Nature Plants

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.

Plants lack specialized immune cells and instead rely on coordinated cellular responses to restrict pathogen invasion while preserving tissue integrity. How plant immunity spatially organizes these responses remains unclear. Using live-cell reporters in Arabidopsis infected with Pseudomonas syringae, we show that effector-triggered immunity, superimposed on pattern-triggered immunity, establishes a sustained yet spatially confined immune architecture at the infection front. Defense activation persists for days but remains restricted to a narrow ring of cells surrounding viable bacterial microcolonies. Over time, immune activity spreads to adjacent layers, forming a coordinated, multilayered defense zone. This zonation extends beyond transcriptional activation to polarized callose deposition at pathogen-facing cell walls, reinforcing a localized containment boundary that limits pathogen spread. Consistent with previous single-reporter studies, simultaneous visualization of salicylic acid (SA) and jasmonic acid (JA) biosynthesis and response markers reveals a radial hormone gradient, with SA-enriched cells proximal to bacterial colonies and JA-enriched cells in surrounding regions. Individual cells predominantly activate one pathway, indicating that SA-JA antagonism is resolved through spatial compartmentalization across neighboring cells. Together, these findings establish immune zonation as a strategy for robust pathogen containment while minimizing collateral tissue damage. Significance statementPlants lack specialized immune cells and must coordinate defense responses across tissues to contain infection. Although plant immune responses are known to be locally activated, how they are organized across cells to form a stable containment boundary has remained unclear. Using live imaging of fluorescent bacterial microcolonies, we show that plant immunity forms a spatially organized defense zone surrounding viable infection sites. Within this zone, distinct defense activities are arranged in a radial gradient, with salicylic acid-associated responses enriched in cells near the pathogen and jasmonic acid-associated responses in surrounding cells. Rather than being resolved solely within individual cells, antagonistic hormone pathways are separated across neighboring cells. This spatial organization reveals immune zonation as a strategy for confining pathogen spread while preserving tissue integrity.

Chloroplast protein import is essential for photosynthesis, yet whether and how cytosolic signaling pathways dynamically regulate this process remains largely unknown. Here we uncover a signaling module that links mitogen activated protein kinase (MAPK) activity to fine tune the import of small subunit of Rubisco (RbcS) into the chloroplast. We show that MPK3 negatively regulates the cytosolic Raf-like kinase ACTPK1, which directly phosphorylates the transit peptide of RbcS precursor at Thr12. MPK3 directly phosphorylates ACTPK1, attenuating its kinase activity and thereby limiting RbcS transit peptide phosphorylation. Genetic and physiological analyses demonstrate that loss of MPK3 elevates ACTPK1 activity, increases RbcS phosphorylation and enhances Rubisco accumulation and CO2 assimilation. On the other hand, ACTPK1 deficiency compromises these processes and photosynthetic performance. Phospho-mutant analyses further reveal that reversible phosphorylation of the RbcS transit peptide is required for efficient chloroplast import. Together, our findings establish chloroplast protein import as a signaling-regulated process and identify transit peptide phosphorylation a key check point integrating cytosolic MAPK signaling with photosynthetic capacity.

