Nature Plants

Plants acquire iron using two canonical mechanisms: reduction-based uptake (Strategy I) and chelation-based uptake (Strategy II). Although Strategy II is characteristic of grasses, genes associated with chelated-metal transport occur broadly across plant lineages, obscuring how this pathway evolved. Here, we reconstruct the evolutionary history of Yellow Stripe-Like (YSL) transporters and Nicotianamine Synthase (NAS) across Archaeplastida and their closest non-plant homologs. Phylogenomic, distributional, and structural analyses reveal pronounced temporal uncoupling between these gene families. YSL most likely originated early in Viridiplantae and represents the deepest evolutionary module of the chelated-metal transport system. In contrast, NAS appeared much later through independent horizontal gene transfer events from fungi into euphyllophytes and specific moss lineages. This timing indicates that YSL-mediated transport initially functioned independently of nicotianamine, implying ancestral use of alternative siderophores. A pronounced expansion of YSL genes in Poaceae coincides with the emergence of canonical Strategy II, suggesting that this pathway arose by exaptation of pre-existing chelated-metal transport mechanisms.

Perennial crops follow different domestication trajectories from annuals, yet the molecular basis of slow-variable domestication--subtle tuning of conserved regulatory hubs--remains poorly characterized. We reconstructed the evolutionary history of the chloroplast kinase ABC1K7 across 9 seed plant species spanning [~]350 Myr, employing PAML codon models, IQ-TREE robust codon models, and protein-level phylogenetic inference, with AlphaFold2 structural modeling. ABC1K7 was under extreme purifying selection ({omega} = 0.073-0.104) across all seed plants. In coconut, a single Y[->]F substitution at residue 652--located >30 [A] from the catalytic core in a predicted intrinsically disordered region--represents the only non-synonymous change differentiating coconut from 7 of 8 angiosperm orthologs, and exhibits perfect co-segregation with domestication traits across a 17-year breeding panel (n = 327). These findings provide population-level evidence consistent with the slow-variable domestication model, identifying ABC1K orthologs as targets for perennial crop improvement.

Whole-genome duplications (WGDs) reshape plant genomes by generating redundancy, after which lineage-specific architectures emerge through fractionation, gene loss and rearrangement. How specialized metabolic pathways remain functionally integrated after such large-scale restructuring remains poorly understood. This problem is especially relevant for biosynthetic gene clusters (BGCs), which physically organize specialized-metabolism genes yet can be disrupted by post-duplication rearrangement. Here, we present the first chromosome-level genomes for Loganiaceae, including near telomere-to-telomere assemblies of Strychnos ignatii and S. pubescens, together with a draft genome of the extinct species S. ridleyi. Following a lineage-specific WGD, the two extant Strychnos species evolved contrasting genome-evolutionary trajectories and metabolite profiles: S. ignatii shows expansion of monoterpenoid- and monoterpene indole alkaloid (MIA)-associated gene families and strychnine-type MIA dominance, whereas S. pubescens exhibits elevated transposable element activity associated with DNA-binding with one finger (DOF)-linked regulatory rewiring and broader sesquiterpenoid- and triterpenoid-rich chemistry. Crucially, both species retain active strychnine biosynthesis despite fragmentation of a deeply conserved alkaloid BGC in MIA-producing Gentianales, revealing how pathway function can persist after disruption of ancestral BGC architecture. Comparative metabolomic and transcriptomic pathway analyses indicate norfluorocurarine oxidase (NO) as a major divergence point associated with strychnine accumulation. Promoter analyses, yeast one-hybrid assays, and electrophoretic mobility shift assays support a model in which S. ignatii retains the canonical jasmonate-responsive MYB, MYC2/bHLH, and AP2/ERF cis-regulatory module at NO, whereas the orthologous S. pubescens promoter shows reduced capacity to recruit these activators and instead exhibits a DOF-associated architecture. Together, our results show that WGD can decouple physical cluster architecture from pathway function, allowing specialized metabolic pathways to remain active while divergent chemical phenotypes evolve through lineage-specific combinations of coding-space expansion and transposable-element-associated cis-regulatory rewiring.

