Wiley-Online-Library: New Phytologist: Table of Contents

Global distribution and biogeography of ericoid mycorrhizal fungi

Fri, 12 Jun 2026 20:22:49 -0700

Global predictions of local ericoid mycorrhizal fungal richness, its latitudinal trends and environmental predictors.

Summary

Ericoid mycorrhizal (ErM) fungi play a crucial role across terrestrial ecosystems, forming mutualistic symbiosis with Ericaceae and contributing to soil organic matter dynamics. However, compared to other fungal groups, their biogeography remains unknown. Here, we combined several analytical approaches to analyze a newly compiled, large-scale dataset comprising 39 163 soil samples and more than 13 million ITS rRNA sequences assigned to ErM fungi. Specifically, we asked: What are the global patterns of ErM fungal species richness and relative abundance (out of all fungi) and their predictors, and how is the distribution of ErM fungi associated with soil carbon content at the global scale? We show that ErM fungi reach their highest species richness in very high latitudes. Soil chemistry is a stronger predictor of ErM fungal species richness than climate or ericoid vegetation cover. The relative abundance of ErM fungi is highest in soils with high surface carbon content, supporting their proposed role in soil carbon storage. Furthermore, we predict that climate change will reduce ErM fungal abundance across 38% of the land cover of their current global distribution. Our study shows distinct biogeographic patterns of ErM fungi compared with arbuscular and ectomycorrhizal fungi and indicates the vulnerability of ErM fungi to climate change.

Time‐delayed activator–repressor regulation of ginsenoside biosynthesis in Gynostemma pentaphyllum

Fri, 12 Jun 2026 20:21:27 -0700

Jasmonic acid (JA)-induced antagonistic regulation of ginsenoside biosynthesis in Gynostemma pentaphyllum.

Summary

Jasmonic acid (JA) signaling is a key regulator of plant secondary metabolism, yet how it balances rapid activation with timely repression of ginsenoside biosynthesis remains unclear in Gynostemma pentaphyllum. Here, we investigated the transcriptional regulation mechanism of ginsenoside biosynthesis by JA–responsive basic helix–loop–helix (bHLH) transcription factors. By integrating transcriptome and phylogenetic analyses with yeast one-hybrid, electrophoretic mobility shift assays, dual-luciferase assays, transgenic hairy root overexpression, and RNA interference, together with metabolite profiling, we identified key regulators and defined their roles in the ginsenoside biosynthesis pathway of G. pentaphyllum. We characterized an antagonistic bHLH pair, GpGAB (g36559, Activator), and GpGIB (g21771, Inhibitor). GpGAB activated ginsenoside biosynthetic genes GpDS, GpPPDS, and GpUGT94AT1, whereas GpGIB repressed the expression of GpDS and GpPPDS. GpGAB also upregulated the expression of GpGIB, with GpGAB responding earlier than GpGIB to JA treatment. Taken together, our results support a model in which GpGAB and GpGIB form a time-delayed negative feedback loop that fine-tunes ginsenoside biosynthesis after JA induction, providing a mechanistic framework for dynamic transcriptional regulation of ginsenoside in G. pentaphyllum.

Correction to ‘Marchantia polymorpha GOLDEN2‐LIKE transcriptional factor; a central regulator of chloroplast and plant vegetative development’

Fri, 12 Jun 2026 20:21:26 -0700

New Phytologist, EarlyView.

Small‐scale adaptation to geothermal soil heating in a perennial herb revealed by combining crosses and transplantations

Alicia Valdés, Vigdís F. Helmutsdóttir, Bryndís Marteinsdóttir, Johan Ehrlén — Fri, 12 Jun 2026 20:19:27 -0700

Path diagrams showing the results of piecewise structural equation models examining how fitness (total number of seeds in flowering individuals) of Cerastium fontanum depended on temperature at planting site, temperature difference, mating type, and flowering time (FFD, first flowering date) in each of the two study years.

Summary

Identifying environmental factors associated with local adaptation and traits under selection is key to linking evolutionary processes to the environment. While reciprocal transplantation studies and provenance experiments often have demonstrated adaptation at relatively large spatial scales, adaptation can also occur at very small spatial scales. Combining a crossing experiment with field transplantations, we investigated whether Cerastium fontanum has adapted to geothermally induced small-scale soil temperature differences. Offspring representing a wide range of parental soil temperatures were transplanted across the same temperature range, and traits and fitness components were measured over 2 yr. We evaluated the relationship between plant performance and soil temperatures, the degree of adaptation to their source thermal environment, and the dependence of adaptation on flowering time. Survival, flowering incidence, and overall fitness were lower in warmer soils. However, adaptation to temperature was asymmetric; while all plants performed well at colder sites, individuals from colder origins performed poorly at warmer sites. Flowering time and fitness varied in relation to soil temperature, as well as the difference between planting and source thermal environments. Our findings indicate that small-scale variation in soil temperature underlies fine-scale adaptation and provides important knowledge to understand evolutionary effects of microclimatic variation.