Recombination in polyploid genomes is generally constrained to homologous or homoeologous chromosomes; however, how chromosomal rearrangements influence recombination between chromosomes remains unclear. Here, we demonstrate that large-scale chromosomal rearrangements in the wild relatives of wheat are associated with recombination involving non-homoeologous chromosomes or arms during alien gene introgression under conditions that permit homoeologous recombination mediated by ph1b. Using a wheat chromosome 6A monosomic-induced 6AS*6CL Robertsonian translocation combined with ph1b-mediated recombination, we generated 17 independent recombinants carrying a new stem rust resistance gene, Sr69, from Aegilops caudata chromosome arm 6CL. Unexpectedly, 94.1% (16 of 17) of recombinants resulted from exchanges with wheat group-7 chromosomes rather than with the homoeologous group-6 chromosome. Comparative sequence- and marker-based analyses identified a 67-Mb rearranged interval on Ae. caudata 6CL that corresponds to telomeric regions of the long arms of wheat group-7 chromosomes. Sequence similarity within this interval was quantitatively associated with recombination frequency, with higher similarity corresponding to more frequent translocations. Physical and optical mapping showed that recombination within the rearranged interval generated compensating 7A/6C, 7B/6C, and 7D/6C translocations, whereas recombination outside this region produced non-compensating 6A/6C exchanges. An independent case involving the powdery mildew resistance gene Pm7C showed a similar correspondence between a rearranged 7CL region and preferential introgression into wheat 7DS. Together, these results indicate that ph1b-mediated recombination involving structurally altered chromosomes is driven by local chromosomal structure and sequence similarity rather than strict homoeologous group identity. This provides a mechanistic basis for harnessing untapped beneficial genes from structurally rearranged alien genomes. Significance StatementAlien gene introgression is a powerful strategy for wheat improvement, typically relying on ph1b-mediated recombination between homoeologous chromosomes. The genomic basis and outcomes of introgression from structurally rearranged alien chromosomes remain unclear. Here, we show that ph1b-induced recombination can efficiently target wheat-allosyntenic blocks in rearranged alien genomes, preferentially transferring genes from structurally altered alien segments into their syntenic regions on wheat chromosomes of different homoeologous groups. Crossover formation is governed by extended sequence similarity within corresponding intervals rather than strict collinearity across entire homoeologous chromosomes. As many wild species exhibit extensive genome rearrangement, these findings and methodologies expand access to underexploited genetic diversity embedded within highly rearranged wild genomes for wheat improvement.

Plant immune responses must balance effective pathogen restriction to prevent excessive tissue damage and rely on potentiation between pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). However, how these immune responses are spatially organized across different cell-types and coordinated by intracellular pathways remains incompletely understood. Here, we show that autophagy functions as a central organizer of this spatial immune response during Pseudomonas syringae infection in Arabidopsis thaliana. Combining single-cell transcriptomics, cell-type-specific complementation, and live-cell imaging, we uncover distinct and opposing roles of autophagy across tissues. In guard cells, autophagy promotes pathogen-induced stomatal reopening by supressing abscisic acid (ABA) signaling through selective degradation of the ABA receptor PYL4. In contrast, in mesophyll cells, autophagy restricts immune activation and is required for effective immune execution: its loss enhances expression of the EDS1-PAD4-ADR1 immune pathway but compromises canonical PTI outputs, likely impacting PTI-ETI potentiation. This uncoupling reveals that immune activation alone is insufficient for effective defense. Together, our findings resolve the longstanding ambiguity surrounding the role of autophagy in plant immunity and establish autophagy as a spatial organizer that partitions immune strategies between stomata and mesophyll during bacterial infection.

The evolution of the water-conducting xylem and sugar-conducting phloem tissues were key innovations in land plant evolution, enabling the origin of long-distance transport networks1. In extant vascular plants, phloem and xylem are linked functionally and always occur together2, though their evolutionary origin is unclear. This uncertainty is owed to the greater fossilisation potential of lignified xylem tracheids compared to thin-walled phloem cells3, 4, 5. Therefore, the fossil record of xylem is far more extensive than that of phloem, with the first definitive record of xylem being around 40 million years earlier6 than phloem7. This bias in the fossil record obscures characterisation of the origins of plant vasculature. In this study, this limitation is overcome by re-describing the "phloem-like" tissues of exceptionally preserved plants from the 407-million-year-old Rhynie chert8-15. We report that this tissue differs markedly from the phloem of extant plants, and propose its identification as a tissue of food-conducting cells (FCCs). Major histological differences were observed in the fossil plants, including no evidence for a pericycle, which in extant species delimits vascular from ground tissues, and the FCCs of the Rhynie chert plants were significantly larger in diameter than phloem cells. These differences suggest that early vascular plants lacked true phloem. However, putative sieve pores in the FCCs of Asteroxylon mackiei were identified. This represents to our knowledge the earliest record of sieve pores in the fossil record. Our results suggest an evolutionary scenario in which phloem features assembled gradually within FCCs, asynchronous to the evolution of xylem.

