The pollen exine serves as a protective barrier and signaling interface essential for male fertility in flowering plants. Its precise patterning depends on coordinated interactions between microspores and tapetal cells. While the CLAVATA3/EMBRYO SURROUNDING REGION-related 19 (CLE19) peptide has been identified as a microspore-derived “brake” that restricts tapetal activity to maintain exine developmental homeostasis, how CLE19 integrates with hormonal signaling pathways remains poorly understood. Here, we demonstrate that CLE19 attenuates brassinosteroid (BR) signaling output by engaging a defined BSL–BIN2–BES1 signaling cascade. Through quantitative phosphoproteomic analysis, we identified that CLE19 affects the phosphorylation of multiple BR signaling components, including BSL-type phosphatases BSL1/2/3, the GSK3-like kinase BIN2, and the transcription factor BES1. We show that CLE19 is perceived by its receptor PXL1, which directly interacts with BSL-type phosphatases to activate the GSK3-like kinase BIN2, leading to phosphorylation of BES1 at serine residues S219 and S223. Functional analyses using phospho-dead and phospho-mimic BES1 variants confirm that CLE19-dependent phosphorylation controls BES1 nuclear export and degradation, ultimately suppressing BR-responsive transcriptional outputs required for pollen exine patterning. Together, our findings define a peptide–hormone signaling axis that regulates transcription factor activity through post-translational regulation, providing mechanistic insight into how developmental robustness is maintained via intercellular signal integration in plant reproduction.

Symbiotic nitrogen fixation in legumes requires the exquisite regulation of the environment within the infected region of the nodule. The microaerobic environment critical for nitrogenase activity is maintained through the physical oxygen diffusion barrier of the cortex and locally the oxygen-binding protein leghemoglobin (Lb). Leghemoglobin binds and releases oxygen with heme moiety to maintain oxygen gradients inside the infected cell (IC) during nitrogen fixation. Heme binds to diverse proteins and plays critical roles in different redox reactions. However, the role and regulation of host-controlled heme production during symbiotic nitrogen fixation are not clear. Here, we identified coproporphyrinogen III oxidase plastid related 1 (CPOP1) as a key regulator of symbiotic heme biosynthesis in Lotus japonicus. CPOP1 is specifically highly expressed in nitrogen-fixing nodules, and knocking out CPOP1 alone causes leaf etiolation and dwarfism which could be recovered by the exogenous application of nitrogen source, indicating nitrogen fixation defect. The IC-specific expression of CPOP1 was directed by the −881 to −740 bp promoter region. The cpop1 mutant shows significantly increased nodule oxygen level and decreased nitrogen fixation activity compared to the wild-type. Intriguingly, bacteria proliferation is inhibited due to the down-regulation of cell division-related gene expression upon CPOP1 knockout. Our data showed that CPOP1 is essential for the microaerobic environment control of ICs and the activation of rhizobial nitrogenase required for symbiotic nitrogen fixation, through host-regulated nodule heme synthesis.

Multiple factors control primary seed dormancy established during seed maturation and secondary seed dormancy initiated when a non-dormant imbibed seed is exposed to adverse conditions. A key player in the control of primary and secondary dormancy in Arabidopsis thaliana is the Delay of Germination 1 (DOG1) gene, the expression of which is extensively regulated at the transcriptional and co-transcriptional levels. Despite its importance, the influence of post-transcriptional messenger RNA (mRNA) processing and mRNA storage of DOG1 on the determination of dormancy depth remains elusive. Here, we show that the UBA2A protein, a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, negatively regulates primary and secondary seed dormancy through the regulation of the DOG1 gene expression at the post-transcriptional level. uba2a mutants show higher levels of the DOG1 mRNA. Surprisingly, DOG1 gene transcription is not affected, as demonstrated by single-molecule fluorescent in situ hybridization, chromatin-attached mRNA analysis and Pol II chromatin immunoprecipitation (ChIP). Instead, our results show that the UBA2A protein decreases the stability of both chromatin-bound and cytoplasmic DOG1 mRNA pools, and results in higher chromatin retention of DOG1 mRNA in the uba2a mutant. Our study highlights chromatin retention and mRNA stability as important features of DOG1 gene expression regulation with a profound impact on dormancy establishment and shows that UBA2A protein, like its human homolog hnRNPAB, is most likely implicated in mRNA transport in the cell.