Cell polarity is an ancient organizing principle across kingdoms. As in animal epithelial cells, plant cells asymmetrically distribute proteins to establish functionally distinct membrane domains. In roots, radial polarity distinguishes inner and outer cell surfaces and supports directional nutrient transport, yet its molecular basis remains poorly understood. Here, we show that the leucine-rich repeat receptor-like kinases CaMRLK and IRK occupy complementary lateral plasma membrane domains in Arabidopsis thaliana roots. Polarity-guided proximity labeling identified previously uncharacterized proteins associated with inner- and outer-lateral domains. Clade VII LRR-RLKs, protein S-acyltransferases, SICK, IRKI1, and a distinct group of NPH3/RPT2-LIKEs assemble into the Lateral Protein Cluster (LPC) through multivalent interactions. LPC components are conserved across land plants, and disruption of NRL function impairs morphogenesis in Arabidopsis and Marchantia polymorpha. Together, these findings establish the LPC as an evolutionarily conserved molecular machinery linking radial cell polarity to plant morphogenesis.

Highly diversified specialized metabolism enables plant communication with pollinators, herbivores, and protectors1-4. Its chemodiversity, under which evenness, richness and variation is summarized5-7, includes many compounds without known function1-4 and presents an evolutionary conundrum about how and what is selected for8,9. Due to its complexity, it is frequently unknown how it is encoded in genomes. To produce population level chemodiversity, the traits need to allow for highly chemodiverse and highly specific individuals in the same population. Here we use metabolomics, transcriptomics, and genomics combined with field analyses and functional assays of monoterpene synthases in the Asteraceae Tanacetum vulgare (tansy) and identify forces which produce high population level chemodiversity: selection for product specificity in enzymes, loss-of-expression alleles, absence variation, and specialized metabolism islands drive individuals towards low chemodiversity while unlinked enzyme loci, expression variation alleles, presence variation, and de novo enzyme evolution enable high individual chemodiversity. Since the molecular data suggests selection for mechanisms that increase chemodiversity itself at the population level, the screening hypothesis which posited plants produce a reservoir of diverse chemicals prior to selection8 should be replaced by a chemodiversity selection hypothesis. The results demonstrate that, in addition to plant protection via individual chemicals with known targeting mechanisms for predators, being different from your neighbors even if you are closely related is likely an important element in plant protection.

Plants have evolved unconventional shoot systems with a "fuzzy" character that blurs organ boundaries, but the developmental programs driving this morphological diversity remain a mystery. One-leaf plants of the genus Monophyllaea are a striking example of this diversity: they develop a single indeterminate cotyledon instead of a conventional shoot system to form a unique structural unit termed a phyllomorph. Here, we integrate tissue-specific and single-nucleus transcriptomics with spatial gene expression analyses to characterize the meristems underlying this developmental system. The Monophyllaea-specific meristem of the phyllomorph retains a conserved shoot apical meristem-like transcriptional core but has a leaf lamina program superimposed. This chimeric transcriptional state integrates normally distinct developmental programs alongside altered phytohormone regulation. The one-leaf morphology emerges through the rewiring of conserved meristem regulatory networks rather than the passive suppression of meristem activity. The findings highlight the remarkable plasticity of developmental modules in plant morphological evolution.

Fluctuating light strongly limits photosynthetic efficiency in plants, yet the mechanisms coordinating stomatal dynamics with rapid photosynthetic induction remain incompletely understood. Here, through a forward physiological screen in Arabidopsis, we identify the abscisic acid (ABA) transporters NPF2.4 and NPF2.5 as regulators of photosynthetic responses to fluctuating light. Loss-of-function npf2.4 and npf2.5 mutants exhibited accelerated stomatal opening and photosynthetic induction during light transitions, resulting in enhanced biomass accumulation and seed yield without compromising long-term drought tolerance. NPF2.4 and NPF2.5 mediated ABA uptake in yeast and were predominantly expressed in the root pericycle and cortex/epidermal tissues, respectively. Reciprocal grafting, xylem sap ABA measurements, and ABA treatment to the roots demonstrated that both transporters regulate root-to-shoot ABA transport. Our findings reveal that root-derived ABA modulates stomatal dynamics and photosynthetic efficiency under fluctuating light, establishing long-distance hormone transport as a key regulator of plant carbon gain in dynamic environments.

