Molecular Plant

Flag leaf angle (FLA) critically determines rice yield potential under dense planting conditions. As two pivotal phytohormones determine rice FLA, the antagonistic interaction between brassinosteroid (BR) and auxin remains largely uncharacterized. We here demonstrate that BR signaling reduces auxin biosynthesis to control FLA via regulating the biosynthesis of secondary cell wall (SCW). Genetic evidence demonstrates OsYUC8 mutants disrupt SCW formation, leading to increased FLA. At the molecular level, the BR-related transcription factor OsBZR1 directly binds to and represses OsYUC8 promoter activity, thereby fine-tuning auxin-mediated SCW biosynthesis. Field evaluations reveal that osbzr1 mutants display optimized flag leaf architecture and improved yield performance under high-density cultivation. Our study not only delineates the antagonistic BR-auxin interaction governing FLA but also establishes a genetic strategy for manipulating crop architecture to maximize yield in dense planting conditions. One-sentence summaryOsBZR1-mediated repression of OsYUC8-driven auxin biosynthesis modulates secondary cell wall formation to optimize flag leaf architecture, providing a genetic strategy for maximizing yield under high-density cultivation.

The medicinal herb Panax notoginseng produces a structurally diverse array of triterpene saponins (ginsenosides), yet the genetic basis of this chemical complexity remains unclear. Here we present a high-quality chromosome-level genome of diploid P. notoginseng and integrate comparative genomics with multi-tissue, multi-year metabolomics and transcriptomics. Surprisingly, unlike tetraploid Panax species, P. notoginseng shows no general expansion of core saponin biosynthetic gene families. Instead, lineage-specific diversification of UDP-glycosyltransferase (UGT) families, a recent burst of LTR retrotransposons, and enrichment of species-specific genes in metabolic modification pathways point to an alternative evolutionary route. Saponin accumulation follows strict spatiotemporal compartmentalisation, and co-expression network analysis reveals that the biosynthetic machinery is not static but continuously rewired during development-from a basic synthesis module in the first year to a modular pattern supporting both broad accumulation and branch-specific modification by the third year. Seventeen differentially expressed UGTs show clear tissue preferences and saponin-branch correlations. As a representative example, PnUGT33 is tightly linked to the PPD-type saponin branch; structural modelling, molecular docking and 100 ns molecular dynamics simulations demonstrate its differential recognition of diverse triterpene skeletons. Collectively, our findings establish that ginsenoside diversity in diploid P. notoginseng arises primarily from UGT lineage diversification, developmentally rewired regulatory networks and UGT mediated branch selective post-modification, rather than from expansion of core pathway genes. This work provides a new paradigm for understanding how plants achieve metabolic complexity without whole genome duplication or massive gene amplification.

Plants detect neighbours through a reduced red-to-far-red ratio (R:FR), triggering elongation growth that reduces crop yield. Although Gibberellin (GA) is required for the neighbour-proximity (NP) elongation response, bioactive GA levels do not increase sufficiently to account for elongation magnitude, suggesting GA sensitivity as an additional regulated variable. Here, we show that GID1C, one of three Arabidopsis GA receptors, is the primary GA receptor involved in NP-induced elongation. GID1C protein accumulates selectively in hypocotyls and root tips under low R:FR without an increase in bioactive GA. The gid1c mutant shows a reduced elongation response that exogenous GA treatment cannot rescue. Transcriptome profiling reveals that GID1C controls 86% of the NP-responsive transcriptome, including genes for cell growth, division, and transcriptional regulation. Hub analysis identifies ICE1 as a GID1C-repressed transcriptional brake. ICE1 transcript is suppressed under low R:FR in a GID1C-dependent manner, and a phosphorylation-resistant ICE1 allele blocks NP-induced elongation. Together, these findings establish GA perception as an additional regulatory layer in NP, with subfunctionalisation among GID1 paralogs shaping the response to neighbouring plants.