Inositol pyrophosphates (PP-InsPs) are important signaling molecules that regulate diverse cellular processes in eukaryotes, including energy homeostasis, phosphate (P_i) signaling, and phytohormone perception. Yet, in plants, the enzymes responsible for their turnover remain largely unknown. Using a non-hydrolysable PP-InsP analog in a pull-down approach, we identified a family of Arabidopsis NUDIX-type hydrolases (NUDTs) that group into two closely related subclades. Through in vitro assays, heterologous expression systems, and higher order gene-edited mutants, we explored the substrate specificities and physiological roles of these hydrolases. Using a combination of strong anion exchange high-performance liquid chromatography (SAX-HPLC), polyacrylamide gel electrophoresis (PAGE), and capillary electrophoresis electrospray ionization mass spectrometry (CE-ESI-MS), we found that their PP-InsP pyrophosphatase activity is enantiomer selective and Mg²⁺ dependent. Specifically, Subclade I NUDTs preferentially hydrolyze 4-InsP₇, while Subclade II NUDTs target 3-InsP₇, with minor activity against other PP-InsPs, including 5-InsP₇. In higher order mutants of Subclade II NUDTs, we observed defects in both P_i and iron homeostasis, accompanied by increased levels of 1/3-InsP₇ and 5-InsP₇, with a markedly larger increase in 1/3-InsP₇. Ectopic expression of NUDTs from both subclades induced local Pi starvation responses (PSRs), while RNA-seq analysis comparing wild-type (WT) and Subclade II nudt12/13/16 loss-of-function plants indicates additional PSR-independent roles, potentially involving 1/3-InsP₇ in the regulation of plant defense. Consistently, nudt12/13/16 mutants displayed enhanced resistance to Pseudomonas syringae infection, indicating a role in bacterial pathogen susceptibility. Expanding beyond Subclade II NUDTs, we demonstrated susceptibility of the 3PP-position of PP-InsPs to enzymatic activities unrelated to NUDTs, and found that such activities are conserved across plants and humans. Additionally, we observed that NUDT effectors from pathogenic ascomycete fungi exhibit a substrate specificity similar to Subclade I NUDTs. Collectively, our findings reveal new roles for NUDTs in PP-InsP signaling, plant nutrient and immune responses, and highlight a cross-kingdom conservation of PP-InsP-metabolizing enzymes.

The phytohormone abscisic acid (ABA) regulates plant responses to environmental stresses, development, and immunity. Under unfavorable conditions, ABA forms a complex with its receptor proteins Pyrabactin Resistance 1 (PYR1)/PYR1-likes (PYLs)/Regulatory Component of ABA Receptors (RCARs), inhibiting Clade A Protein Phosphatases Type 2C (PP2Cs) and releasing Sucrose Non-Fermenting-1-Related Protein Kinase 2s (SnRK2s) from PP2C-mediated inhibition. Rapidly Accelerated Fibrosarcoma (RAF) kinases from the B1, B2, and B3 subgroups phosphorylate and reactivate SnRK2s, initiating ABA responses. While ABA does not significantly activate B-RAFs, their basal activity is essential for initiating ABA signaling. However, the mechanisms sustaining this basal B-RAF activity are not fully understood. In this study, we revealed that Clade A PP2Cs interact with and dephosphorylate a certain number of B3 subgroup RAFs at a conserved serine residue, corresponding to Ser619 in RAF3, within the phosphate-binding loop. A phosphomimicking mutation at this residue, RAF3^S619D, failed to bind ATP and exhibited diminished kinase activity in vitro and in vivo. Ser619 in RAF3 is an autophosphorylation site, phosphorylated by recombinant RAF3-KD but not by its substrate SnRK2.6. The RAF3^S619A mutant, abolishing Ser619 autophosphorylation, displayed increased kinase activity in vitro. The B-RAF high-order mutant OK¹⁰⁰-B3 carrying RAF3^S619A showed enhanced ABA sensitivity compared with those with wild-type RAF3. Thus, PP2C-mediated dephosphorylation and the autophosphorylation of this unique serine residue dynamically regulate ATP binding affinity and tightly control RAF3 activity during various ABA signaling phases. This intricate mechanism ensures rapid RAF–SnRK2 cascade activation during stress while promptly desensitizing RAFs once stress signaling commences.