Precise quantitative and spatial control of plant gene expression is typically attributed to cis-regulatory elements in promoters and other non-coding sequences. The extent to which exon-encoded regulatory information shapes plant gene expression and how remains unclear. Here we used BRASSINOSTEROID INSENSITIVE 1 (BRI1) as a model locus and found that it contains an exonic enhancer (EE), which is essential to establish the spatial BRI1 expression pattern. Its disruption restricts BRI1 expression and impairs BRI1-dependent root growth, linking exon-encoded regulatory information and development. The BRI1 EE acts in concert with its promoter, and related receptor kinase genes likewise harbor regulatory information within their coding sequences. Genome-wide surveys show that candidate EEs are associated with highly connected chromatin interaction networks and transcriptionally active loci. Moreover, species comparisons suggest that common features of exon-encoded regulatory information extend across diverse plant lineages. Thus, exon-encoded regulatory information is a vital component of plant gene regulation.

Cellulose synthase complexes build the load-bearing cellulose microfibrils of plant cell walls, yet how the abundance of their catalytic CELLULOSE SYNTHASE A (CESA) subunits is maintained remains unclear. Here, we used multi-bait TurboID proximity labelling with ten cellulose-synthesis-associated baits and six subcellular controls to define a high-confidence cellulose synthase neighbourhood. Stringent spatial and recurrence-based filtering yielded a core network of 119 interactions among 44 proteins and identified three members of the conserved Bcl-2-associated athanogene (BAG) family as previously unrecognised regulators of cellulose synthase homeostasis. BAG1-3 associated with primary-wall CESAs in reciprocal proximity-labelling experiments. Arabidopsis bag mutants showed reduced cellulose accumulation, hypersensitivity to cellulose-synthesis inhibitors, and markedly decreased CESA protein abundance without corresponding changes in CESA transcript levels. Loss of BAG function also increased the accumulation of CESA6 in vacuolar compartments. These findings identify BAG proteins as previously unrecognised regulators of cellulose synthase homeostasis and link a conserved proteostasis-associated protein family to plant cell wall biosynthesis. More broadly, the study establishes multi-bait proximity labelling, combined with cell location-specific controls, as a strategy for resolving dynamic protein networks whose components traffic through multiple subcellular compartments.

Coordinated organogenesis and rhythmic stem development determine shoot morphogenesis, which governs distinct plant architecture and crop yield. The shoot apical meristem (SAM) drives organ initiation and stem growth, with its activity sustained by the spatially defined CLAVATA3 (CLV3)-WUSCHEL (WUS) feedback loop. However, how the temporal CLV3-WUS module modulates SAM activity remains elusive. Here, we demonstrate that both CLV3 and WUS are required for circadian stem elongation. The clock component TIMING OF CAB EXPRESSION1 (TOC1) directly activates and sustains the circadian expression of CLV3, and this regulatory process is controlled by the APETALA1-CIRCADIAN CLOCK-ASSOCIATED1 module. Notably, the rhythmic expression pattern of CLV3, rather than its transcript abundance, plays a more important role in regulating WUS expression and sustaining SAM activity, and CLV3 confers circadian rhythmicity to WUS protein accumulation. Transcriptome and ChIP seq analyses reveal that WUS modulates multiple developmental programs, including meristem homeostasis, phytohormone responses, and cell wall remodeling. Mechanistically, WUS directly activates PECTIN METHYLESTERASE5 expression to promote stem elongation. Collectively, our findings uncover a spatiotemporal regulatory cascade that fine-tunes SAM activity to coordinate rhythmic organogenesis and stem development, thereby establishing optimal phyllotactic patterning in plants.