Root anatomical traits modulate the assembly and nitrogen‐transformation potential of root‐associated microbiomes in a temperate steppe

Thu, 11 Jun 2026 20:32:07 -0700

Root traits regulate microbially mediated nitrogen (N) transformation potential.

Summary

Plants have evolved numerous belowground strategies to capture nutrients. While root functional differentiation between absorption and transportation has been inferred from order-based traits, the role of microbiomes in mediating this differentiation remains unclear. We measured traits (anatomical, chemical, and morphological) of lower order (absorption-dominated) and higher order (transportation-dominated) roots of 37 herbaceous species (13 monocots and 24 dicots) in a temperate grassland. Furthermore, we employed high-throughput quantitative polymerase chain reaction and 16S rRNA gene sequencing to investigate bacterial nitrogen-transformation gene abundance, diversity, and community assembly along the soil-root continuum (rhizosphere, rhizoplane, and endosphere) and analyzed their relationships with root traits. Monocot roots exhibited greater bacterial diversity and nitrogen-transformation gene abundances than dicots. Within dicots, lower order roots showed higher bacterial diversity and nitrogen-transformation gene abundances than higher order roots, a pattern not observed in monocots. Lower order roots, characterized by higher cortex proportion, facilitated the enrichment of diverse bacteria and recruitment of nitrogen-transformation microorganisms. These patterns were associated with a decrease in homogeneous selection from lower order to higher order roots. This study reveals the mechanisms of functional differences among herbaceous root orders from a microbiome perspective, offering further insights into how root–microbe interactions underpin nitrogen-transformation potential in terrestrial ecosystems.

Evidence for a trade‐off between growth rate and xylem embolism resistance in 22 Eucalyptus species

Thu, 11 Jun 2026 20:30:45 -0700

Examples of cross-sectional images of branchlets at 4× and 40×.

Summary

Within the growth–survival trade-off framework, embolism resistance is considered a contributor to survival, yet whether greater embolism resistance inherently limits growth remains unclear. We investigated this relationship among 22 Eucalyptus species spanning wide precipitation and temperature gradients, grown under controlled conditions for 6–10 months. We quantified embolism resistance (drought-induced stem P₅₀), growth, and wood anatomy. Our experimental results reveal a clear trade-off between embolism resistance and growth rate, consistently supported by both cross-species and phylogenetic (correlated-divergence) analyses. Faster growing species exhibited less negative P₅₀ and higher vessel lumen fraction, driven by wider vessels, enhancing hydraulic conductivity. Conversely, slower growing species had more negative P₅₀, characterised by thicker vessel walls and a greater density of narrower vessels, reducing hydraulic conductivity. P₅₀ and growth rate were significantly related to climate-of-origin, with species from drier or colder regions exhibiting greater embolism resistance and slower growth. Furthermore, we conducted a global vote-counting review of 34 studies, showing weak but context-dependent support for the growth rate–P₅₀ trade-off, with no evidence of concurrent faster growth and greater embolism resistance. These findings advance understanding of growth rate–embolism resistance trade-offs, reveal climatic adaptation mechanisms in woody species, and inform predictions of plant persistence under climate change.

Anthocyanin biosynthesis in blueberry is regulated by light and abscisic acid signaling via a VcABF2‐miR156‐VcSPL9 feedback loop

Wed, 10 Jun 2026 20:40:02 -0700

Proposed model explaining how the VcABF2-miR156-VcSPL9 feedback loop regulates anthocyanin biosynthesis via the crosstalk between light and abscisic acid signaling.

Summary

The crosstalk between light and abscisic acid (ABA) signaling orchestrates fruit coloration in horticultural crops, including blueberry (Vaccinium spp.). Although the miR156–SPL module is known to post-transcriptionally regulate anthocyanin biosynthesis, its role in integrating light and ABA signaling remains elusive. In this study, we treated blueberry fruits with fluridone (Flu), an ABA biosynthesis inhibitor, which compromised the induction of anthocyanin biosynthesis by high-light (HL) intensity in the fruits. We determined that the ABA-responsive transcription factor (TF) VcABF2 participates in HL-mediated anthocyanin accumulation by transcriptionally activating VcANS expression. We determined that the low-light (LL)-induced SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) TF VcSPL9 directly binds to the promoters of VcABF2, VcDFR, and VcUFGT and transcriptionally represses their expression. However, ABA treatment antagonized the negative regulatory function of VcSPL9 in anthocyanin biosynthesis. Small-RNA transcriptome analysis revealed that miR156 is targeted and activated by VcABF2. This microRNA specifically cleaves VcSPL9 transcripts to relieve VcSPL9-mediated inhibition of VcABF2, ultimately forming a feedback loop that regulates anthocyanin biosynthesis. Our findings elucidate a mechanism by which the VcABF2-miR156-VcSPL9 loop coordinates light and ABA signaling to precisely modulate anthocyanin biosynthesis in blueberry.