Plants monitor daylength to synchronize their flowering time with their surroundings and thus maximize reproductive fitness. In Arabidopsis (Arabidopsis thaliana), CONSTANS (CO) activates the expression of FLOWERING LOCUS T (FT); this activation is a crucial aspect of the daylength-dependent regulation of flowering time. Here, we demonstrate that the basic leucine zipper 3 (bZIP3) transcription factor is important for CO-induced FT expression under long photoperiod conditions in Arabidopsis. We isolated bZIP3 as a CO-interacting protein by yeast two-hybrid screening and verified bZIP3–CO complex formation in Arabidopsis through co-immunoprecipitation assays. The temporal and spatial expression patterns of bZIP3 are very similar to those of CO, and bZIP3 protein levels fluctuate throughout the day, with high abundance in the late afternoon. The bzip3 mutant displayed delayed flowering under long photoperiods, whereas bZIP3 overexpression accelerated flowering regardless of daylength. bZIP3 directly binds to the FT promoter region containing CO-responsive elements in vivo. FT messenger RNA (mRNA) levels in the bzip3 mutant and bZIP3 overexpression lines correlated with their flowering times and changed only during the daytime. bZIP3 overexpression resulted in significantly lower FT transcript levels in the co mutant background than in the wild type. Furthermore, bZIP3 forms a complex with ASYMMETRIC LEAVES1 (AS1), a CO partner that helps CO induce FT expression. The bzip3 as1 double mutant flowered later than the two single mutants under longer daylengths, and FT mRNA levels were much lower in the double mutant than in the bzip3 single mutant. Collectively, our findings uncover a new layer of photoperiod-dependent FT regulation in which bZIP3 facilitates CO to activate FT transcription by forming a complex with AS1.

While many plant lineages display remarkable diversity in morphological form, our understanding of how phenotypic diversity, or disparity, arises in relation to genomic evolution over geologic scales remains poorly understood. Here, we investigated the relationship between phenotypic and genomic evolution in the Fagales, a lineage of woody plants that has been a dominant component of temperate and subtropical forests since the Late Cretaceous. We examine newly generated transcriptomic and trait datasets representing most extant genera and a rich diversity of Cretaceous fossil representatives. Our phylogenomic analyses identify recurrent hotspots of gene duplication and genomic conflict across the order. Our phenotypic analyses showed that the morphospace occupied by Fagales was largely filled by the early Cenozoic, and rates of evolution were highest during the early radiation of the Fagales crown and its major families. These results suggest that Fagales conforms to an “early-burst” model of disparification, with morphospace being filled early in the order's diversification history, and that elevated levels of phenotypic evolution also often correspond to hotspots of gene duplication. Species diversification appears decoupled from patterns of both phenotypic and genomic evolution, highlighting the multidimensional nature of the evolution of plant diversity across geological timescales.

Soybean (Glycine max) provides vegetable oils and proteins for human consumption. Its production depends on seeds and other production-related agronomic traits. How the seed traits are regulated in soybean remains largely unclear. In this study, we identified a miR172a-ERF416/413 module for the regulation of seed traits. The miR172a can cleave the targets ERF416 and ERF413 to affect the downstream gene expression for the reduction of soybean seed size and weight. Both the MIR172a-overexpressing transgenic soybean plants and the erf416/413 mutants produced smaller seeds than the control. Consistently, the ERF416-overexpressing transgenic soybean plants generated larger seeds. ERF416 and ERF413 were directly targeted to the promoter of GmKIX8-1 and GmSWEET10a to regulate their gene expression for seed size/weight control. Interestingly, the erf416/413 mutants showed higher seed yield per plant and higher total seed fatty acid (FA) content, whereas the MIR172a-transgenic soybean had lower total seed FA content compared with the control cultivar, suggesting that miR172a and ERF416/413 may function in FA accumulation through different pathways. Haplotypes of the ERF416 promoter region were further analyzed and Hap1 was correlated with higher gene expression and higher seed weight, while Hap3 was correlated with higher total seed lipid content. Our study revealed a new module for seed trait control. Manipulation of such alleles should facilitate breeding for high-oil and high-yield soybean cultivars.

