Nature Plants

Controlling the deleterious effects of immune responses is as vital as fighting infection. In plants, this is achieved, in part, by circadian clock-mediated regulation, such as the synthesis of and response to the immune hormone salicylic acid (SA)1,2. Application of SA at the same concentration under light/dark cycles induces immunity with minimal impact on growth, however, prolonged darkness leads to plant death2. To uncover what determines this life-or-death outcome, we identified twenty survival of SA-induced death (ssd) mutants through genetic screening. These mutants are defective in starch, glucose, and nitrate metabolism, and circadian regulation, and accumulate excessive starch and/or glucose. Likewise, glucose application rescues SA-treated plants in prolonged darkness. Surprisingly, SA treatment does not deplete glucose, but instead, induces amino acid and fatty acid catabolism. Through transcriptomic analyses of glucose-rescued WT plants and ssd mutants for shared pathways, we found that SA triggers plant death in darkness by inducing oxidative stress, and water loss, while glucose antagonizes these processes, boosts ER protein processing and re-establishes the anabolism-catabolism balance. Interestingly, the programmed cell death induced by effector-triggered immunity shares common transcriptomic patterns with those observed during SA-induced cell death in darkness and could also be attenuated by glucose treatment. Therefore, coordination with the cellular metabolic context plays a central role in determining immune outcomes and optimizing plant health.

Polyploidy provides adaptive advantages in plants by buffering deleterious mutations1,2. While polyploidization can enhance agronomic traits such as increased biomass, known as the gigas effect1-4, increasing genetic gain in polyploid crops remains a critical but difficult goal due to the difficulty in dissecting complex trait inheritance5,6. Here we present chromosome-scale genome assemblies for 26 Avena taxa, spanning diploid, tetraploid, and hexaploid lineages. We traced four independent polyploidization events across the genus, including the formation of A. agadiriana as an allotetraploid (AgAgAg'Ag'), and revealed a reticulate evolutionary history shaped by gene flow involving four subgenomes (A, B, C, D), for example, the hybrid speciation of A. hirtula. Transcriptomic analysis of 286 samples across 11 tissues, combined with deleterious mutation analysis from a cultivated population of 112 accessions, showed that polyploidization led to widespread functional redundancy among homoeologs, supporting a genome-wide buffering effect. However, derived allele frequency analysis revealed that, while disrupting functional genes may yield desirable traits, the buffering effect impedes the fixation of beneficial loss-of-function mutations and thereby limits breeding efficiency. Based on these integrative analyses, we propose breeding strategies to circumvent these limitations by targeting beneficial loss-of-function alleles within the complex polyploid background of oat. Our study highlights broader challenges in the improvement of polyploid crops and provides a foundation for future breeding strategies.

The terrestrialization of plants was accompanied by exposure to several environmental stresses. Adaptation to these stresses required numerous changes at the cellular and molecular level. One such adaptation in the leaves of Arabidopsis thaliana is the movement of cell nuclei to avoid UV damage. In the dark, the nuclei locate to the bottom walls of leaf cells to distance genetic material from external stresses, but in response to intense blue light (an indication of the presence of UV), they move to the side walls to escape UV-induced DNA damage1. The movement is driven by the photoreceptor phototropin and the actin cytoskeleton2. However, how this protective mechanism evolved in land plants remains unclear. Here, we show that in the liverwort Marchantia polymorpha, nuclei show a similar, but less stable movement in response to intense blue light. In the dark, M. polymorpha positioned nuclei on the upper walls of epidermal cells in young thalli, but in response to intense blue light, the nuclei immediately moved to the side walls, similar to A. thaliana. However, the movement was transient and the nuclei returned to the upper walls through both the actin and microtubule cytoskeletons. Unlike A. thaliana, M. polymorpha responded to prolonged (> 1 day) exposure to low light by moving nuclei from the upper to the side walls through both the actin and microtubule cytoskeletons and two photoreceptors (phototropin and phytochrome). However, no light-dependent nuclear relocation was observed in charophyte algae, suggesting that light-dependent nuclear relocation was initially established in the common ancestor of land plants as a result of terrestrialization and then diverged during land plant evolution.