Conserved symbiosis‐associated genes in the cycad Encephalartos natalensis suggest co‐option for cyanobacterial symbiosis

Tue, 09 Jun 2026 20:22:41 -0700

The heterocyst-rich Encephalartos natalensis cyanobacterial zone in coralloid root suggests co-option of conserved symbiosis-associated genes. This figure was created in BioRender (BioRender.com/https://BioRender.com/n3qveqc).

Summary

Plant-cyanobacterial symbioses have evolved independently at least four times across land plants, yet their underlying molecular mechanisms remain largely elusive. Here, we elucidate the pathways involved in this specialised symbiosis and nutrient exchange within coralloid roots (CRs) of Encephalartos natalensis. Using anatomical analysis and RNA sequencing, we characterise the structural and transcriptional features of CRs harbouring active, heterocyst-rich, nitrogen-fixing Nostoc cyanobacteria. Notably, no fungal hyphae or arbuscular structures were observed under the sampled conditions. CR-associated upregulation of core common symbiosis signalling pathway (CSSP) genes was evident, genes shared across multiple nodulating symbioses. Transcriptome-wide analysis further revealed elevated expression of citrulline and ornithine biosynthesis genes, indicating host assimilation of Nostoc-fixed ammonia. Together, these findings demonstrate that cycads retain and transcriptionally upregulate conserved symbiosis signalling genes during cyanobacterial associations. Building on the evolutionary link between CSSP genes and the ancient arbuscular mycorrhizal (AM) signalling toolkit, our results support differential retention of these genes across plant lineages. Specifically, in E. natalensis, CSSP gene expression in CRs suggests transcriptional co-option for cyanobacterial symbiosis in CRs. This study provides a framework for understanding the role of ancient molecular pathways in driving plant–microbe symbiosis evolution and diversification.

The cost of a meal: an ancestral plant strategy turns fatty acids into weapons against insect herbivores

Udita Acharya, Debora Gasperini — Tue, 09 Jun 2026 20:20:07 -0700

New Phytologist, EarlyView.

Turnip mosaic virus utilizes the lipid droplet biogenesis machinery to facilitate its propagation in plants

Tue, 09 Jun 2026 20:18:09 -0700

Potyvirus turnip mosaic virus induces neutral lipid accumulation and lipid droplet biogenesis in infected leaves for its own benefit.

Summary

Lipid droplets (LDs), which are dedicated to storing neutral lipids (NLs), are dynamic organelles involved in numerous other functions, including membrane remodeling during abiotic stress. While the hijacking of LDs by animal viruses is well documented, their role(s) in plant virus infection remains largely unexplored. Similar to animal viruses, plant potyviruses reroute host proteins, intracellular membranes, and lipids to create an optimized microenvironment for their efficient viral replication compartment (VRC) assembly and movement. We therefore investigated whether potyviruses can also exploit the LD biogenesis machinery for their own benefit, akin to some animal viruses. Utilizing lipid analyses, confocal and transmission electron microscopy, and viral propagation surveys in plants impaired in LD biogenesis, we show that potyvirus turnip mosaic virus (TuMV) infection induces a significant accumulation of NLs and a proliferation of LDs in Nicotiana benthamiana or Arabidopsis thaliana-infected leaves, which are often located in close proximity to VRCs. This suggests that there is a spatial and functional relationship between LDs and TuMV. We demonstrate also that two protein families crucial for LD biogenesis, namely the lipid droplet-associated proteins and SEIPINs, facilitate TuMV propagation in Arabidopsis thaliana. Taken together, our results indicate a pro-viral function for LDs in potyvirus-infected plants.

Ectomycorrhizal fungi and forest management timelines: do we understand what to conserve?

Asko Lõhmus — Tue, 09 Jun 2026 20:15:49 -0700

New Phytologist, EarlyView.

Homology of the dark cells of Paleozoic liverworts with the specialized oil body cells of modern liverworts (Marchantiophyta)

Susan Tremblay, Josep Mercadal — Mon, 08 Jun 2026 21:54:27 -0700

Examples of oil bodies of extant liverworts of the Jungermanniopsida (Bazzania sp., Riccardia chamedryfoli, and Pallavicinia sp.), Marchantiopsida (Conocephalum sp., Marchantia polymorpha), and Haplomitriopsida (Treubia lacunosa and Haplomitrium sp.) and dark cells of Devonian liverworts Pallaviciniites devonicus and Metzgeriothallus sharonae.