Rates of protein evolution (d_N/d_S) vary widely across the tree of life. In plants, both life-history traits and GC-biased gene conversion (gBGC) are thought to contribute to this variation, although disentangling their individual contributions remains a challenge. Using information on variation in life-history traits and molecular data in 148 species from Poaceae subfamilies Bambusoideae (mostly woody) and Pooideae (exclusively herbaceous), we investigated the relative importance of modes of reproduction and the non-selective forces of gBGC on protein evolutionary rates between the two subfamilies. Elevated rates of protein evolution associated with relaxed purifying selection were more evident in woody bamboos than in Pooideae and were better explained by reproductive modes than by traits that are likely proxies of effective population size. Although gBGC slightly reduced protein evolutionary rates in both subfamilies, its contribution had only a limited effect on molecular divergence between the groups. Forward simulations generally supported our empirical results on the influence of reproductive mode on selection and gBGC. Our findings from two sister lineages of the grass family provide evidence for association between protein evolution and life-history traits governing reproductive mode and enhance understanding of molecular evolution in plants with contrasting reproductive strategies.

Bananas and plantains of the genus Musa constitute the most vital fruits and staple foods. Cultivated bananas may have originated from intraspecific and interspecific hybridizations of four wild species, namely Musa acuminata (A), M. balbisiana (B), M. schizocarpa (S), and the Australimusa species (T). Here, we appraise the advances made in banana genomics, genetics, and breeding over the past few decades. The sequencing of Musa genomes has been a major breakthrough in banana research programs, presenting unprecedented possibilities for gaining deeper insights into the evolution, domestication, breeding, and genetics of indispensable agronomic traits of bananas. Also, we delve into how these genetic facets, coupled with innovative genomic-assisted tools, including genomic selection and gene editing, propel advancements in banana breeding endeavors. Ultimately, we propose the forthcoming prospects within the domain of banana genetics and breeding.

The evolution of spermatophytes (seed plants) is relatively well known in their evolutionary relationships over temporal changes, but their spatial evolution is another critical yet often neglected lens, especially using a taxon-based approach. Here, by integrating geographic distributions and origin locations across 429 spermatophyte families worldwide with unsupervised machine learning approaches, we constructed a Spermatophyte Spatial Evolutionary System that classifies global spermatophytes into 18 distribution types and six distribution supertypes within three primary floristic elements: cosmopolitan, tropical, and temperate. We found that the three elements all primarily originated from Gondwana, with the cosmopolitan element being the youngest and the temperate element being the oldest in terms of origin. They primarily formed during the Tertiary, particularly between the Eocene and Miocene, driven mainly by climate, long-distance dispersal, and tectonic movement, while each exhibited distinct migration routes and formation models. Our results provide novel insights into the spatial evolution of global spermatophytes and highlight that similar distribution patterns of spermatophytes were driven by their comparable formation processes and mechanisms at the levels of floristic element, distribution supertype, and type.