Although mitochondrial DNA (mtDNA) is subject to damage and high mutation rates in many eukaryotes, plants have a variety of mtDNA repair pathways that somehow result in exceptionally low mutation rates. However, the stoichiometry of biomolecules in plant mitochondria raises challenges for the DNA repair process. The protein complexes responsible for repair pathways contain subunits present at low copy numbers per mitochondrion. Mitochondria on average contain less than a full genome, limiting the capacity for templated repair, and raising the risk that repair machinery is localised to a DNA-empty mitochondrion where it cannot be used. Here we build on recent experimental characterisation of the copy numbers and physical processes involved to model the capacity for DNA repair in plant mitochondria. We find that targeted import of protein machinery, biased fusion of mitochondria bearing DNA, and exchange of biomolecules upon fusion can improve repair capacity through different mechanisms. Specifically, our model indicates that base excision repair can keep ~95% of mtDNA intact even without targetting or exchange rules and that targetting protein import to DNA-bearing mitochondria or exchanging protein content drives this to effectively 100%. In contrast, template repair cannot keep a majority of mtDNA intact unless mtDNA is shared across mitochondria through fusion, in which case its efficacy increases. Exchanging of metabolons (repair protein complexes) increases repair efficiency across all circumstances. We discuss the implications of our model for plant development and organelle inheritance.

Aerial roots of certain maize (Zea mays) and sorghum (Sorghum bicolor) genotypes secrete a carbohydrate-rich mucilage that sustains nitrogen-fixing bacteria, and the underground roots of most plants secrete mucilage at their tips. In both settings, border cells released from the root cap produce this mucilage, yet the genes controlling their formation remain largely unknown. We sequenced the RNA of about 23,000 nuclei from mucilage-secreting roots of maize, sorghum, and Medicago truncatula, sampled before and after secretion. Each species yielded 10 to 15 clusters, which we annotated with published markers and with new markers that we validated by in situ hybridization in the two cereals and by promoter-reporter fusions in M. truncatula. We then inferred modular and cell type-specific gene regulatory networks. Transcriptional programs diverged across the three species except in the quiescent center and the meristem, and in the clusters containing border cells, where a shared set of regulators emerged. Silencing three of five candidate regulators reduced border cell number, while silencing a partially overlapping set of three regulators reduced root diameter in M. truncatula. Silencing the C2H2 zinc finger protein MtrunA17_Chr1g0148421 also reduced border cell viability. A maize insertion mutant of bzip89 released fewer border cells than the wild type. These networks offer entry points for tuning mucilage production in cereal and legume crops.

Decoding how plants integrate multiple hormone signals to coordinate growth requires tools capable of resolving pathway interactions at cellular resolution in living tissue. Here we present ACE (Auxin-Cytokinin-Ethylene) and ACE2, proof-of-concept single-locus reporters to simultaneously capture activity of multiple hormones. Deploying ACE alongside well-established reporters, exogenous hormone treatments, and reverse-genetic perturbations of hormone biosynthesis, signaling, and transport in three-day-old etiolated Arabidopsis seedlings, we dissect the spatiotemporal hierarchy governing primary root elongation and root apical meristem (RAM) size. We demonstrate that both ethylene- and cytokinin-triggered root growth inhibition involve a boost of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1 (TAA1)-mediated auxin biosynthesis and AUXIN RESISTANT1 (AUX1)-dependent auxin redistribution. Two spatially distinct auxin responses underlie the respective root growth effects: ethylene expands TAA1-dependent auxin biosynthesis from the root vasculature into the epidermis and promotes AUX1-mediated auxin import into the transition and elongation zones to inhibit cell elongation, while cytokinin confines ethylene-dependent TAA1-boosted activity to the vasculature and drives auxin accumulation in lateral root cap cells to reduce RAM size. Together, these data establish a reciprocal regulatory loop between these hormones, positioning ethylene as a convergence node in auxin-cytokinin crosstalk, and cytokinin as a modulator of the ethylene-auxin interaction. Critically, the changes in cross-activated reporter patterns described for different genetic backgrounds, alongside quantitative assessment of hormone-specific inhibition of the mutants growth, were consistent with the multi-hormone network established over two decades of research, and added cell-type-resolved spatial detail and a proposed hierarchy for the etiolated seedling root. Finally, a second-generation reporter, ACE2, overcomes key technical limitations of ACE, expanding the platforms capacity toward a higher-order multi-hormone monitoring system. These resources expand the Arabidopsis genetic toolkit and provide a generalizable framework instrumental for dissecting multi-hormone signaling hierarchies at the cellular level.