Summary

Oil bodies are a synapomorphy of liverworts (Marchantiophyta), a major group of land plants with a sparse fossil record. Paleozoic liverworts sometimes possess dark cells that appear similar in distribution to liverwort oil body cells. The Middle Devonian Metzgeriothallus sharonae provides an opportunity for comparison with modern liverworts. Shale samples were collected, and the carbonaceous fossils were isolated by acid maceration. Museum shale specimens of Pallaviciniites devonicus were also obtained and processed. The relative location, frequency, and spatial distribution of the fossil dark cells were compared to those of oil body cells in extant taxa. Quantitative analyses revealed that the frequency and spatial distribution of dark cells are comparable to those of oil body cells. Microscopy results show evidence of oil body membranes within dark cells. The dark cells of M. sharonae show clumping near the thallus margin, suggesting an anti-herbivore function. These results support the hypothesis that the dark cells of Paleozoic liverworts and the oil body cells of extant lineages are homologous structures with a shared developmental origin, providing a new character that can aid in the classification of fossils and that sheds light on the evolution and function of liverwort oil bodies.

Apple ZAT11, a C2H2‐type zinc finger protein, enhances resistance to Penicillium expansum by affecting jasmonic acid biosynthesis in apple

Mon, 08 Jun 2026 20:19:54 -0700

A working model illustrating the role and mechanism of MdZAT11 in response to Penicillium expansum infection.

Summary

Blue mold, caused by Penicillium expansum, is a prevalent postharvest disease of apple and significantly limits apple quality. Apple have key genes underlying their biological stress responses and corresponding functions that remain largely unexplored. Here, we identified MdZAT11, a Cys2/His2 (C2H2)-type zinc finger protein, as a crucial positive regulator of apple resistance to P. expansum infection. Utilizing transcription factor-centered yeast one-hybrid (TF-centered Y1H) and RNA sequencing analyses, we discovered 1059 potential target genes of MdZAT11, with Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicating significant enrichment in stress-responsive pathways, particularly jasmonic acid (JA) biosynthesis. Further investigation revealed that MdZAT11 enhances the expression of JA biosynthesis genes (MdAOS, MdAOC, MdLOX6, and MdLOX3.1) by directly binding to their promoters, as demonstrated by electrophoretic mobility shift assays (EMSA), dual-luciferase reporter (DLR) assays, and RT-qPCR analysis, thereby augmenting JA biosynthesis. Taken together, our findings advance understanding of the transcriptional regulation of defense against P. expansum in apple and identify MdZAT11 as a candidate gene worth further investigation for disease resistance in this species.

A cyclo‐DOPA 6‐O‐glucosyltransferase‐mediated route for gomphrenin I biosynthesis in Basella alba and Gomphrena globosa

Sun, 07 Jun 2026 22:05:34 -0700

Pigment analysis of Basella alba plants.

Summary

Betacyanins are red pigments characteristic of Caryophyllales and show considerable structural diversity, yet the enzymatic basis underlying 6-O-glucosylated betacyanins, such as gomphrenin I, has remained unclear. In particular, how alternative glucosylation patterns contribute to betacyanin diversification is poorly understood. Here, we identified cyclo-DOPA glucosyltransferases from Basella alba and Gomphrena globosa and examined their roles in gomphrenin I biosynthesis using transient expression assays and tobacco BY-2 cell systems. Phylogenetic analyses, structural modelling, and site-directed mutagenesis were employed to investigate their functional and structural characteristics. BacDOPA5/6GTs catalysed both 5-O- and 6-O-glucosylation of cyclo-DOPA, leading to the production of betanin and gomphrenin I, whereas GgcDOPA6GT specifically mediated gomphrenin I formation. These enzymes belong to distinct subclades within the cDOPA-GT family, and mutational analyses demonstrated essential roles for conserved histidine residues and an α-helical region adjacent to the catalytic site. Thermal stability analyses further showed that gomphrenin I is more thermally stable than betanin, likely due to the formation of an intramolecular hydrogen bond. Together, these results reveal an additional cDOPA6GT-mediated route for gomphrenin I biosynthesis and provide insight into the diversification and functional specialisation of betacyanins, linking the position of glucosylation to pigment stability and biochemical properties.

ESN3, a nodule‐specific small peptide essential for symbiotic nitrogen fixation in Medicago truncatula

Sun, 07 Jun 2026 22:03:49 -0700

Symbiotic nitrogen fixation–defective (fix⁻) phenotypes of Medicago truncatula esn3 mutant.

Summary

Symbiotic interactions between legumes and rhizobia rely on the symbiotic interface, the symbiosome membrane. However, the regulatory mechanisms for symbiosome membrane maintenance remain largely elusive. Methods include forward genetics screenings of mutants, transcript-based cloning and genetic complementation, yeast two-hybrid library screening and Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 gene editing. We characterized Early Senescent Nodule 3 (ESN3), a key regulator of symbiotic nitrogen fixation (SNF) encoding a nodule-specific, 54 aa-long small peptide, which localizes to the symbiosome membrane in Medicago truncatula. We identified SYPTAXIN132 as an ESN3-interacting protein. We showed that syp132a mutants exhibited premature nodule senescence and upregulation of senescence-associated gene expression, similar to the esn3 mutant. Our proteomic studies revealed significant alterations of a large number of membrane proteins in the symbiosome fraction of the esn3 mutant, consistent with a key role of ESN3 in symbiosome maintenance. Furthermore, our data indicated that the expression of ESN3, but not SYP132A, is responsive to gibberellic acid (GA) treatments and DELLA proteins are positive regulators of ESN3 gene expression. In this study, we demonstrated that ESN3 encodes a novel nodule-specific small peptide, playing a key role in SNF. In conjunction with the syntaxin SYP132A, GA signaling plays a negative role in SNF at a later stage of nodule development.