Understanding why sex chromosomes repeatedly evolve recombination suppression, gene loss, and repeat accumulation remains a central challenge in evolutionary genomics. Plant sex chromosomes may be particularly informative, because they have often evolved recently from hermaphroditic ancestors. We studied the sex-linked region of the dioecious annual Mercurialis annua using new long-read genome assemblies of an XX female and a YY male, a published female assembly, linkage maps, and population-genomic data from several Mercurialis species. We identify two discrete nested evolutionary strata on the Y chromosome of diploid M. annua. A young stratum was generated by a large inversion and shows little degeneration, whereas an older stratum nested within it exhibits substantial gene loss, transposable-element accumulation, insertion of paralogous gene copies, and elevated X-Y sequence divergence. These findings indicate that recombination suppression evolved in at least two stages, with a recent inversion expanding an older non-recombining region. Comparative analyses among several Mercurialis species further show that the extent of sex-linked differentiation varies markedly among them. We also identify APRR7 as the only gene showing consistent male-specific inheritance across the genus; this gene is a strong candidate master sex-determination gene. Together, our results refine the structure and gene content of the sex-linked region in M. annua and contribute to our understanding of the diversity of sex chromosomes in plants.

Identifying plant disease resistance proteins remains challenging, particularly for cell-surface receptors that perceive apoplastic pathogen effectors through transient or indirect interactions. Here, we establish effector-centred proximity-dependent labelling using TurboID as a protein-level approach to identify immune receptors and guarded host targets in planta. We fused three apoplastic effectors, Avr2 and Avr4 from Fulvia fulva and XEG1 from Phytophthora sojae, to TurboID and transiently expressed these fusion proteins in leaves of Nicotiana benthamiana and tomato (Solanum lycopersicum). The fusions significantly biotinylate their matching receptors, including Cf-4 by Avr4-TurboID and Cf-2 by Avr2-TurboID, as well as the guarded virulence target of Avr2, the Rcr3 protease, demonstrating that both direct and indirect recognition systems can be captured. Application of this approach to XEG1 revealed SlEix1 as the functional ortholog of NbRXEG1. Functional assays and structural modelling support SlEix1 as a signalling-competent receptor contributing to XEG1-triggered immunity. Together with previous studies, these findings position the tomato EIX locus as a multi-effector immune hub encoding closely related receptor-like proteins with distinct ligand specificities. Collectively, this study establishes effector-TurboID-mediated proximity-dependent labelling as a versatile approach for identifying cell surface plant immune receptors and apoplastic virulence targets, providing a scalable route to accelerate resistance gene discovery in crop species.

Plant amino acids function as both pathogen nutrients and essential drivers of systemic immunity. The regulation of amino acid homeostasis through transporters is a essential for mounting a robust and coordinated immune response in plants during pathogen infection. Using systems biology and integrative network science, we investigated bacterial virulence in Arabidopsis. By comparing gene coexpression networks of effector-triggered susceptibility (ETS) and pattern-triggered immunity (PTI), we uncovered a plant amino acid-related processes specifically linked to ETS. Integrating time-series transcriptomics, protein-DNA interactions, and mathematical simulations, we identified ANAC046 as a transcriptional regulator of amino acid processes during ETS. Single-cell RNA-Seq revealed that amino acid transporters are primarily expressed in companion and mesophyll cells, while functional validation confirmed ANAC046s roles in promoting susceptibility. Further integration of transcriptome and interactome data showed that amino acid-related genes interact with key immune hub proteins. Network topology analysis enabled the characterization of seven additional genes involved in plant defense. To support community-wide research, we developed MIData, an open-access platform for pre-analyzed Arabidopsis networks. Together, our findings demonstrate the power of systems-level approaches in uncovering hierarchical regulatory mechanisms underlying plant susceptibility to bacterial pathogens.