Tomato (Solanum lycopersicum) is classified as a day-neutral plant, whereas its wild relatives exhibit delayed flowering under long day (LD) conditions due to higher activity of the SELF-PRUNING 5G (SP5G). In Arabidopsis thaliana, CONSTANS (CO) activates FLOWERING LOCUS T (FT), a homolog of SP5G, but whether and how CO integrates with SP5G in tomato flowering was unclear. Here, we demonstrate that SlCOL1 (the tomato CO homolog) delays flowering by directly activating SP5G in a PHYTOCHROME B1 (PHYB1)-dependent manner. Importantly, genetic and molecular analyses combining a photoperiod-responsive tomato line carrying the wild SP5G allele from S. pennellii, together with SlCOL1 and flowering-pathway mutants, revealed synergistic crosstalk among the photoperiodic SlCOL1-SP5G module, age-dependent pathway (mediated mainly by the microRNA156-SlSBP module), gibberellin (GA) pathway, and SINGLE FLOWER TRUSS (SFT) pathway. Mechanistically, we show that SP5G forms a complex with miR156-targeted SlSBP13 to directly regulate SFT expression, and that GA may interfere with SP5G activity. Together, these findings revealed a coordinated network that integrates multiple flowering signals to modulate both shared and pathway-specific targets. Our findings provide a significant advance in understanding the molecular regulation of tomato flowering and offer promising avenues for breeding strategies optimized for diverse environmental conditions and latitudes.

Heavy metal-associated isoprenylated plant proteins (HIPPs) are encoded by large gene families, which have diversified specifically in vascular plants. Their physiological functions and molecular mode of activity are currently largely unknown. In this study, we characterize a group of phylogenetically closely related genes HIPP32, HIPP33, and HIPP34 in Arabidopsis thaliana, revealing their essential roles in controlling diverse developmental pathways. Through comprehensive genetic analyses, we demonstrate that these genes exhibit partially overlapping pleiotropic functions, influencing multiple aspects of plant growth such as embryogenesis, maintenance of apical meristems, root architecture, shoot branching, leaf morphogenesis and floral organ formation. Transcriptomic profiling of hipp mutants identified significant deregulation in several regulatory pathways involved in plant hormone responses, with a specific impact on auxin signaling processes. Interestingly, we show that the analyzed HIPP proteins localize very specifically to plasmodesmata, suggesting their potential function in regulating intercellular communication in shaping plant development.

Transcription factors (TFs) orchestrate environmental responses by activating target genes, yet how they reshape epigenome architecture to coordinate gene expression remains poorly understood. We previously identified SIENA (Stimulus-Induced ENhancer Acetylation) domains as large regions of jasmonic acid (JA)-induced H3K9 hyperacetylation surrounding MYC2 TF binding sites in Arabidopsis and tomato. However, the mechanisms underlying the formation of SIENA domains (SIENAs) and their functional significance remained unknown. Here, we show that SIENAs also form at major JA-responsive genes and gene clusters in soybean, extending this phenomenon to an evolutionarily distant crop species. Comprehensive chromatin profiling revealed that SIENAs accumulate multiple histone acetylation marks, including H3K9ac, H3K27ac, H3K56ac, H2BK20ac, and H2A.Zac, establishing them as regions of broad histone hyperacetylation. Pharmacological disruption of proteasomal turnover and histone acetylation dynamics compromised SIENA formation. Chromatin accessibility analyses further showed that inducible accessibility within SIENAs is tightly associated with MYC2 binding sites, supporting a model in which MYCs nucleate localized chromatin reprogramming events. Together, our findings establish SIENAs as MYC2-dependent chromatin-organizing domains and identify histone hyperacetylation as a central feature of MYC2-mediated gene activation.

Ribosome biogenesis is critical for plant development and environmental responses. A large number of ribosomal proteins (RPs) and ribosomal biogenesis factors (RBFs) are required for ribosome biogenesis, many of which remain uncharacterized in plants. We report here the identification of Arabidopsis RBF FAN and its interacting partner FAN-INTERACTING PROTEIN 1 (FIP1). As their human and yeast orthologues, FAN-FIP1 interact. Both FAN and FIP1 participate in the processing of pre-rRNAs. Functional loss of FAN or FIP1 knock-down results in developmental retardation and hypersensitivity to heat stresses. We demonstrate that FAN-FIP1 positively mediates brassinosteroid (BR) signaling by ensuring the translation efficiency of the BR receptor-coding gene BRASSINOSTEROID INSENSITIVE 1 (BRI1) through the presence of its upstream open reading frame (uORF). Importantly, BR signaling positively mediates the processing of pre-rRNAs, which may be critical not only for development but also for heat tolerance.

