves, roots, stalks, and rhizomes across two seasons, from mid-growing season to senescence. Using a photosynthetic index to align the leafs transition from nitrogen sink to source across species, co-expression network analysis revealed that the subnetworks driving leaf nitrogen recycling are preserved across annuals and perennials. However, we discovered that the subnetworks associated with underground sink establishment, specifically those associated with seed-like dormancy and desiccation tolerance pathways, have diverged among annual crop accessions. Our work identifies conserved gene candidates and networks that could be used to reintroduce perennial-like nutrient recycling into annual crops to enhance long-term nutrient retention in the field.

Wild relatives of wheat harbour genetic diversity essential for improving resilience to climate-driven stresses, yet their deployment is hampered by unresolved evolutionary relationships and the absence of reference genomes. Here we present a chromosome-scale reference genome for Thinopyrum bessarabicum, a diploid halophyte and high-priority donor for wheat salt tolerance breeding. A key unresolved question is whether the diploid J genome contributed directly to the subgenome composition of extant polyploid Thinopyrum species, and which genomic features underpin its exceptional salt tolerance. Using this resource, we show that the diploid J genome of Th. bessarabicum is not represented among the subgenomes of polyploid Thinopyrum species, resolving a long-standing ambiguity in Triticeae genomics. Gene-level resolution of the reciprocal 4/5 chromosomal translocation across six related Triticeae species identifies conserved breakpoint gene pairs, supporting a single ancestral rearrangement. Genome-wide gene content analysis shows that halophytic capacity is underpinned by quantitative expansion of conserved stress-response gene families. Salt tolerance phenotyping validates chromosome 5J as a tolerance locus in both Th. bessarabicum and wheat introgression lines. A physically anchored marker framework and dual-reference skim-sequencing pipeline enable precise megabase-resolution characterisation of Th. bessarabicum introgressions in wheat, providing a genomic foundation for deploying J-genome diversity in crop improvement.

Cellulose, a primary component of plant cell walls, is synthesized by cellulose synthase complexes (CSCs) at the plasma membrane. Targeting this process with cellulose biosynthesis inhibitors (CBIs) has significantly advanced our understanding of plant cell wall formation and provided valuable compounds for herbicide development. Here, we identified a fungal natural product, 8-methyldichlorodiaporthin (MDD), as a broad-spectrum plant CBI. Structure-activity relationship analyses demonstrate that methylation modifications on the isocoumarin ring and chlorination of side chain are crucial for MDD-induced growth inhibition. A chemical forward genetic screen in Arabidopsis thaliana revealed two semi-dominant CESA1 mutations, causing A903T and H1024Y substitutions, that confer insensitivity to MDD. Both mutations locate to transmembrane domains of CESA1, and we show that MDD depletes CSCs from the plasma membrane and reduces cellulose content. Further genetic analyses indicate that the cesa1mddi1-1 A903T mutant also confers resistance to CBIs quinoxyphen and C17, but not to CBIs isoxaben, indaziflam, or ES20. Stacking additional point mutations conferring resistance to other CBIs, cesa3ixr1-1 G998D, and cesa6es20-r3 G935E into the cesa1mddi1-1 A903T background yields multiple-drugs resistant lines that maintain normal growth. These findings establish MDD, as a novel, natural CBI that likely targets CESA1, thereby extending our understanding of CSC regulation and abilities to develop multi-drugs resistant crop varieties. These findings offer new perspectives for weed management and plant biotechnology. Significance StatementCellulose, a fundamental structural component of plant cell walls, is synthesized by cellulose synthase complexes (CSCs) and represents a critical herbicide target. While synthetic cellulose biosynthesis inhibitors (CBIs) like isoxaben and quinoxyphen have helped in the elucidation of CSC function and aided in weed control, natural CBIs remain largely undiscovered. Here, we identify 8-methyldichlorodiaporthin (MDD), a fungal-derived isocoumarin natural product, as a CBI that inhibits plant growth by depleting CSCs from the plasma membrane. Genetic screens reveal MDD-resistant cesa1 mutations, and combining these with other CBI-resistant alleles yields multi-herbicide resistant plants that can grow normally. This research enhances our understanding of cellulose biosynthesis and paves the way for multi-herbicide resistant crops with agricultural benefits.