Rice black-streaked dwarf virus (RBSDV) is a major viral pathogen threatening rice production worldwide. However, the molecular mechanisms underlying the arms race between RBSDV and its host remain largely elusive. Here, we demonstrate that RBSDV infection, or the expression of viral RNA-silencing suppressor protein P6, promotes the ubiquitination and degradation of rice small ubiquitin-like modifiers (SUMO) conjugating enzyme 1b (OsSCE1b). OsSCE1b catalyzes the SUMOylation of OsPelota, a protein involved in plant antiviral RNA decay. Furthermore, RBSDV P6 enhances the interaction between rice ubiquitin E3 ligases SINAT3/4/5 and OsSCE1b in the cytoplasm, leading to increased ubiquitination and degradation of OsSCE1b. Rice plants overexpressing OsSCE1b exhibited reduced susceptibility to RBSDV infection. Conversely, OsSCE1b knockdown and knockout lines, as well as OsPelota knockout lines, were more susceptible, indicating that both OsSCE1b and OsPelota negatively regulate RBSDV infection. Additionally, our findings show that OsSCE1b-catalyzed SUMOylated OsPelota interacts with the Hsp70 subfamily B suppressor OsHBS1, forming a complex that degrades RBSDV genomic RNAs containing one or more GA₆ motifs. Taken together, our data demonstrate that OsSCE1b negatively regulates RBSDV infection by promoting OsPelota SUMOylation and activating the antiviral RNA decay activity of the OsPelota–OsHBS1 complex. Conversely, RBSDV P6 promotes viral infection by enhancing OsSCE1b ubiquitination and degradation, thereby suppressing OsPelota SUMOylation and the rice antiviral RNA decay defense response.

Base editing technologies can improve crops, but their efficiency in maize remains suboptimal. This study attempts to overcome these limitations by examining optimized cytosine and adenine base editors (CBEs and ABEs), namely evoAPOBEC1, evoFERNY, evoCDA1, TadA8.20, and TadA8e, for precise genome editing in transient and stable expression maize cells. Employing a seed fluorescence reporter (SFR) system for rapid screening of BE transformants and transgene-free progenies, we enhanced editing efficiencies and heritability. Notably, TadA8.20 and evoCDA1 attained multiplexed editing efficiencies of up to 100.0% and 79.0% at the tested loci, respectively, with some homozygous and bi-allelic mutants exceeding 72.4% and 73.7%. Precise editing of ZmACC1/2 (acetyl-CoA carboxylase) improved herbicide resistance, with ZmACC2 mutants displaying improved performance. This study advances crop genetic engineering by facilitating robust, multi-locus modifications without altered agronomic performance, enhancing herbicide tolerance in maize. The successful utilization of these BE is a significant step forward in agricultural biotechnology and precision breeding.

Understanding plant adaptive strategies that determine species distributions and ecological optima is crucial for predicting responses to global change drivers. While functional traits provide mechanistic insights into distribution patterns, the specific trait syndromes that best predict elevational optima, particularly in less-studied regions such as the Himalayas, remain unclear. This study employs a novel hierarchical framework integrating morphological, anatomical, and physiological traits to explain elevational distributions among 310 plant species across a 3,500-m gradient (2,650–6,150 m). We analyzed 95,000 floristic records collected from 4,062 localities spanning 80,000 km² in Ladakh, NW Himalayas, India, to define elevational optima and link them with 17 functional traits from over 7,800 individuals. We assessed the roles of moisture and cold limitations on trait–optima relationships by comparing two contrasting habitats (dry steppe and wetter, colder alpine). The predictive power of functional traits was more pronounced in the alpine species facing more extreme abiotic stress than the steppe species. Our results indicate that conservative life history strategies strongly predict elevational optima in alpine areas, while drought avoidance and competitive dominance are key in steppe habitats. Trait syndromes combining short stature, compact growth forms, enhanced storage tissues, and features promoting water-use efficiency (δ¹³C), freezing resistance (fructan levels), and nutrient retention (high root nitrogen and leaf phosphorus) explained 61% of the variation in alpine species' optima. Conversely, lifespan and clonal propagation determined the optima of steppe species at lower elevations. The study emphasizes the importance of functional trait combinations in determining elevational optima, highlighting that alpine species prioritize resource conservation and stress tolerance, while steppe species focus on competitive growth strategies. This multi-trait approach contrasts with previous research focusing on single trait–elevation relationships, providing novel insights into the diverse mechanisms shaping elevational distributions and offering valuable predictive power for assessing vegetation responses to future climate change.