Sugar is both an essential energy source and the major substrate for cell wall biosynthesis during plant growth, yet how growth-promoting hormones regulate sugar synthesis remains unclear. Here, we show that the brassinosteroids (BRs) promote gluconeogenic and photosynthetic sugar synthesis by activating phosphoenolpyruvate carboxykinase (PCK), which catalyzes the conversion of oxaloacetate to phosphoenolpyruvate, a central step in primary metabolism. Arabidopsis BR-deficient mutants display reduced PCK1 activity and elevated phosphorylation at conserved Ser-62 and Thr-66 residues. BR treatment induces PCK1 dephosphorylation and activation, whereas the GSK3-like kinase BIN2 phosphorylates these sites, altering quaternary structure and inhibiting PCK1. Phospho-blocking mutations of Ser-62/Thr-66 confer BR-independent PCK1 activity and enhance seedling growth, while phosphomimetic mutations reduce PCK1 activity and impair seedling growth and establishment. BR also promotes PCK dephosphorylation and activation in photosynthetic leaves of maize and sorghum. Our study demonstrates that BR regulates primary metabolism via GSK3/BIN2-mediated phosphorylation of PCK, thereby promoting gluconeogenesis and photosynthesis.

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

Progressive climate change is driving increasingly devastating crop losses through droughts, heatwaves and other adverse weather. Combined with shrinking arable land and spreading plant diseases, this makes it crucial to enable crops to grow efficiently in unfavorable, dynamic environments. Because stressors demand prompt, highly coordinated responses, plant stress adaptations rely heavily on epigenetic regulation. Histone deacetylases (HDAs), particularly class I, were recently shown to repress these responses. As constitutive defense is energetically costly, tools enabling temporal modulation of such mechanisms are highly sought after in crop biotechnology. This study evaluated whether valeric acid (VA), a five-carbon carboxylic acid, can inhibit HDA and activate plant defense responses. Here we show that VA is a potent HDA inhibitor that confers resistance to multiple abiotic and biotic stresses in Arabidopsis, and further validate the abiotic component in maize and tomato. Despite its simple chemical structure, structural and transcriptomic evidence shows that VA acts by selectively inhibiting two major stress-repressing deacetylases, HDA19 and HDA6. By targeting these epigenetic switches, VA activates natural defense and acclimation responses. Time-course transcriptomic analyses further revealed that priming with VA induces transcriptional memory, which, together with VA-induced metabolic rewiring, enables rapid and efficient responses to future stressors. Most importantly, despite activating energetically demanding defenses, VA promotes vegetative growth and increases yield under normal conditions, thereby breaking the growth-defense trade-off. These findings establish VA as the first epigenetic biostimulant of its kind, capable of improving plant performance under both abiotic and biotic stress while simultaneously increasing crop yield. As the epigenetic mechanisms underlying its action are evolutionarily conserved, VA priming emerges as a promising universal strategy to mitigate the climate-driven global crisis of crop losses.

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 ATP-binding cassette (ABC) transporter ABCB1 transports both auxins and the brassinosteroid brassinolide (BL). ABCB1-mediated auxin (IAA) transport depends on interaction with the FKBP42 protein TWISTED DWARF1 (TWD1), yet the mechanism underlying substrate selectivity remains unclear. Here, we confirm dual IAA and BL transport by ABCB1 and show that the two substrates compete for ABCB1-mediated transport. We demonstrate that a conserved proline residue (P1008) is required for IAA, but not BL, transport. Furthermore, we identify TWD1 as a calmodulin-activated peptidyl-prolyl cis-trans isomerase (PPIase) that selectively enhances IAA, but not BL, transport through isomerization of the E1007-P1008 peptide bond. Loss of TWD1 PPIase activity abolishes ABCB1-mediated IAA export without affecting BL transport, revealing a regulatory mechanism that prioritizes auxin over brassinosteroid transport. Cryo-EM, molecular docking, and molecular dynamics simulations of wild-type ABCB1 and the ABCB1P1008G variant suggest that the P1008 loop mediates long-range communication between the nucleotide-binding domain surface and the substrate-binding pocket, thereby providing a structural mechanism by which TWD1 modulates substrate specificity. In summary, our findings establish the structural basis of ABCB1 substrate selectivity and uncover a post-translational mechanism that selectively regulates auxin transport while preserving brassinosteroid transport. One Sentence SummaryTWD1 prioritizes ABCB1-mediated auxin over brassinosteroid transport