The shikimate pathway provides precursors for phenolic metabolites in plant primary and secondary metabolism. Carbon flux measurements in intact Arabidopsis leaves using a novel isotopologue MS/MS methodology revealed unexpected dynamics between chorismate and isochorismate pools. 13CO2 labeling kinetics point to chloroplast-derived shikimate as a major bifurcation point, with approximately one third diverted away from the chloroplast. In contrast, the small pool of chorismate was almost exclusively chloroplast-localized and turned over rapidly, reaching more than 70% labeling within minutes. Isochorismate, a precursor to salicylic acid (SA) in the Brassicales, was present at 50-fold molar excess over chorismate but labeled much more slowly and appeared primarily extra-chloroplastic. Total isochorismate declined by 90% in the Arabidopsis enhanced disease susceptibility mutant, which lacks the isochorismate exporter. Non-aqueous fractionation further supported a primarily chloroplast-localized chorismate pool but extra-plastidic isochorismate. Populus trichocarpa and Nicotiana benthamiana leaves contained chorismate but only trace isochorismate, consistent with their use of the benzoyl-CoA route to SA. Carbon commitment calculations indicated that one third of the total chorismate pool in Arabidopsis leaves is diverted to isochorismate. Global leaf calculations based on elemental analysis-isotope ratio mass spectrometry and targeted isotope recovery indicate that only 0.03% of total assimilated carbon (5.27 pmol{middle dot}mg-1 D.W.{middle dot}min-1) enters the shikimate pathway in photosynthetically active mesophyll. For comparison [~]0.05% (7.75 pmol{middle dot}mg-1 D.W.{middle dot}min-1) enters the 2-C-methyl-D-erythritol 4-phosphate pathway, which provides precursors for photosynthetic pigments and electron carriers. The compartmentalization and turnover dynamics of shikimate, chorismate, and isochorismate suggest continuous demand for aromatic precursors in mesophyll tissue is comparable to demand for MEP-pathway derived pigments.

Plants detect proximity to neighboring vegetation by light spectral signatures which are sensed by phytochrome photoreceptors. As a response, many species grow taller to out-compete their neighbors. In seedlings, the rapid elongation of hypocotyls requires enhanced supply of carbon resources from the cotyledons, transported as sucrose. The mechanisms of how phytochrome signaling regulates carbon allocation are unknown. We show that sucrose biosynthesis, particularly the step catalyzed by sucrose phosphate synthase (SPS), is a key determinant of hypocotyl elongation. Moreover, we show that auxin directs resource allocation to the elongating hypocotyl. Increased sucrose availability enhances elongation only when auxin levels are sufficient, highlighting the interdependence between sugar supply and auxin. In contrast, our data reveal that reduced sucrose availability does not impair neighbor-proximity-induced auxin synthesis and signaling in hypocotyls and cotyledons. Our findings shed light on the regulation of carbon allocation -- a process which is poorly understood, despite its importance for crop yield.

ABSTRACTCallose synthase is responsible for the targeted deposition of the {beta}-1,3-glucan polymer, callose which underlines essential plant developmental processes, including cell division, pathogen defense or cell-cell communication. The architecture of the callose synthase complex (CALSC) as well as the molecular mechanisms of callose synthesis remain unknown. Here we report an integrative characterisation of the Arabidopsis CALS complex, with the most enriched subunits, CALS1, CALS2 and CALS3, forming its core. Structurally, CALSC assembles into a trimer, requiring the plant-specific Bag domain to mediate inter-subunit associations. The biological importance of CALSC assembly is highlighted by the simultaneous loss of CALS1 and CALS3, which abolishes plasmodesmal callose deposition and affects symplastic transport. Site-directed mutagenesis and molecular dynamics simulations depict the topology of the CALS1 active site in detail, including the components of the enzymatic reaction. We pinpoint the translocating tunnel through which the nascent glucan is delivered and mechanistically confirm the role of transmembrane helix 8 in regulating glucan export. Our work provides unprecedented insight into the molecular architecture of the CALSC and the distinct changes from maturation to activity at the plasma membrane, while showcasing the mechanisms involved in callose synthesis at the molecular level.