Combined phylogenetic and geographic data can predict plant–pest interactions with high accuracy

Elvira Hernández‐Gutiérrez, Richard A. Nichols, Laura J. Kelly — Sun, 07 Jun 2026 22:02:05 -0700

Schematic overview of the study pipeline.

Summary

Non-native plant pests can pose major threats to biodiversity, with destructive ecological and economic consequences. The ability to predict future threats would allow limited resources to be concentrated on managing the most serious risks. We built a Bayesian model to predict hosts at risk from Agrilus, a beetle genus of over 3000 species including one of the world's worst tree pests, using phylogenetic and geographic relationships between known and potential hosts. We assess risk to Quercus (oak), their most common host, by predicting the probability of over 7000 possible oak–Agrilus interactions to identify species at risk and inform future prevention efforts. Our model detects known hosts with 83.6% accuracy under Leave-One-Out cross-validation, and successfully classifies novel hosts of Agrilus species in new areas, indicating strong predictive performance on independent or misclassified data. Geographic proximity is a strong predictor of host sharing, with the likelihood declining rapidly with distance. In general, hosts cluster phylogenetically, with a tendency for closely related oaks to share the same Agrilus species. Our approach uses readily available data and could be implemented to assess Agrilus interactions with other plant genera, and extended to additional host–pest systems to help prioritise countermeasures against threats world-wide.

Resumen

Las plagas no nativas de plantas pueden representar graves amenazas para la biodiversidad, con consecuencias ecológica y económicamente devastadoras. La predicción de futuras amenazas permitiría concentrar los limitados recursos disponibles para la gestión de los riesgos más graves. Aquí, desarrollamos un modelo bayesiano para predecir posibles nuevas plantas huésped de Agrilus, un género de escarabajo con más de 3.000 especies que incluye a una de las peores plagas arbóreas del mundo, usando relaciones filogenéticas y geográficas entre huéspedes conocidos y potenciales. Evaluamos el riesgo para Quercus (roble), su huésped más común, prediciendo la probabilidad de más de 7.000 posibles interacciones roble–Agrilus, para identificar especies en riesgo e informar futuras medidas de prevención. Nuestro modelo detecta huéspedes conocidos con una precisión de 83,6% en validación cruzada dejando uno fuera (‘Leave-One-Out’), y clasifica con éxito nuevos huéspedes de especies de Agrilus que ya han invadido áreas nuevas. Esto indica un sólido rendimiento predictivo sobre datos independientes o mal clasificados. La proximidad geográfica es un fuerte predictor del uso compartido de huéspedes, cuya probabilidad disminuye rápidamente con la distancia. En general, las especies huésped se agrupan filogenéticamente. Los robles estrechamente emparentados suelen compartir la misma especie de Agrilus. Nuestro enfoque utiliza datos fácilmente disponibles y puede implementarse para evaluar interacciones de Agrilus con otros géneros de plantas, así como ser extendido a otros sistemas huésped–plaga para ayudar a priorizar medidas de control frente a riesgos a escala mundial.

Exploring thylakoid emergence: evolution of membrane biogenesis and photosystem II assembly in early‐diverging cyanobacteria

Louise Hambücken, Denis Baurain, Luc Cornet — Fri, 05 Jun 2026 20:39:41 -0700

Overview of the results. Phylogenetic analyses of 36 assembly factors of photosystem II (PSII) and 13 proteins involved in membrane dynamics summarized in Siebenaller & Schneider (2023) were performed to investigate the taxonomic distributions and structural differences between the thylakoid-less Gloeobacterales and the Phycobacteria.

Summary

Thylakoid membranes (TM) in cyanobacteria and chloroplasts host the light-dependent reactions of oxygenic photosynthesis. Gloeobacterales, the earliest-diverging cyanobacterial lineage, lack TM and perform photosynthesis in the cytoplasmic membrane (CM), representing an ancestral state relative to other cyanobacteria (Phycobacteria). This study investigates the evolutionary origin of TM. Phylogenomic analyses were performed across a phylogenetically diverse set of cyanobacteria, including extensive representation of basal lineages (Gloeobacterales, Thermostichales, Gloeomargaritales, and Pseudanabaenales), as well as micro- and macrocyanobacteria, using orthologous proteins involved in membrane dynamics and photosystem II (PSII) assembly, together with structural modeling using AlphaFold3. We identified two candidate proteins associated with membrane trafficking that may contribute to TM biogenesis, including the SPFH (Stomatin, Prohibitin, Flotillin, en HflK/C) family member Slr1106, proposed to have been acquired by lateral gene transfer. Analysis of 36 PSII assembly factors revealed modifications in late-stage assembly, notably in manganese homeostasis. Structural changes in the YidC translocase may have facilitated the relocation of linear electron transfer components from the CM to TM. Altogether, these phylogenetic and functional prediction analyses provide new insight into the molecular innovations that led to TM emergence, including membrane trafficking systems, PSII assembly changes, and protein targeting adaptations.