Introductory Paragraph (Nature Plants format)Parthenogenesis or fertilization-independent embryogenesis occurs at low frequency in sexual plants. Expression of BABYBOOM-like (BBML) and PARTHENOGENESIS (PAR) genes in the egg cell of several diploid dicot crops induce parthenogenesis at varying frequency; however, recovery of viable haploid seeds has rarely been reported, perhaps due to a lack of viable endosperm formation. In the legume cowpea (Vigna unguiculata L. Walp), ectopic egg cell expression of the endogenous BBML homolog (VuBBML1) and PAR from Taraxacum officinale induces parthenogenesis; however, seeds abort as endosperm formation is blocked following self-pollination. Expression of VuBBML1 in both the egg cell and central cell, together with central cell fertilization following self-pollination, results in viable seeds that germinate and give rise to haploid plants. VuBBML1 has a functional role in the formation of cowpea embryo and endosperm seed compartments. This finding opens possibilities for establishing double haploid production during homozygous parental breeding, and asexual seed induction for fixing hybrid vigor in cowpea.

Gene functional descriptions, which are typically derived from sequence similarity to experimentally validated genes in a handful of model species, offer a crucial line of evidence when searching for candidate genes that underlie trait variation. Plant responses to environmental cues, including gene expression regulatory variation, represent important resources for understanding gene function and crucial targets for plant improvement through gene editing and other biotechnologies. However, even after years of effort and numerous large-scale functional characterization studies, biological roles of large proportions of protein coding genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, a public and updateable data resource consisting of transcript abundance assays from 2,090 samples derived from 604 tissues or conditions across 18 diverse species. We integrated across these diverse conditions and genotypes by analyzing expression profiles, building gene clusters that exhibited tissue/condition specific expression, and testing for transcriptional modulation in response to environmental queues. For example, we discovered extensive phylogenetically constrained and condition-specific expression profiles across many gene families and genes without any functional annotation. Such conserved expression patterns and other tightly co-expressed gene clusters let us assign expression derived functional descriptions to 64,620 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome-next.jgi.doe.gov), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.

The middle lamellae (ML) of plant cells, enriched in Homogalacturonan (HG) is considered to function as a crucial glue responsible for cell-cell cohesion (for review see 1). Mutants with defective HG content exhibit cell adhesion defects2,3. Despite advances, the mechanisms governing cell adhesion during plant development remain elusive. We previously hypothesized that cell-cell cohesion relies on cell wall integrity signaling, yet the specifics remain undefined4. OligoGalacturonans (OG), degradation products of HG, are prime candidates for informing cells about ML status and thereby influencing cell adhesion. This integrity signal is crucial for adhesion homeostasis 4. OGs serve as signaling molecules, recognized by membrane-bound cell wall receptors. Notably, restoring adhesion in qua2-1 mutants by modulating pectin response gene expression in esmd/qua2 mutants underscores potential OGs importance4-6. Deciphering the diversity and role of endogenous OGs is imperative for understanding cell adhesion modulation. Our study aims to identify compounds in this signalling pathway that regulate cell adhesion. We focused on characterizing HG degradation products in dark-grown hypocotyls. Our findings highlight various oligomers, along with two key monomers: galacturonic acid and its oxidized form, galactaric acid. These monomers appear to play a pivotal role in controlling cell adhesion by indirectly enhancing the crosslinking of extensin, a cell wall structural protein. This crosslinking leads to the densification of extensin-based cell wall networks, ultimately restoring cell adhesion in defective mutants. Our research sheds light on the intricate interplay between HG degradation product monomer and cell adhesion mechanisms.

Branching of root systems enables the exploration and colonization of the soil environment. In Arabidopsis roots, de novo organogenesis of lateral roots is patterned by an oscillatory mechanism called the root clock, which is dependent on metabolites derived from the {beta}-carotene pathway1, 2. Retinoids are {beta}-carotene-derived regulators of organogenesis in the animal kingdom. To determine if retinoids function in plant development, we conducted time-lapse imaging of a chemical reporter for retinoid binding proteins. We found that it oscillates with a comparable frequency to the root clock and accurately predicts sites of lateral root organogenesis. Exogenous application of retinal to wild-type plants is sufficient to induce root clock oscillations and lateral root organogenesis. A homology search yielded a potential Arabidopsis homolog, TEMPERATURE INDUCED LIPOCALIN (TIL) to vertebrate retinoid binding proteins. Genetic analysis indicates that TIL is necessary for normal lateral root development and a til mutant has decreased retinal sensitivity. TIL expression in a heterologous system conferred retinal binding activity, suggesting that it may directly interact with this molecule. Together, these results demonstrate an essential role for retinal and for plant retinal binding proteins in lateral root organogenesis.