Strigolactones (SLs) are plant hormones regulating shoot branching and symbiotic interactions, but their trace-level abundance limits research and applications. Here, we optimized a Nicotiana benthamiana transient expression system for SL production by tuning agroinfiltration parameters and co-expressing rate-limiting carotenoid biosynthetic genes. Overexpression of Zea mays PSY1 or an Arabidopsis PSY-GGPS11 fusion increased carlactone production over 2-fold and enhanced downstream SL accumulation. Using this platform, we discovered that sorghum cytochrome P450 SbCYP728B35 catalyzes conversion of 5-deoxystrigol to sorgolactone, revealing a previously unknown function. These results establish metabolic engineering of precursor supply as an effective strategy for boosting SL production and demonstrate N. benthamiana as a robust system for pathway elucidation and biotechnological synthesis of bioactive strigolactones.

The plant kingdom exhibits a wide range of phenotypic variation in capacity to regenerate tissues and organs, from whole-plant vegetative propagation via cuttings, to recalcitrance even under optimized tissue culture. Currently, the molecular pathways underpinning this phenotypic variation are poorly understood. Here, we report that Arabidopsis mutants of the DNA demethylase pathway exhibit dramatically enhanced regeneration and the ability to propagate whole plants from cuttings without the use of exogenous hormones. Vegetatively propagated plants possess a shared regeneration signature of de novo DNA methylation gains at the transcription start sites of many genes, including approximately 30 genes involved in cellular pluripotency and tissue regeneration. These methylation changes can be inherited through sexual reproduction and result in exacerbated transcriptomic changes. We propose that loss of the DNA demethylase pathway unlocks a path on the epigenetic landscape towards increased pluripotency and tissue-culture-free regeneration.

The plant cuticle is a key adaptation acquired during the colonization of land. It forms a hydrophobic barrier at the interface with the environment, fulfilling essential protective and developmental functions. Despite its evolutionary significance and central role in land plant biology, the determinants that drove the emergence of the cuticle remain poorly understood. Here, we show that the CUTIN SYNTHASE (CUS) enzyme family, which synthesises the lipidic polyester that forms the structural framework of the cuticle in flowering plants, originated in a common ancestor of land plants, concomitant with terrestrialization. Using the moss Physcomitrium patens, we further demonstrate that CUS function is conserved among land plants. Inactivation of CUS genes disrupts gametophore development, the first tissue forming a cuticle during the moss life cycle, and compromises cuticle integrity. We also show that P. patens CUS enzymes localize to the apoplast, where they mediate the formation of a 10,16-dihydroxyhexadecanoic acid polyester using 2-mono-(10,16-dihydroxyhexadecanoyl)glycerol as substrate. Overall, our results reveal the conservation of CUS catalytic and physiological functions over 500 million years and support a pivotal role for this enzyme family in the emergence of the cuticle in an ancestral land plant during terrestrialization. SIGNIFICANCEThe cuticle is a hallmark of land plants that fulfills essential roles, ranging from protection to development. Elucidating the mechanisms underlying its emergence and formation therefore has the potential to reveal fundamental aspects of land plant evolution and biology. Here, we show that the CUTIN SYNTHASE (CUS) enzyme family, which catalyzes the formation of the cuticle framework in flowering plants, arose in an ancestor of land plants during terrestrialization. Using the moss Physcomitrium patens, we further demonstrate that CUS function has been conserved for 500 million years across bryophytes and tracheophytes. We propose that the emergence of the CUS family was a key event in establishing the plant cuticle during terrestrialization.