A fundamental question in developmental biology is how highly complex, yet reproducible multicellular body plans form from a single cell. The multicellular haploid body of the land plant Marchantia polymorpha develops from a single isolated cell - the spore - that divides asymmetrically. This produces a small terminally differentiating basal cell, and a large proliferative apical cell that gives rise to the multicellular sporeling body. The genetic basis for the establishment of asymmetry, first within the spore, and later within the sporeling body has remained virtually unknown. Here, we show that the plant specific RHO-type GTPase - RHO OF PLANTS (ROP) - polarises to the spore basal pole to ensure spore division is highly and reproducibly asymmetric. We demonstrate this highly asymmetric division is necessary to specify the terminal differentiation of the basal cell. Furthermore, we show that ROP-mediated polarised outgrowth is required to establish asymmetry within the sporeling body derived from the apical cell. Our discovery highlights how ROP function confers developmental robustness and contributes to the establishment of asymmetry during plant development from a single isolated cell.

Plant regeneration underpins plant developmental plasticity, tissue culture, genetic transformation and crop improvement. Although numerous related omics datasets have been generated, specialized multi-omics databases for this field are still scarce. Here, we constructed PlantRegMoD, an AI-powered integrated database dedicated to plant regeneration. This platform hosts 20.54 TB standardized multi-omics data from 147 projects across 32 plant species and 2,593 samples. We established a unified hierarchical classification system covering five major categories and nine regeneration models, and curated 236 regeneration genes as well as their 28,190 homologs across 58 representative plant species. It contains extensive transcriptomic resources across all regeneration models, together with 196,423 single cells and over 8.81 million epigenetic peaks to dissect cellular heterogeneity and multi-layered epigenetic regulation. Equipped with nine online omics-related tools and a RAG-based intelligent Q&A system, PlantRegMoD greatly reduces bioinformatic barriers and serves as a robust resource for mechanistic, functional and evolutionary studies of plant regeneration.

Plant body organization depends on the coordinated development and function of shoots and roots, yet their functional specialization and interdependence remain incompletely understood. Whereas shoot senescence and death, as well as root regeneration from shoot tissues, are well studied, what capacities roots retain in the absence of the shoot remain unclear. To address this question, we tracked Arabidopsis roots after complete shoot excision. Initially, the remaining roots entered a growth-arrested but viable state. Despite broad repression of growth-associated programs, auxin and cytokinin signaling persisted, and the roots retained developmental responsiveness. This arrested state, however, was not developmentally terminal. By approximately 20 days after excision, green structures emerged from lateral root-associated domains. They accumulated chlorophyll and starch, assimilated carbon in response to light, and developed persistent cuticle-covered surfaces. Based on their origin and shoot-like characteristics, we termed them lateral root-derived shoots (LRSs). LRSs arose preferentially in the most shoot-proximal region, where cytokinin signaling progressively accumulated. Excision of this region repositioned LRS formation to the newly established proximal boundary, indicating spatial redefinition of shoot-forming competence. Auxin and cytokinin antagonistically governed the choice between continued lateral root growth and LRS identity, with cytokinin further promoting leaf-like differentiation. LRSs subsequently formed roots and developed into fertile plants under appropriate conditions. These findings reveal that roots retain developmental competence after shoot loss and can reorganize positional and hormonal programs to acquire shoot identity and reconstruct a complete plant body.