Protein-protein interactions (PPIs) play a crucial role in enabling proteins to carry out their functions within various biological processes (Hui et al., 2003). Since the introduction of the yeast two-hybrid (Y2H) method for PPI detection in 1989 (Fields and Song, 1989), the identification of PPIs has become a significant focus in modern biological research. PPI goes beyond examining individual proteins, allowing researchers to establish a comprehensive network that regulates biological processes. Rice, as a key model organism in plant biological studies, has been at the forefront of PPI research. In 2008, prominent rice scientists in China called for concerted efforts to define a comprehensive protein-protein interaction network experimentally, which aimed to facilitate the prediction of the functional mechanisms operating throughout a plants lifecycle (Zhang et al., 2008). With efforts for 2 decades, the experimentally identified rice PPIs have reached over ten thousand. Several public databases have been established to systematically collate and store PPIs, including STRING (Szklarczyk et al., 2019), BioGRID (Oughtred et al., 2020), IntAct (del Toro et al., 2022), PRIN (Gu et al., 2011), RicePPINet (Liu et al., 2017) and RiceNet v2 (Lee et al., 2015). However, most PPI datasets in rice stem from computational predictions, while experiment-based rice PPI datasets are fragmented due to the lack of systematic profiling at the rice PPIome level, which largely hinders information sharing in the rice research community. To bridge this gap, we constructed the Port of Protein-Protein Interactomes (POPPIN; https://riceome.hzau.edu.cn/poppin/), an integrated database dedicated to sharing experimentally verified PPIs and functional clues in rice. Empowered by high-throughput PPIome profiling technologies and text mining assisted by a large language model (Huang et al., 2025; Liu et al., 2025), POPPIN currently has deposited over 150,451 pieces of rice PPI-related information. Additionally, POPPIN provides detailed protein information, including GO annotations, subcellular localizations, domains, trait ontology (TO) information, and hyperlinks to external biological databases. Through offering a user-friendly web interface for search and dynamic network visualization, POPPIN serves as the first large-scale, experiment-based database for searchable PPIs in rice, and has the potential to be extended to other species under this structural framework.

Copper (Cu) is an essential micronutrient whose bioavailability is strongly affected by soil physicochemical properties. During evolution, plants have developed mechanisms to flexibly adjust their metabolism to Cu status. Superoxide dismutases (SODs), including Cu/ZnSOD1 (CSD1) and FeSOD1 (FSD1), are key antioxidant enzymes regulated in Cu dependent manner in Arabidopsis thaliana. Examination of CSD1 cellular distribution and activity revealed that CSD1 is a nuclear and cytosolic SOD whose abundance and activity respond to Cu availability inversely to FSD1. Combined microscopic and biochemical analyses of Cu-dependent dynamics revealed that, unlike FSD1, CSD1 localization in guard cells (GCs) remains independent of Cu availability. CSD1 escapes miR398-mediated regulation in GCs through a cell type-specific splice variant (CSD1.2) that carries an altered miR398-binding site. In silico analyses indicate that this mechanism is also present in crop species. Functionally, the csd1 mutant showed reduced sensitivity to abscisic acid (ABA)-induced stomatal closure, a phenotype rescued by reintroducing CSD1. Biochemical and reactive oxygen species (ROS) level analyses indicate that CSD1.2 most likely acts independently of its canonical enzymatic activity in GCs and functions upstream of the ROS burst in the ABA signaling pathway. Together, we present a novel, cell-type-specific mechanism that safeguards ABA-driven stomatal closure under fluctuating Cu supply.