Plant cell wall enlargement is fundamental to crop productivity and its sensitivity to drought1. Tip growth and diffuse growth are contrasting wall enlargement patterns often proposed to be limited by different processes: localized secretion and remodeling of pectins for tip growth versus loosening and sliding of cellulosic networks by -expansins (EXPAs) for diffuse growth2,3. Here, we knocked out root-hair specific EXPA7 and EXPA18 in Arabidopsis, abolishing root-hair tip growth which was restored by complementation with genes from some, but not all, expansin clades. Notably, EXPA13 and EXPA20 failed to complement; they belong to two ancient clades lacking a highly conserved Asp considered essential for expansin activity. Mutation of this Asp in EXPA7 confirmed its requirement for wall enlargement. EXPA-mCherry fusions revealed widely contrasting patterns of subcellular trafficking and wall-binding for different EXPAs. The results demonstrate an essential EXPA requirement for root-hair tip growth and uncover a greater diversity of expansin functions than previously recognized.

Photosynthesis by which plants convert carbon dioxide to sugars using the energy of light is fundamental to life as it forms the basis of nearly all food chains. Surprisingly, our knowledge about its transcriptional regulation remains incomplete. Effort for its agricultural optimization have mostly focused on post-translational regulatory processes1-3 but photosynthesis is regulated at the post-transcriptional4 and the transcriptional level5. Stacked transcription factor mutations remain photosynthetically active5,6 and additional transcription factors have been difficult to identify possibly due to redundancy6 or lethality. Using a random forest decision tree-based machine learning approach for gene regulatory network calculation7 we determined ranked candidate transcription factors and validated five out of five tested transcription factors as controlling photosynthesis in vivo. The detailed analyses of previously published and newly identified transcription factors suggest that photosynthesis is transcriptionally regulated in a partitioned, non-hierarchical, interlooped network.

Bacteria can trigger protein mistranslation to survive stress conditions 1. Mitochondria and plastids evolved from bacteria and therefore also use prokaryotic-type expression machineries to synthesize proteins. However, fungi and animal mitochondria are highly sensitive to mistranslation, which for instance manifests in lethal mitochondrial cardiomyopathy disorder 2. The response in plant cells is unknown. Glutaminyl-transferRNAs (Gln-tRNAGln) of bacteria, mitochondria, and plastids are synthesized indirectly 3,4. Initially, tRNAGln gets charged with glutamate. Subsequently, Gln is produced through trans-amidation by the aminoacyl-tRNA amido-transferase complex GatCAB. Consequentially, affected GatCAB activity results in pools of misloaded Glu-tRNAGln. Here we show that Arabidopsis mutants with decreased GatCAB level provide global insights into organellar mistranslation in plants. Proteomics revealed Gln-to-Glu misincorporation in plastid- and mitochondrially-expressed protein complexes with only modest abundance changes in mutant plants. Plastids appear more lenient to mistranslation as they exhibit much higher Gln-to-Glu misincorporation. Through efficient compensatory mechanisms, mutant plants display surprisingly subtle phenotypes. However, their acclimation to temperature stress differs. Interestingly, wild-type plants under similar stress also have altered Gln-to- Glu misincorporation. Our study shows that the response towards organellar mistranslation varies among eukaryotes. In plants, this knowledge can be used to improve stress tolerance.

Meiotic recombination ensures accurate chromosome segregation and promotes genetic diversity by generating crossovers between homologous chromosomes1. While essential in most sexually reproducing organisms, recombination is variably regulated and can be absent in some lineages, a condition known as achiasmy2. However, obligate achiasmy in both sexes of a sexual species has not been previously documented. Here, we investigate the beak-sedge Rhynchospora tenuis, a holocentric plant with the lowest known chromosome number among flowering plants (n = 2) and inverted meiosis3. Using chromosome-scale genome assemblies from nine accessions, molecular cytogenetics, immunocytochemistry, high-throughput single-gamete sequencing and whole-genome sequencing of controlled crosses, we show that R. tenuis undergoes obligate, genome-wide achiasmy in both male and female meiosis. Despite normal early meiotic axis formation, synapsis fails, crossovers are not detected cytologically or genetically, and univalents persist at metaphase I. Extensive haplotype-specific accumulation of transposable elements (TEs) generates segregation distortion (e.g. meiotic drive), favouring the transmission of larger, TE-rich chromosomes. Remarkably, sexual reproduction is retained with fertilisation producing viable seeds only when translocation-compatible gametes meet, indicating strong post-meiotic selection that eliminates incompatible homozygous combinations. As a result, all surviving offspring are genetically identical to the maternal genotype, effectively restoring heterozygosity each generation and mimicking clonal reproduction. We propose that the combined effects of recombination loss, low chromosome number, holocentricity, inverted meiosis, and selective transmission of longer chromosomes enable faithful segregation and clonal-like inheritance despite sexual reproduction. These findings challenge the boundary between sex and clonality, revealing a unique evolutionary strategy linking genome architecture, recombination loss, and transmission bias.