DNAs from the cytoplasmic genomes often communicate with the nuclear genome during regulation, development, and evolution. However, the dynamics of cytonuclear interaction during crop domestication have still been rarely investigated. Here, we examine cytonuclear interactions during grapevine domestication using pan-mitogenome, pan-plastome, and haplotype-resolved nuclear genomes, all assembled from long-read sequences across 33 wild and domesticated grapevine accessions. Structural variation shaped the mitogenomic variation in gene contents, leading to duplications of three specific genes during grapevine domestication (one cox and two rpl genes). Extensive genomic signals of cytonuclear interactions were detected, including a total of 212–431 nuclear–mitochondrial segments (NUMTs) and 95–205 nuclear–plastid segments (NUPTs). These results showed that NUMTs were under strong selection and were more abundant in cultivated grapes, whereas NUPTs dominated in wild grapes, indicating the evolutionary trajectories of cytonuclear interactions during grape domestication. Through Genome-Wide Association Study (GWAS), we identified 84 candidate genes associated with mitochondrial–nuclear genome interactions. Among these, the PFD1 gene acts as a signaling regulator, modulating specific signaling pathways regulated by the mitochondria. Interestingly, there are significantly more cytonuclear interaction genes near NUMTs than in other genomic regions, suggesting NUMT-mediated interactions between the nuclear and mitochondrial genomes. Overall, our study provides evidence that NUMTs promote cytonuclear interaction during grapevine domestication, offering new insight into the impact of cytonuclear interactions on plant evolution, genetics, and breeding.

Bananas (Musa ssp.) are globally important staple crops increasingly constrained by biotic stressors, climatic instability, and the high labor demands of cultivation. The genetic improvement of dwarf phenotypes offers a strategic pathway to enhance mechanization and reduce production costs. In this study, we have carried out whole-genome resequencing of 300 Musa accessions to analyze genome-wide allelic diversity and identify loci associated with shoot architecture. Our analysis uncovered extensive genetic variation within the A subgenome, pivotal for environmental adaptability, and detected introgression from Musa itinerans (subgroup A) into cultivated varieties (subgroup F), suggesting a broadened genetic base amenable to breeding. A genome-wide association study (GWAS) pinpointed MabHLH30 as a crucial gene associated plant stature. Functional validation confirmed MabHLH30 as a critical regulator of plant stature and leaf morphology. Leveraging this finding, we developed molecular markers for MabHLH30, enabling marker-assisted selection (MAS) to accelerate the breeding of compact, high-yielding cultivars. Collectively, these results provide a genomic framework for the targeted improvement of banana architecture and represent a valuable resource for cultivar development under diverse agroecological conditions.

Root nodules are specialized organs formed by the symbiotic relationship between legumes and soil-borne rhizobia, facilitating an exchange of energy and nutrients essential for both organisms. This process is accompanied by dynamic changes in genomic organization and gene expression. While the three-dimensional (3D) architecture of the genome is known to influence gene regulation, its role in nodulation and symbiotic nitrogen fixation remains largely unexplored. In this study, we present the first high-resolution (40 kb) 3D genomic map of peanut roots and root nodules, generated using a high-throughput/resolution chromosome conformation capture strategy. Compared to roots, ∼2.0% of chromosomal regions in nodules transition from a repressive (B) to an active (A) compartment and exhibit significant alterations in topologically associated domains (TADs). Peanut nodules also show more extensive cis-interactions, with 100s of differentially expressed genes enriched in symbiotic pathways and nitrate metabolism. Additionally, assay for transposase-accessible chromatin with high-throughput sequencing identifies 25,863 and 14,703 open chromatin regions (OCRs) in roots and nodules, respectively. By integrating OCR mapping with epigenomic modifications, we reveal dynamic local OCRs (LoOCRs) and histone modifications associated with nodulation-related genes. Notably, novel TADs and long-range chromatin loops are detected in peanut nodules, including an H3K27me3 modification-mediated loop that may regulate the expression of Nodule Inception. Another altered chromatin loop highlights the nodule highly expressed AhMsrA gene, which positively influences nodulation. Together, these findings shed new light on how chromatin architecture shapes gene expression during legume nodulation and nitrogen fixation.