In Asteraceae species, the capitulum is a compact inflorescence, featuring a characteristic reproductive structure. Despite the identification of a few key regulatory factors, the transcriptome-level information on the developing capitulum remains limited. Here, we applied single-cell and spatial transcriptome sequencing to investigate the developing Gerbera hybridas capitulum during floret differentiation. We obtained a transcriptomics atlas encompassing different stages of the Gerbera capitulum and analyzed the cellular and spatial dynamics of gene expression. Using marker gene expression and GO enrichment of cluster-specific DEGs, we annotated putative cell types and described changes in gene expression across sampled stages, potentially associated with ongoing developmental processes. We detected activity of previously undescribed MADS-box genes and defined their spatial expression patterns. Notably, the MADS-box gene GAGL12 was found to be enriched in the putative capitulum phloem cells. The GAGL12 protein was shown in yeast two-hybrid assays to interact with several other MADS-domain proteins with hypothesized functions in vasculature development, and further detailed in silico analyses supported a candidate role in the development of capitulum vasculature. Altogether, we provide integrative and dynamic transcriptomic insight into capitulum and floret development and lay a basis for future functional studies of the control and development of this intriguing reproductive structure.

The phytohormone auxin is a central coordinator of plant growth and development. Besides its canonical effect on gene transcription1,2, auxin triggers an ultra-rapid calcium ion influx that initiates the root gravitropic response3. The nature of the so-called rapid auxin pathway connecting the AFB1 auxin receptor3,4 and plasma membrane calcium channels remained unknown. Here, we show that auxin induces the direct interaction of the AFB1 receptor with the CNGC14 calcium channel. As the AFB1 receptor is independent of the ubiquitin ligase complex5, the auxin-induced interaction translates into relocalization of the receptor to the plasma membrane. We identify the interaction interface and provide evidence that the docking of the receptor to the channel complex activates Ca2+ influx and triggers growth inhibition. These findings position a calcium channel as an unprecedented component of the AFB1 auxin receptor complex. The ligand-dependent localization shift of a TIR1/AFB family receptor represents a novel paradigm in signal transduction and opens the possibility of unforeseen branches of auxin signaling pathways.

Nucleotide-binding leucine-rich repeat (NLR) immune receptor genes are of significant value in disease resistance breeding and the control of viral diseases. Soybean mosaic virus (SMV) poses a serious threat to soybean production and the Rsv1 locus in soybean cultivar Suweon 97 confers broad-spectrum resistance against SMV strains G1 to G7; however, this locus harbors no fewer than 18 NLR genes, and thus the broad-spectrum antiviral mechanisms underlying the Rsv1 locus remain poorly understood to date. Here, we established a rapid and highly efficient screening system for cloning NLR genes from soybean Rsv1 locus and identified a broad-spectrum antiviral NLR gene 13g184900 from this highly complicated locus. The NLR encoded by 13g184900 can recognize viral P3 protein from all SMV strains (G1-G7) and another potyvirus Bean common mosaic virus (BCMV). The coiled-coil (CC) domain of this NLR directly interacts with viral P3 protein. Additionally, we showed that this NLR originated from wild soybean accession in East China and has been introduced into several soybean cultivars during domestication. Collectively, we developed a high-throughput screening system for identifying NLR genes in soybean and our study provides new mechanistic perspective on how the Rsv1 locus mediates the broad-spectrum resistance to all SMV G1-G7 strains.

Brown spot (BS), caused by the fungal pathogen Bipolaris oryzae, is a major disease threatening global rice production. However, the genetic basis of host BS resistance remains unclear. Here, we identified brown spot resistance 1 (bsr1), a quantitative trait locus conferring BS resistance, by map-based cloning. We show that bsr1 encodes a sucrose transporter and that a near-isogenic line carrying bsr1 (bsr1-NIL) in the susceptible Koshihikari genetic background exhibited resistance to BS by suppressing sucrose efflux into the apoplast after pathogen attack. Furthermore, bsr1-NIL also showed strain-specific resistance to bacterial blight caused by Xanthomonas oryzae pv. oryzae through the same mechanism. These findings demonstrate that bsr1 confers dual resistance to fungal and bacterial diseases by regulating sucrose efflux. Our study identifies a previously unrecognized mechanism underlying resistance to both BS and bacterial blight and highlights bsr1 as a promising target for breeding disease-resistance rice cultivars. Rice (Oryza sativa L.) is a staple food for more than half of the worlds population1. Brown spot (BS), caused by the fungus Bipolaris oryzae, is one of the most prevalent fungal diseases of rice, and its incidence has increased under global warming2. BS infects coleoptiles, leaves, leaf sheaths, panicle branches, glumes, and spikelets, and severe infection can substantially reduce grain yield.