Stomata in motion: How temperature shapes guard cell function and developmental plasticity

Shao‐Li Yang, Martijn van Zanten, Ive De Smet — Fri, 05 Jun 2026 20:36:40 -0700

The micropores, namely stomata, on the plant leaf surface are crucial for dealing with stressful conditions. Stomatal development (density) and dynamics (opening and closing) are tightly regulated by temperature. Stomatal development is primarily regulated by the transcription factor SPCH, which is inhibited by PIF4 under heat but activated by SCRM/ICE1 under cold. Stomatal dynamics, on the contrary, are regulated by complex signalling networks in response to temperatures, allowing stomata to open under heat and close under cold rapidly. This precise regulation of stomata enables plants to adapt to fluctuating environments.

Summary

Stomata, the micropores on plant epidermal surfaces, balance the gain of inorganic carbon with evaporative loss of water. Stomata consist of two specialised guard cells that regulate aperture in a turgor-driven manner. Stomatal development (number and size) and dynamics (opening and closing) are both factors determining performance and survival under stressful conditions. Understanding the regulatory mechanisms of stomatal development and dynamics is thus key for developing crops that are resilient to climate warming. This Tansley insight summarises the current knowledge of how temperature cues control stomatal dynamics for rapid responses and feed into stomatal developmental programmes for long-term adaptation.

Accessory regions and horizontal gene transfer shape the evolution of clonal Colletotrichum nymphaeae infecting strawberry

Joris A. Alkemade, Alan G. Buddie, Anthony Kermode, Timothy G. Barraclough — Fri, 05 Jun 2026 20:35:22 -0700

Genetic diversity of strawberry-infecting Colletotrichum isolates.

Summary

Rapid adaptation in fungal plant pathogens is often attributed to sexual recombination, yet many important pathogens are largely clonal. We investigated how genetic and phenotypic diversity arises in the predominantly asexual fungus Colletotrichum nymphaeae, the main cause of strawberry anthracnose in Europe and North America. We performed comparative genomics on 36 C. nymphaeae genomes and 45 other Colletotrichum genomes sampled from strawberry or from closely related species, assessing population structure, transposable element (TE) content, genome compartmentalisation and signatures of horizontal transfer, and linked these features to phenotypic variation and virulence. Colletotrichum nymphaeae consists of three major lineages, with a globally distributed clonal lineage showing high variability in morphology and virulence. Extensive variation in TE content was detected among and within lineages. Genomes are compartmentalised into core regions and TE-rich accessory regions (ARs) that cluster by lineage and are enriched for gene duplications, genes under relaxed selection and genes linked to stress, virulence and fungicide resistance. We identified a Starship element and a 2 kb region containing two effector genes that were horizontally acquired. TE-rich ARs and horizontal gene transfer drive diversification in this largely asexual pathogen, shaping its evolution and posing challenges for durable strawberry anthracnose management.

Overcoming redundancy in the Arabidopsis TREHALOSE‐6‐PHOSPHATE PHOSPHATASE family reveals connections to development and iron homeostasis

Fri, 05 Jun 2026 20:34:08 -0700

Arabidopsis plants mutant for all TREHALOSE-6-PHOSPHATE PHOSPHATASE genes are smaller with enhanced branching.

Summary

Arabidopsis encodes 10 TREHALOSE-6-PHOSPHATE PHOSPHATASE (TPP) genes, homologous to maize RAMOSA3 (RA3), which controls shoot branching. Here, we explored the functions of the Arabidopsis TPPs. We used expression profiling, multiplex CRISPR-Cas9 editing and metabolite profiling to explore the function of Arabidopsis TPP genes. The Arabidopsis TPP genes had distinct expression patterns in shoot apices, with TPPI and TPPJ expressed in shoot meristem boundaries, reminiscent of RA3 expression. Single and double mutants in these genes lacked obvious phenotypes; however, a CRISPR-Cas9 knockout of all 10 TPP genes led to increased branching and earlier flowering. Native expression of GFP-tagged TPPI partially complemented these defects, with protein localization in meristems, vascular tissues and in nuclei. Metabolite profiling revealed higher trehalose 6-phosphate (Tre6P), lower trehalose and altered sugar and iron-associated metabolites. The 10× tpp mutants were also chlorotic, had low iron levels and could be rescued by iron supplementation. Consistently, developmental and iron-responsive genes were upregulated in the 10× tpp mutants, while photosynthesis-related genes were repressed. Our findings suggest that TPP genes redundantly regulate shoot architecture, sugar metabolism, iron homeostasis and photosynthesis in Arabidopsis, and support a role for TPP-mediated Tre6P signaling in coordinating developmental and physiological pathways.