The Arabidopsis PWWP-DOMAIN INTERACTOR OF POLYCOMBS1 (PWO1) and Telomere Repeat-Binding Proteins 1-3 (TRB1-3, TRBs) associate with distinct and shared protein complexes involved in epigenetic regulation, yet their cooperative roles in chromatin control and plant development remain largely unexplored. Here, we show that the interaction between PWO1 and TRBs is evolutionarily conserved. Both PWO1 and TRBs associate with plant telomeres, interact at these regions, and are co-enriched at subsets of interspersed telo-box motifs across regulatory regions genome-wide. TRBs facilitate PWO1 binding at shared genomic regions, including telo-box motifs. PWO1 and TRBs share a substantial number of genomic targets and preferentially bind chromatin regions associated with transcriptionally active states, whereas TRBs alone associate with repressive marks at thousands of loci. Genetic analyses show that the pwo1 trb1 trb3 triple mutant displays severe developmental defects, including main stem arrest and early maturation associated with aberrant lignin deposition in interfascicular tissues. In the triple mutant, key enzymes in the lignin biosynthesis pathway are upregulated, indicating that PWO1, TRB1, and TRB3 cooperatively regulate secondary cell wall formation. Together, our findings provide new insights into how PWO1 and TRBs cooperate to regulate chromatin states and orchestrate plant development, highlighting their central role in controlling gene expression programs. Significance statementThis study shows that PWO1 and TRB proteins co-occupy telomeres, including interspersed telo-box motifs, to regulate chromatin organization and plant development, particularly ectopic lignin deposition. Our findings reveal how these nuclear protein factors coordinate epigenetic states in Arabidopsis thaliana, providing a framework for understanding the control of developmental programs. O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/740627v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1370171org.highwire.dtl.DTLVardef@3faea5org.highwire.dtl.DTLVardef@e30921org.highwire.dtl.DTLVardef@16c948e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Evolutionarily conserved PWO-TRB interactions and their shared roles in chromatin regulation and plant development. Created with BioRender.com. C_FIG

The evolution of indoleacetic acid (IAA) into the plant hormone auxin remains unclear. Here, we compared IAA response and metabolism in land plants and their closest living relatives, the streptophyte algae, using chemical treatments, phytohormone profiling, and targeted and untargeted metabolomics. Streptophyte algae showed neither plant-like auxin responses nor canonical IAA metabolism. Here, we demonstrate IAA side-chain decarboxylation as a novel pathway of cellular IAA metabolism, operating in streptophyte algae and land plants alike. Decarboxylation also underpinned IAA's innate photolability and yielded cytotoxic intermediates, which also accumulated endogenously under simulated sunlight. Together, these findings establish IAA decarboxylation as a major, conserved metabolic pathway, and suggest that the metabolic constraints arising from IAA's instability and indirect cytotoxicity contributed to its adoption as a plant hormone.

Nitrogen (N) is a major determinant of plant growth and productivity. Because soil N availability and internal N demand fluctuate, plants have evolved sophisticated mechanisms to coordinate N acquisition and utilization at the whole-plant level. However, how this coordination is achieved remains poorly understood. Here, we show that N-inducible LATERAL ORGAN BOUNDARIES DOMAIN transcription factors LBD37, LBD38, and LBD39 (LBDs) function as repressors of local N uptake and assimilation and systemic N-demand signaling in Arabidopsis. Triple mutants lacking these three LBDs displayed enhanced nitrate influx and increased accumulation of nitrate, amino acids, and total N. Transcriptome analysis identified an array of N-starvation- and nitrate-inducible genes derepressed in shoots and roots, including C-TERMINALLY ENCODED PEPTIDE (CEP) and CEP DOWNSTREAM (CEPD) genes, as well as genes involved in N uptake and assimilation. Grafting and genetic analyses revealed that LBDs gate the systemic N-demand signaling relay by repressing CEP and CEPD expression organ-autonomously. We also found that LBDs locally repress genes involved in N uptake and assimilation through a distinct regulatory mechanism. We propose that LBDs are key transcriptional repressors in a regulatory framework for optimizing N acquisition and utilization under fluctuating N conditions at the whole-plant level.

The domestication of maize from teosinte involved dramatic remodeling of the ear, yet the cellular and genetic bases of this transformation remain unclear. Here, we generate a single-nucleus and spatial transcriptome atlas of developing maize and teosinte ears. Comparative analysis reveals divergence in cob-associated cell types, with enhanced cytokinin signaling and reduced growth-inhibitory signals collectively driving cob thickening and enlargement in maize. We further demonstrate that domestication expanded the spatial expression domain of key transcription factors in maize meristem cells, enhancing the potential for increasing kernel number. Additionally, we verified a major domestication gene, ZmSPD1, in which two nonsynonymous SNPs differentiate maize from teosinte and alter jasmonic acid (JA) levels in the ear, thereby suppressing spikelet abortion to effectively double kernel production. These findings provide a cell-resolved mechanistic framework for how cob architecture and kernel number were shaped during maize domestication, offering new insights into the formation of key agronomic traits.