Climate change-enforced drought stress conditions and diseases caused by pathogens often co-occur and represent one of the greatest challenges in plant science1-3. Wilt pathogens that colonize water-conducting plant tissues can aggravate the problem and affect a wide range of agricultural crops4,5. However, whilst fungal infections with the vascular pathogen Verticillium dahliae are typically associated with wilt symptoms due to occlusion of xylem tissues, the related V. longisporum induces de novo formation of tracheary elements6,7. This promotes not only its virulence but also enables elevated water storage capacity of the infected host plant and resilience against drought stress conditions6,7. Here, we identified a secreted Verticillium protein, TRANSDIFFERENTIATION EFFECTOR (TRADE), which triggers cell identity switches of bundle sheath cells into tracheary elements. We show that TRADE interacts with the intracellular plant protein VARICOSE (VCS), a conserved component of the mRNA turnover machinery and ortholog of the metazoan protein ENHANCER OF DECAPPING 4 (EDC4/HEDLS/Ge-1)8. The TRADE-VCS interaction induces SUCROSE NON-FERMENTING 1 (SNF1)-related protein kinase (SRK)-dependent phosphorylation and thus dysfunction of VCS. This affects the abundance of mRNAs encoding master regulators of xylem differentiation and demonstrates how a single pathogen effector protein triggers complex tissue-specific developmental reprogramming and thus promotes abiotic stress resilience.

Streptophytes constitute a major organismal clade comprised of land plants (embryophytes) and several related green algal lineages. Their seemingly well-studied phylogenetic diversity was recently enriched by the discovery of Streptofilum capillaum, a simple filamentous alga forming a novel deep streptophyte lineage in a two-gene phylogeny1. A subsequent phylogenetic analysis of plastid genome-encoded proteins resolved Streptofilum as a sister group of nearly all known streptophytes, including Klebsormidiophyceae and Phragmoplastophyta (Charophyceae, Coleochaetophyceae, Zygnematophyceae, and embryophytes)2. In a stark contrast, another recent report, published in Current Biology by Bierenbroodspot et al.3, presented a phylogenetic analysis of 845 nuclear loci resolving S. capillatum as a member of Klebsormidiophyceae, nested among species of the genus Interfilum. Here we demonstrate that the latter result is an artefact stemming from an unrecognized contamination of the transcriptome assembly from S. capillatum by sequences from Interfilum paradoxum. When genuine S. capillatum sequences are employed in the analysis, the position of the alga in the nuclear genes-based tree fully agrees with the plastid genes-based phylogeny. The "intermediate" phylogenetic position of S. capillatum predicts it to possess a unique combination of derived and plesiomorphic traits, here exemplified, respectively, by the "Rho of plants" (ROP) signaling system and the cyanobacteria-derived plastidial transfer-messenger ribonucleoprotein complex (tmRNP). Our results underscore S. capillatum as a lineage pivotal for the understanding of the evolutionary genesis of streptophyte, and ultimately embryophyte, traits.

Acclimation to high temperature increases plants tolerance of subsequent lethal high temperatures1-3. Although epigenetic regulation of plant gene expression is well studied, how plants maintain a memory of environmental changes over time remains unclear. Here, we show that JUMONJI (JMJ) proteins4-8, demethylases involved in histone H3 lysine 27 trimethylation (H3K27me3), are necessary for Arabidopsis thaliana heat acclimation. Acclimation induces sustained H3K27me3 demethylation at key HEAT SHOCK PROTEIN (HSP) loci by JMJs, poising the HSP genes for subsequent activation. Upon sensing heat after a 3-day interval, JMJs directly reactivate HSP genes. Finally, jmj mutants fail to maintain heat memory under fluctuating field temperature conditions. Our findings of an epigenetic memory mechanism involving histone demethylases may have implications for environmental adaptation of field plants.