The GSK3/SHAGGY‐like OsGSK3 phosphorylates and inhibits phase separation of OsFCA at Ser‐43 and Ser‐45 to regulate brassinosteroid signaling and rice architecture

Thu, 04 Jun 2026 22:22:39 -0700

A working model for GLYCOGEN SYNTHASE KINASE 3-mediated phosphorylation of FLOWERING CONTROL LOCUS A in the regulation of brassinosteroid signaling and rice growth and development.

Summary

Brassinosteroid (BR) signaling plays a critical role in rice (Oryza sativa L.) grain development. GLYCOGEN SYNTHASE KINASE 3 (OsGSK3), a negative regulator of BR signaling, suppresses the transcriptional activity of OsBZR1 through phosphorylation. In this study, we employed a phosphoproteomic approach to construct an OsGSK3-mediated regulatory network. Within this network, we identified FLOWERING CONTROL LOCUS A (OsFCA) as a positive regulator of BR signaling and grain length, with m-Osfca mutants exhibiting significantly lower sensitivity to brassinolide treatment. Importantly, OsGSK3 interacts with and phosphorylates OsFCA on serine residues S43 and S45, and then forms condensates via liquid–liquid phase separation. Phosphorylated OsFCA promotes the translocation of the OsGSK3-OsFCA complex into the cytoplasm. Within the cytoplasm, OsGSK3 and OsFCA no longer exist in a condensate state. This mechanism provides precise regulation of grain length in rice. Notably, Osfca mutants are late-flowering, with OsFCA promoting heading under long-day conditions by repressing the expression of Grain number, plant height and heading date 7 (Ghd7) while activating that of Early heading date 1 (Ehd1), Heading date 3a (Hd3a), and RICE FLOWERING LOCUS T 1 (RFT1), which is potentially modulated by OsGSK3. This study clarifies the BR signaling transduction network by identifying OsFCA as a positive BR signaling component that regulates grain development and heading date, providing theoretical foundations for molecular breeding design in rice.

Dynamic microbiome turnover and glycerol‐3‐phosphate‐linked metabolic adjustments underlie resilience to desiccation in intertidal algae

Thu, 04 Jun 2026 22:19:25 -0700

A holobiont-level desiccation strategy in intertidal red algae. Rapid dehydration restructures the microbiome, enriching stress-tolerant taxa, like Sulfitobacter and Alteromonas, while host-secreted G3P sustains key epiphytic bacteria that enhance antioxidant and osmoprotective functions. This cross-domain metabolic coupling highlights a co-evolved strategy for intertidal resilience.

Summary

Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host–microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.

The feedback regulation between DREB2C and E3 ligases DEL1/DEL2 for balancing the initial growth and ABA signaling in Arabidopsis

Thu, 04 Jun 2026 22:19:20 -0700

Schematic diagram of the feedback regulation between DREB2C and E3 ligases DEL1/DEL2 for balancing the initial growth and ABA signaling in Arabidopsis.

Summary

Dehydration-Responsive Element Binding Protein 2C (DREB2C) is a vital transcription factor that responds to drought, cold and heat stresses in Arabidopsis. Previous studies have suggested that DREB2C might be involved in abscisic acid (ABA) signaling, but the detailed molecular mechanism remains unclear. In this study, we find that DREB2C positively regulates ABA-mediated seed germination and root elongation. Degradation assays show that the degradation of DREB2C relies on the 26S proteasome pathway and ABA promotes the accumulation of DREB2C. Further analyses confirm that two novel E3 ligases DREB2C-Degrading E3 Ligase 1/2 (DEL1/2) interact with DREB2C and mediate its ubiquitination. Functional analyses demonstrate that DEL1 or DEL2 negatively regulates ABA-mediated seed germination and root elongation, while overexpression of DEL1 or DEL2 in DREB2C-overexpressing lines results in reduced ABA hypersensitivity. Genetic analysis indicates that DEL1 and DEL2 function redundantly in the degradation of DREB2C and act upstream of DREB2C in the ABA signaling pathway. In addition, DREB2C directly binds to the promoters of DEL1 and DEL2 and activates their expression, thereby shutting down the transmission of ABA signals. Collectively, we uncover a novel feedback regulatory loop between DREB2C and DEL1/DEL2 that balances the initial growth stage and ABA responses in Arabidopsis.

A root–soil association index reveals life‐history strategies of arbuscular mycorrhizal fungi

Thu, 04 Jun 2026 22:18:22 -0700

Phylogenetic tree of Glomeromycota, including all studied virtual taxa, based on the small subunit region. The bar plot in the external part of the phylogeny depicts the log-transformed arbuscular mycorrhizal root–soil association index, with values > 0 indicating rhizophilic lifestyle, < 0 edaphophilic lifestyle, and close to 0 no preference. The color of the bars depicts the statistical support, which indicates the posterior support for the rhizophilic or edaphophilic strategy of each virtual taxon.