Calcium signalling and structural roles are fundamental for plant growth, development, and environmental adaptation. Recent studies have identified MILDEW RESISTANCE LOCUS O (MLO) proteins as novel calcium-permeable channels with roles in root growth, cell wall development, pollen tube growth, and perception. However, the molecular mechanisms underlying MLO function remain unknown. Here, we demonstrate that multimerisation is essential for MLO activity. Chemical crosslinking, split-ubiquitin interaction assays, and single-molecule photobleaching revealed that MLO proteins form stable dimeric and trimeric assemblies at the plasma membrane. Structural modelling uncovered a molecular architecture of the MLO trimer with a central ion-conducting pore, which was further examined by molecular dynamics simulations in a lipid membrane environment. Computational electrophysiology showed preferential inward Ca2+ transport, confirming that MLO proteins function as calcium influx transporters, and identified a conserved set of pore-lining residues that coordinate ion translocation. Functional and structural analyses indicated that the mechanism of calcium permeation is evolutionarily conserved. Our findings provide mechanistic insight into MLO-mediated calcium influx across the plasma membrane and establish multimerisation as a critical determinant of this calcium channels activity.

Alignment-based detection of transposable element (TE) insertion polymorphisms suffers from reference bias and multi-mapping errors in repetitive genomic regions, creating a fundamental validation bottleneck for population-scale structural variant catalogs. Here, we demonstrate that the OneGenome-Rice (OGR) genomic foundation model (GFM)--a 1.25 billion parameter Mixtral architecture trained on 422 rice genomes without TE annotations--provides an entirely orthogonal, alignment-free approach that resolves TE-mediated structural divergence at chromatin-domain resolution. At the CTB4a cold-tolerance locus on chromosome 4, OGR embeddings revealed that the aus subpopulation (NONA_BOKRA) carries 2.2-fold higher structural divergence from indica than japonica, consistent with its 728 subpopulation-exclusive cold-protective TE insertions. Sliding-window analysis across 4.4 megabases identified a 25.6-fold divergence enhancement at TE clusters relative to the conserved CTB4a gene body. Critically, the minimal effective resolution was established at approximately 20 kilobases--corresponding to the median size of topologically associating domains (TADs) in the rice genome--while individual TE sites at 500 base pairs were undetectable (P = 0.94). Non-neural baselines confirmed the signal derives from learned representations of genomic context rather than simple nucleotide statistics. These findings establish GFMs as orthogonal validation tools for population-scale TE genotyping and provide computational evidence that TE functional effects are organized at the chromatin-domain level, with direct implications for prioritizing functional TE variants in crop breeding.

Chromosome number variation and structural reorganization are key drivers of plant evolution, yet their genomic basis remains unclear due to incomplete representation of repetitive regions in existing assemblies. The Linum genus exhibits exceptional karyotypic diversity (n = 7-43), providing a powerful system to investigate chromosome evolution. Here, we generated near telomere-to-telomere (T2T) genome assemblies for four species, including cultivated flax (L. usitatissimum cv. CDC Bethune; n = 15), its wild progenitor (L. bienne; n = 15), and two related species (L. decumbens and L. grandiflorum; n = 8). Together with published genomes of L. lewisii (n = 9) and L. tenue (n = 10), these enabled reconstruction of chromosome evolution across six lineages. Phylogenomic analyses revealed a shared ancestral whole-genome duplication (WGD) associated with the n = 9 karyotype, followed by lineage-specific WGDs and divergent diploidization. The transition from n = 8 to the derived n = 15 flax lineage not only occurred without chromosome length expansion, but also with genome size reduction, indicating extensive internal restructuring. Comparative analyses showed that this restructuring was associated with lineage-specific expansion of a single DNA transposon family (TE_00003234; hAT), which is highly enriched in expansive pericentromeric regions that are characterized by low gene density and nucleotide diversity, suppressed recombination, segregation distortion, and extensive synteny disruption, unlike the LTR retrotransposon-rich pericentromeres typical of most plant genomes. These findings support a model in which lineage-specific DNA transposon expansion is associated with remodeling of pericentromeric architecture and large-scale chromosome restructuring following polyploidization.