Soybean cyst nematode (SCN) is the most destructive pathogen of soybean, yet the cellular basis of host resistance remains poorly understood. Here, we present a high-quality, cell-type-resolved atlas of root responses during early SCN infection in the highly resistant genotype PI437654, capturing transcriptional states across all major tissues, including rare syncytial cells. Our analyses reveal that resistance is mediated not by a localized defense but by coordinated, multicell reprogramming spanning invasion layers, vascular tissues, and feeding site-associated cells. We identify the vascular cambium as the primary cellular origin of SCN-induced syncytia, resolving a long-standing question in nematology. Mechanistically, resistance arises from disruption of key processes required for feeding site establishment, secretory stress via imbalanced vesicle trafficking, suppression of endoreduplication to prevent hypertrophic syncytial growth, and activation of autophagy to maintain cellular homeostasis. Spatially organized hormone signaling networks, including jasmonic acid, salicylic acid, and ethylene pathways, further reinforce defense, with GmJAZ1 functioning as a central regulator of JA-SA crosstalk. Collectively, PI437654 enforces resistance by targeting host cell identity, nutrient sink formation, and sustained parasitism, deploying a multilayered, tissue-specific defense strategy. This study provides a mechanistic, systems-level framework for SCN resistance and establishes a single-cell resource capturing rare root cell states, offering actionable targets for engineering durable nematode resistance. Key pointsO_LISoybean cyst nematode (SCN) is the most destructive pathogen of soybean worldwide, yet the cellular basis of early host responses and feeding site initiation remains poorly understood. C_LIO_LIUsing single-nucleus RNA sequencing (snRNA-seq), we generated a cell-type-resolved atlas of early SCN infection in roots of a unique and highly resistant soybean genotype PI437654. Trajectory analysis integrated with syncytium marker genes revealed that cambium cells are selectively targeted as the cellular origin of syncytium formation. C_LIO_LISCN infection triggers extensive cell-type-specific transcriptional reprogramming, particularly in vascular tissues (xylem, phloem, and cambium), involving pathways related to cell cycle and endoreduplication, vesicle trafficking, autophagy, and phytohormone signaling. C_LIO_LIFunctional validation demonstrated enhanced autophagy activation in infected roots via increased GFP-GmATG8a-labeled autophagic puncta, while overexpression of the jasmonic acid regulator GmJAZ1 significantly enhanced SCN resistance in susceptible soybean. C_LIO_LITogether, these findings define the cellular origin of SCN-induced syncytia and reveal coordinated cell-type-specific defense programs, providing a mechanistic framework for engineering durable resistance to SCN. C_LI

Macroautophagy is a conserved intracellular catabolic process in eukaryotes that participates in chloroplast degradation, through the selective breakdown of chloroplast components. Selective autophagy of membrane-bound organelles typically requires receptors that bridge organelle membranes and pre-autophagosomal structures. Here we identify OEP24.1 as a new receptor in the selective chloroplast piecemeal autophagy, supporting the degradation of stromal proteins. We found that the {beta}-barrel protein OEP24.1 is located at the outer membrane of plastid envelopes and on bodies budding off plastids into the cytosol and containing stroma proteins. OEP24.1 interacts physically with ATG8 autophagy proteins in a UIM dependent manner. OEP24.1-GFP and RFP-ATG8 colocalize with in mobile autophagosome-like puncta in the cytosol and in autophagic bodies within the vacuole. Delivery of OEP24.1 to vacuole lumen is dependent on active autophagy. OEP24.1 controls carbon allocation at the whole plant level, carbon concentrations in flowering stems and xylem composition. These phenotypes can be explained by the role of OEP24.1 in metabolite diffusion across the chloroplast envelope, and by its involvement in the facilitation of chloroplast quality control through piecemeal autophagy.

Chloroplast HSP70 is an essential component of the plastid proteostasis network, supporting protein folding, complex assembly and disassembly, and stress acclimation. Despite extensive genetic evidence for its essentiality, the cellular consequences of reduced chloroplast HSP70 activity remain poorly defined. Here, we investigated the function of the sole chloroplast HSP70 in Chlamydomonas reinhardtii, HSP70B, using an inducible artificial microRNA approach that reduced HSP70B abundance to below 30% of wild-type levels. HSP70B depletion resulted in cell division arrest and extensive proteome remodeling, characterized by strong upregulation of proteins involved in chloroplast protein quality control and membrane remodeling. Notably, this response was accompanied by increased abundance of protein quality control components in the endoplasmic reticulum, cytosol, and mitochondria, indicating pronounced proteostasis cross-talk between cellular compartments. In contrast, chloroplast and cytosolic ribosomes, photosynthetic and respiratory protein complexes, and central metabolic enzymes were broadly depleted, consistent with a collapse of cellular proteostasis. At the ultrastructural level, HSP70B-depleted cells exhibited lesions at thylakoid membrane conversion zones previously described in VIPP1-depleted cells. Accordingly, higher-order oligomeric forms of VIPP1 accumulated, and cells displayed extreme sensitivity to high-light stress. These findings confirm HSP70B as a key regulator of VIPP1 oligomer dynamics and highlight its central role in coordinating chloroplast membrane remodeling with cellular proteostasis in Chlamydomonas. One-sentence summaryDepletion of chloroplast HSP70B causes cell division arrest, proteostasis collapse, impaired VIPP1 oligomer dynamics with aberrant thylakoid structures, and increased light sensitivity.