C4 and CAM photosynthesis have repeatedly evolved in plants over the past 30 million years. Because both repurpose the same set of enzymes but differ in their spatial and temporal deployment, they have long been considered as distinct and incompatible adaptations. Remarkably, Portulaca contains multiple C4 species that perform CAM when droughted. Spatially explicit analyses of gene expression reveal that C4 and CAM systems are completely integrated in P. oleracea, with CAM and C4 carbon fixation occurring in the same cells and CAM-generated metabolites likely incorporated directly into the C4 cycle. Flux balance analysis corroborates the gene expression and predicts an integrated C4+CAM system under drought. This first spatially explicit description of a C4+CAM photosynthetic metabolism presents a new blueprint for crop improvement.

Large language models (LLMs) are rapidly permeating scientific research, yet their capabilities in plant molecular biology remain largely uncharacterized. Here, we present MO_SCPLOWOC_SCPLOWBO_SCPLOWIC_SCPLOWPO_SCPLOWLANTC_SCPLOW, the first comprehensive benchmark for evaluating LLMs in this domain, developed by a consortium of 112 plant scientists across 19 countries. MO_SCPLOWOC_SCPLOWBO_SCPLOWIC_SCPLOWPO_SCPLOWLANTC_SCPLOW comprises 565 expert-curated multiple-choice questions and 1,075 synthetically generated questions, spanning core topics from gene regulation to plant-environment interactions. We benchmarked seven leading chat-based LLMs using both automated scoring and human evaluation of open-ended answers. Models performed well on multiple-choice tasks (exceeding 75% accuracy), although most of them exhibited a consistent bias towards option A. In contrast, expert reviews exposed persistent limitations, including factual misalignment, hallucinations, and low self-awareness. Critically, we found that model performance strongly correlated with the citation frequency of source literature, suggesting that LLMs do not simply encode plant biology knowledge uniformly, but are instead shaped by the visibility and frequency of information in their training corpora. This understanding is key to guiding both the development of next-generation models and the informed use of current tools in the everyday work of plant researchers. MO_SCPLOWOC_SCPLOWBO_SCPLOWIC_SCPLOWPO_SCPLOWLANTC_SCPLOW is publicly available online in this link.

In plant development, key receptor kinases are often active in disparate cell types, with each requiring vastly different signalling outputs. The ERECTA (ER) receptor kinase and its homologs ERL1 and ERL2 exemplify this pleiotropy. In Arabidopsis, they influence stomatal patterning, shoot meristem function, ovule morphogenesis, xylem fiber differentiation, and cell division in the vascular cambium1-6. Such diverse expression and functionality raises the question of how ER signalling can specify such distinct cell behaviours. One mechanism is via cell-type specific interactions with co-receptors, ligands, or other proteins that modulate signalling. However, little is known about ER interactors in the vascular cambium, a bifacial stem cell niche that generates phloem and xylem (Figure 1A). Combinatorial mutations between ER, ERL1 and ERL2 and receptor kinases of a second family, PXY, PXL1, and PXL2, show severe cambial defects5,7, but the mechanism underpinning these phenotypes is not known. Here we discovered that PXY proteins form protein complexes with ER and ERL2. PXY signalling can be manipulated by altering levels of its cognate ligand, TDIF. In genetic analysis, plant lines in which TDIF levels were altered had dramatic phenotypic changes that required the presence of ER or ERL2. Our results demonstrate that PXY signalling mediated cambium regulation depends on ER signalling and explains ER function in the cambium. Because the cambium produces xylem, which constitutes the wood in vascular plants, our findings position PXY-ER complexes at the centre of the accumulation of this versatile biomaterial and essential carbon sink. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/594489v1_fig1.gif" ALT="Figure 1"> View larger version (79K): org.highwire.dtl.DTLVardef@289bb6org.highwire.dtl.DTLVardef@6d0fdorg.highwire.dtl.DTLVardef@1829836org.highwire.dtl.DTLVardef@d70b3b_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO PXY forms heterodimers with ER and ERL2 (A) Transverse sections of a wild type hypocotyl showing the region of secondary growth. Black rectangle marks the area of cambium shown in the diagrammatic representation on the lower left. (B-D) Localisation of PXY-CFP (B), ER-YFP (C) and overlap (D) in Nicotiana epidermal cells. (E) FRET signal. (F) Graph showing FRET efficiencies of PXY-CFP and ER/ERL1/ERL2-YFP pairs. (G-H) Coimmunoprecipitation of PXY-FLAG with ER-HA or ERL2-HA and vice versa in Arabidopsis cells. Scales (A) are 50 M. C_FIG