Positioning of the division plane is a critical step during cellular development. While in animal cells the plane of cell division is defined during metaphase, in plants this decision is made before mitosis and includes the formation of a cytoskeletal structure termed the preprophase band (PPB). Although not essential, the PPB constitutes the earliest mark for the plane of cell division and coincides with the sites where the cell plate fuses with the parental plasma membrane during cytokinesis. Recent studies indicate that endo- and exocytosis are involved in remodelling of the cortical division zone. Here we show that PPBs, phragmoplasts, cell plates and cell walls are misplaced in Arabidopsis mutants of Atvps2.2/hyade (hya), a plant-specific component of the Endosomal Sorting Complex Required for Transport (ESCRT)-III. We demonstrate that the amino acid substitution Q71P of the hya-3 allele abolishes the homo- and heteromerization with other ESCRT-III components. Functional HYA-GFP fusion proteins are excluded from the canonical location of ESCRT-III complexes at multivesicular bodies (MVBs) and are absent from Brefeldin A (BFA) and Wortmannin (WM) sensitive compartments in Arabidopsis. HYA-GFP neither localize to early nor late endosomes but colocalizes with markers of secretory compartments such as the Qc-SNARE, SYP61 and with trans-Golgi-network (TGN) derived secretory Rab-A3 vesicles. Moreover, HYA-GFP locates to the extracellular space indicating that VPS2.2/HYA is involved in secretion. These results are consistent with a novel, non-canonical function of ESCRT-III in the establishment and maintenance of the cortical division zone via secretion.

Horizontal gene transfer (HGT) allows the movement of DNA across broad evolutionary distances without sexual reproduction. In grasses, HGT is widespread and although a few horizontally transferred genes (HTG) are adaptive, most are purged over time. Within the adaptive HTG, biosynthetic genes encoding enzymes that act together in the same pathway and physically co-localise in clusters have been reported multiple times. The aims of this study are to test whether HGT is bidirectional in a pair of grass species, maize and Zuloagaea bulbosa, and if HTGs are found more than expected by chance in biosynthetic genes organised in clusters. To achieve this, we firstly generated a phased reference genome for Z. bulbosa. Then we identified 56 candidate horizontally transferred genes, of which 45% were from Andropogoneae, including two likely to be of maize origin. Since transfers from Z. bulbosa to maize were previously described, our results show that HGT is bidirectional, although the balance might not be even. After predicting all biosynthetic gene clusters in the Z. bulbosa genome, we found that HTGs are enriched in biosynthetic genes organised in clusters. This correlation between HGT and gene clustering is likely to be a consequence of selection due to the immediate adaptive benefit a whole pathway can provide. Two of the HTGs from Andropogoneae belong to the benzoxazinoid BGC, which previously underwent an ancestral transfer from Panicoideae into Pooideae. The dynamism of biosynthetic gene clusters, including recurrent horizontal gene transfers, contributes to the extraordinary metabolic diversity present in plants. Significance statementHorizontal gene transfer (HGT) is a significant driver of evolution that is widespread in grasses. In this study, we show for the first time reciprocal transfer of DNA between maize and another Mexican grass, Zuloagaea bulbosa. This result represents a proof of concept of bidirectional HGT which allows for limited, recurrent gene flow among distant species. Furthermore, we show that horizontally transferred genes are enriched for biosynthetic genes organised in biosynthetic gene clusters, regions of the genome that encode for multiple enzymes that act in the same biosynthetic pathway. We hypothesise that the transfer of a complete multi-genic pathway, ready to be used and potentially offering an evolutionary advantage, might promote a predominant retention of gene clusters in comparison with background HGT.