Unlike the stable transcription of plant genes with CG gene body methylation alone, genes with methylation in TE-like CHG and CG contexts are poorly transcribed and often missanotated. In contrast, here we describe a set of TE-like methylated genes that are maternally demethylated and expressed toward the extreme high end of the spectrum in endosperm. They are enriched for short, secreted proteins, and about a third encode zeins, the major seed storage proteins of maize. Consistent with their dynamic expression in endosperm, they acquire either activating or repressive gene regulatory modifications when demethylated but are heterochromatic when methylated in other tissues. The majority are expressed both maternally and paternally, but a subset whose methylation/demethylation extends upstream of gene bodies into promoters are strongly imprinted. These and other data indicate that TE-like methylation and associated heterochromatin can be a signature of broad silencing but exceptionally high and specific gene expression in either pollen or endosperm.

AO_SCPLOWBSTRACTC_SCPLOWZizania palustris (Northern Wild Rice) is an aquatic grass native to North America and a crop wild relative of Oryza sativa with ecological, cultural, and agricultural significance. Here, we present a transcriptomic atlas spanning 20 tissues across six major developmental stages. Seed tissues showed shifts in abscisic acid, gibberellin, and ethylene pathways that define the hormonal basis of deep dormancy in this recalcitrant species and its release. Leaf development showed stage-specific reprogramming, from hypoxia-responsive programs in submerged tissues to cell wall remodeling and redox regulation during aquatic-aerial transitions, with photosynthesis and carbohydrate metabolism defining flag leaves and SRG1 divergence emerging as a defining feature of leaf development in Z. palustris. Reproductive tissues expressed duplicated homologs of well-recognized shattering genes with divergent regulation, consistent with subfunctionalization after whole-genome duplication. These findings provide new insight into traits underlying ecological adaptation and domestication in Z. palustris and related grasses. CORE IDEASO_LIA first transcriptomic atlas for Northern Wild Rice maps gene expression across 20 tissues and six developmental stages, providing a foundational functional genomics resource for Zizania palustris. C_LIO_LISeed dormancy and release are driven by coordinated hormone reprogramming, with shifts in ABA, GA, and ethylene pathways across whole seed, embryo, and endosperm. C_LIO_LILeaf development is defined by aquatic-to-aerial transcriptional transitions, moving from hypoxia-responsive programs in submerged tissues to cell wall remodeling, redox regulation, and photosynthesis/metabolism in aerial and flag leaves. C_LIO_LIWhole-genome duplication underlies regulatory divergence in domestication traits, as duplicated homologs of canonical seed shattering genes show paralog- and tissue-specific expression consistent with subfunctionalization. C_LIO_LIThe atlas identifies tissue-specific modules and stable housekeeping candidates, enabling improved experimental design (e.g., expression normalization) and accelerating candidate prioritization for breeding, GWAS/eQTL, and trait discovery. C_LI PLAIN LANGUAGE SUMMARYNorthern Wild Rice (Zizania palustris) is an aquatic grass native to North America that is important for ecosystems, agriculture, and Indigenous cultures. In this study, we created a detailed gene expression map across 20 different tissues and six stages of plant development. We found that seeds strongly regulate plant hormones that control dormancy, helping explain why Northern Wild Rice seeds remain dormant for long periods and how they eventually germinate. Leaves showed clear changes in gene activity as plants moved from underwater growth to above-water growth, shifting from low-oxygen stress responses to processes that support photosynthesis and structural strength. In flowers, we identified duplicated genes involved in seed shattering that are regulated differently, likely due to past genome duplication events. Together, these results improve our understanding of how Northern Wild Rice is adapted to aquatic environments and how key traits relevant to domestication have evolved.