Plants, like other sessile organisms, need to sense many different signals, and in response to them, modify their developmental programs to be able to survive in a highly changing environment. The multistep phosphorelay (MSP) in plants is a good candidate for a response mechanism that integrates multiple signal types both environmental and intrinsic in origin. Recently, ethylene was shown to control MSP activity via the histidine kinase (HK) activity of ETHYLENE RESPONSE 1 (ETR1)1,2, but the underlying molecular mechanism still remains unclear. Here we show that although ETR1 is an active HK, its receiver domain (ETR1RD) is structurally and functionally unable to accept the phosphate from the phosphorylated His in the ETR1 HK domain (ETR1HK) to initiate the phosphorelay to ARABIDOPSIS HISTIDINE-CONTAINING PHOSPHOTRANSMITTERs (AHPs), the next link downstream members in MSP signaling. Instead, ETR1 interacts with another HK ARABIDOPSIS HISTIDINE KINASE 5 (AHK5) and transfers the phosphate from ETR1HK through the receiver domain of AHK5 (AHK5RD), and subsequently to AHP1, AHP2 and AHP3, independently of the HK activity of AHK5. We show that AHK5 is necessary for ethylene-initiated, but not cytokinin-initiated, MSP signaling in planta and that it thus mediates hormonal control of root growth.

The Morelloid clade (black nightshades) is one of the most strongly supported clades within the megadiverse Solanum genus. It comprises 76 globally distributed, non-spiny herbaceous and suffrutescent species. While often erroneously considered poisonous weeds, several species are economically important as orphan crops. The clade is closely related to tomato and potato but, due to a lack of focused breeding efforts, remains a reservoir of genetic diversity for crop improvement. Despite this potential, we lack fundamental knowledge on the evolution of the Morelloid clade. The group includes polyploid species with unknown parental origins--likely reflecting reticulate processes such as hybridization, introgression, and associated backcrossing events. Prior analyses have been unable to disentangle these processes, leaving the mechanisms underlying reticulate evolution in the Morelloid clade poorly understood. Here, we use genome skimming to produce a well-supported maximum likelihood plastid phylogeny from complete circularized plastomes and a coalescent-based species tree from combined Angiosperms353 and conserved ortholog set nuclear markers. Our dataset, composed of previously published data and deep genome skimming from herbarium samples, spans 26 Morelloid species. To investigate patterns of non-treelike evolution, we used a nuclear phylogenetic network, multispecies coalescent simulations, a fused rooted nuclear chloroplast tree, and quantification of nuclear gene tree concordance. We show that incongruence between nuclear and plastid trees is pervasive and cannot be explained by incomplete lineage sorting alone. Instead, our results demonstrate that events consistent with repeated chloroplast capture have shaped the reticulate evolutionary history of the clade, especially among African polyploid and Pan-American diploid lineages.

Arbuscular mycorrhizal fungi (AMF) establish a dynamic and asynchronous symbiosis with a wide range of land plants, involving distinct stages of root colonization and associated cellular responses that co-occur within the same root. Whilst decades of research have significantly advanced our understanding of the plants symbiotic gene repertoire, this spatial and temporal complexity has hindered a detailed dissection of the molecular mechanisms underlying fungal accommodation. Here, we present the first single-nucleus RNA-sequencing (snRNA-seq) dataset of Solanum lycopersicum roots colonized by Rhizophagus irregularis. Unsupervised subclustering of an AM-specific cell population resolves AM-responsive root epidermal cells as well as a developmental gradient of cortical cells across distinct stages of arbuscule formation, unveiling stage-specific transcriptional signatures during AMF colonization. Moreover, using Motif-Informed Network Inference based on single-cell EXpression data (MINI-EX), we put forward candidate transcription factors orchestrating these stage-specific transcriptional programs. Together, our data support novel hypotheses on how diverse plant developmental and physiological processes - including localized cell cycle reactivation and the integration of multiple nutritional cues - are coordinated to facilitate the establishment of a functional symbiosis. As such, this high-resolution dataset serves as a valuable resource for candidate gene prioritization and future reverse genetic studies.