The banana family (Musaceae) exhibits remarkable diversity in both karyotype structure and bract coloration, yet the evolutionary dynamics of chromosomes and the genomic and regulatory basis underlying color diversification remain poorly understood. Here, we present a telomere-to-telomere (T2T), gap-free genome assembly of Musa exotica, an ornamental species with brightly colored bracts occupying an early-branching lineage within sect. Callimusa (Musa L.). By integrating this high-quality genome with other available Musaceae genomes, we reconstruct the ancestral Musaceae karyotype (AMK) for the first time, inferring a haploid chromosome number of n = 17. Comparative genomic analyses reveal recurrent, highly complex lineage-specific inter-chromosome rearrangements across extant Musaceae lineages, leading to inferred stepwise reductions in chromosome number to n = 11, 10, and 9. Notably, closely related species share similar rearrangement patterns, suggesting conserved evolutionary trajectories shaped by lineage-specific structural remodeling. Strikingly, rearrangement-associated regions are enriched for functionally important genes, particularly structural genes (CHS and F3H) and regulatory transcription factors (MYB and bHLH) involved in the anthocyanin biosynthesis pathway. Integrative transcriptomic and regulatory analyses further demonstrate coordinated activation of anthocyanin biosynthetic genes (CHS, CHI, F3'5'H, and ANS) in bracts, with expression divergence largely decoupled from gene dosage and predominantly driven by transcriptional regulation. Co-expression analyses reveal extensive MYB- and bHLH-enzyme interactions, underscoring their central role in modulating pathway activity and bract coloration diversity. Collectively, our findings suggest a link between genome structural evolution to trait diversification, offering a refined framework for understanding genome evolution and phenotypic diversification in Musaceae and other monocots. SignificanceWe reconstructed the ancestral Musaceae karyotype and revealed extensive lineage-specific chromosome rearrangements underlying karyotype evolution. Rearrangement-associated regions are enriched for anthocyanin biosynthetic and regulatory genes, suggesting that genome structural evolution may have contributed to bract coloration diversification in Musaceae. Integrative transcriptomic analyses further indicate that variation in anthocyanin-mediated bract coloration is more closely associated with transcriptional regulation than with gene dosage alone.

Crop nutrition depends on plant-microbe interactions, yet it remains unclear whether conserved genetic pathways impose universal rules on root microbiome assembly across plant hosts. Here, we show that the Common Symbiosis Signalling Pathway (CSSP), a conserved genetic module controlling endosymbiosis with arbuscular mycorrhizal fungi and nitrogen-fixing bacteria, regulates root microbiome assembly in a host-specific manner across contrasting fertilisation regimes. Using Lotus japonicus and Hordeum vulgare, we demonstrate that mutations in orthologous CSSP genes remodel root bacterial communities in both species, but with distinct taxonomic outcomes. In Lotus, CSSP disruption reduces rhizobial colonisation and promotes niche replacement by commensal taxa, whereas in Hordeum, the same mutations broadly restructure bacterial lineages without converging on Lotus-like responses. Root exudate profiling reveals host-specific metabolic differences, particularly in phenylpropanoid (flavonoids and coumarins) and gibberellin pathways, linking CSSP activity to chemically distinct rhizosphere environments that correlate with divergent microbiome assembly patterns across hosts. Moreover, root bacterial community composition accurately predicts plant nutritional status, highlighting tight coupling between host physiology and microbiome composition. Together, our results show that conserved symbiosis signalling regulates root microbiome assembly, while host-specific metabolic environments determine taxonomic outcomes. This extends CSSP function beyond canonical endosymbioses and positions symbiosis signalling as a general determinant of plant-microbiome interactions with implications for crop nutrition. Significance StatementRoot microbiomes influence plant nutrition, yet how conserved host genetic pathways controlling interactions with intracellular symbionts shape root-associated microbiome assembly across divergent plant species remains unresolved. The Common Symbiosis Signalling Pathway (CSSP), conserved across most land plants, regulates root microbiome composition in both a legume and a cereal, but with distinct taxonomic outcomes. These effects correlate with CSSP-dependent differences in root exudate chemistry and host metabolic profiles. Together, our results show that conserved symbiosis signalling operates within host-specific metabolic contexts, providing a framework for understanding why disruption of the same genetic pathway can lead to divergent microbiome configurations across plant species.

O_LIMechanical interaction between guard cells and epidermal pavement cells enables large stomatal apertures and high productivity in angiosperms. We do not know when this response evolved, but over the last 169 years we have found that mechanical advantage has been tested in at least 230 species from 85 families. To date no data on this trait exists among angiosperms outside magnoliids, monocots and eudicots. C_LIO_LITo resolve the evolutionary origins of this critical stomatal response we tested for mechanical advantage across 14 additional species including the earliest diverging lineages of angiosperms. C_LIO_LIWe find that mechanical advantage, while variable in magnitude, is present in all angiosperm species that have been measured, including Amborella trichopoda sister to all angiosperms. C_LIO_LIThis response likely evolved once in flowering plants, in the common ancestor of this clade, remaining widespread across angiosperms today. We hypothesize that angiosperms could not have realized the full potential of physiological innovations in water transport without the evolution of this key trait that increased operational stomatal aperture. C_LI