Durable resistance to soil-borne pathogens remains elusive in cereals, partly because susceptibility (S) genes that facilitate root infection have not been identified in monocots. In the model legume Medicago truncatula, the SCAR/WAVE complex member MtAPI functions as a root S-gene for microbial invasion. Whether SCAR gene associated susceptibility function is conserved in monocots, and whether SCAR gene inactivation can enhance root resistance in cereals, remains unknown. Here, we identify and characterize three SCAR genes in barley: HvSCAR-A, HvSCAR-B, and HvSCAR-C. Cross-species complementation assays indicate that HvSCAR-B and HvSCAR-C are functionally similar to MtAPI. While hscar-b and hvscar-c single mutants exhibited no major growth defects, hvscar-a mutants showed strongly reduced seed production, and a hvscar-b/c double mutant displayed shorter root hairs. Notably, the hvscar-b/c double mutant exhibited increased resistance to the hemibiotrophic pathogen Phytophthora palmivora but greater colonization by the symbiotic arbuscular mycorrhizal fungus Funneliformis mosseae, underscoring a complex role in plant root - microbe interactions. Our findings reveal a conserved susceptibility function of SCAR genes in monocots and identify api monocot homologs as promising targets for engineering disease resistance in cereals. This study offers new insights into SCAR protein functional diversification and its potential for improving root health in crop plants.

Thylakoid membranes are indispensable for oxygenic photosynthesis, yet the mechanisms that protect these membranes from photooxidative damage remain poorly understood. By screening previously uncharacterized proteins induced during the chloroplast unfolded protein response, we identify VIA1 as an essential factor for preserving thylakoid integrity under high light in the model green alga Chlamydomonas reinhardtii. Loss of VIA1 causes hypersensitivity to photo-oxidative stress and rapid thylakoid swelling. VIA1 localizes to thylakoid membranes and directly binds Vesicle-Inducing Protein in Plastids 1 (VIPP1), an ESCRT-III-like protein essential for thylakoid biogenesis and remodeling. Structure-guided mutagenesis shows that this interaction is required for VIA1 function and is mediated by a winged-helix domain interface reminiscent of ESCRT-II/ESCRT-III binding mode. VIA1 orthologs from cyanobacteria and land plants rescue the Chlamydomonas via1 mutant phenotype, and disruption of VIA1 in Synechocystis sp. PCC 6803 impairs growth, especially under light stress. Together, these findings establish VIA1 as an evolutionarily conserved protein that contributes to thylakoid membrane homeostasis via its interaction with VIPP1. Significance StatementFrom cyanobacteria to land plants, all organisms performing oxygenic photosynthesis rely on thylakoid membranes to capture light and and produce oxygen. Yet these membranes are highly susceptible to environmental stress, particularly excess light, which causes oxidative damage to membrane lipids and proteins. How thylakoid integrity is maintained under these conditions remains a key open question. Here we identify VIA1 as a conserved factor required for maintaining thylakoid membrane structure under high light. VIA1 interacts with VIPP1, an ESCRT-III-like protein essential for thylakoid biogenesis, through a functionally indispensable interface reminiscent of ESCRT-II/ESCRT-III binding mode. The conservation of the VIA1-VIPP1 module across photosynthetic prokaryotes and eukaryotes suggests it arose early in the evolution of oxygenic photosynthesis and has been maintained ever since.

The genomic foundation model Evo 2 enables zero-shot variant effect prediction. Here, we evaluate its performance using Arabidopsis thaliana reproductive barrier genes with experimentally confirmed gain- and loss-of-function variants, and show that Evo 2 distinguishes functionally impactful variants. Together with a sign-reversal amplitude metric that recovers a variant missed by standard scoring, these results highlight the potential of Evo 2 for causal variant prioritization in plant GWAS and QTL mapping.