Summary

Arbuscular mycorrhizal (AM) fungal taxa differ in their life-history strategies, including their preferential association with intraradical vs extraradical compartments. We introduce the arbuscular mycorrhizal root–soil association index (AMF-RSI), a novel quantitative index describing the relative association of AM fungi with root vs soil compartments, corresponding to the previously proposed rhizophilic and edaphophilic AM fungi. The AMF-RSI was calculated from metabarcoding data compiled in the GlobalAMFungi database using Hierarchical Modeling of Species Communities and was subsequently applied to assess shifts in AM fungal community traits driven by soil disturbance caused by tillage. We assessed 301 AM fungal taxa and found that AMF-RSI was strongly conserved at the genus level. While the majority of AM fungal taxa from families Archaeosporaceae, Diversisporaceae and Paraglomeraceae exhibited preferential association with soil, taxa within Glomeraceae exhibited high variability in edaphophilic vs rhizophilic strategies. AMF-RSI values predicted AM fungal community responses to soil disturbance, with rhizophilic taxa being more prevalent in tilled soils. The AMF-RSI represents a new quantitative trait distinguishing preferential association of AM fungi with intraradical vs extraradical compartments (edaphophilic vs rhizophilic life-history strategies). Applied at the community level, it provides a tool for characterizing shifts in AM fungal communities in response to environmental conditions.

Organized peripheral vascular strand development in nodules is controlled by a bHLH/HLH heterodimer

Thu, 04 Jun 2026 22:16:57 -0700

Schematic representation of the proposed signaling pathway controlled by NVDs leading to legume-type nodule development.

Summary

The Leguminosae family can develop root nodules with symmetrical peripheral vascular-strands (PVSs). Medicago truncatula forms indeterminate nodules with PVSs. The PVSs elongate directly from the root toward the nodule apex, maintaining a symmetrical organization and facilitating the formation of the cylindrical nodule structure. By combining genetic, biochemical, and genomic tools, we have shown that two basic Helix–Loop–Helix groups of transcription factors, MtbHLH1 (renamed Nodule Vascular bundle Development 1 (NVD1)) and NVD2, control the development of symmetrical PVSs in M. truncatula. In nvd1 nodules, PVSs drift toward the infection zone, generating aberrantly shaped nodules. NVD1 activates its expression along with NVD2, a transcriptional regulator. NVD1 functions downstream of auxin signaling. Transcriptome sequencing of nvd1 and nvd2 nodules, combined with visualization of auxin and cytokinin (CK) signal outputs, revealed disrupted auxin and CK signaling in nvd nodules. Furthermore, ectopic expression of the auxin biosynthetic enzyme (MtYUCCA8) under pMtNVD1 and pMtNVD2 resulted in defective PVSs. Mutant nvd2 nodules display asymmetric PVSs. NVD2 regulates the transcriptional activity of NVD1 by forming heterodimers with it. The formation of symmetrical PVSs depends on the balanced presence of NVD1 and NVD2. Our findings highlight the pivotal role of the NVD1-NVD2 interaction in shaping the development of symmetrical PVSs.

David Johnson

Thu, 04 Jun 2026 22:15:48 -0700

David Johnson, Lancaster University (UK).

Machine learning‐guided multi‐omics suggests iron‐dependent hormonal signaling drives root morphological plasticity in wheat under temperature stress

Wenyuan Shen, Qingming Ren, Xinyu Chen, Yiyang Dai, Yu Zhang, Fei Xiong — Thu, 04 Jun 2026 22:14:46 -0700

Proposed working model of the iron-dependent hormone trade-off.

Summary

Root plasticity is crucial for crop survival under climate change. However, the coordinated regulatory network between metabolic disturbances and hormonal signaling that drives morphological adaptation under temperature fluctuations remains unclear. This study integrated machine learning-driven multi-omics analysis, in situ histochemical localization, and pharmacological validation to decipher the root adaptation strategies of wheat under temperature gradients. Wheat roots exhibited convergent morphological plasticity under temperature stress. However, this convergence was associated with distinct hormonal signaling pathways linked to iron homeostasis. Transcriptome data indicated that temperature stress generally down-regulated genes associated with iron acquisition strategy II. Low-temperature stress induced physiological iron deficiency, which triggered an auxin surge to promote compensatory root hair elongation, coinciding with the transcriptional upregulation of iron acquisition Strategy I. Conversely, high-temperature stress induced jasmonic acid accumulation, which contributed to maintaining root hair growth while potentially mitigating iron overload by promoting iron compartmentalization and restricting local accumulation. Our findings support an ‘iron-dependent hormonal trade-off’ model and identified iron homeostasis as the core metabolic hub connecting environmental perception, hormonal regulation, and root architectural plasticity. This study highlights the powerful role of multi-omics integration approaches in uncovering hidden metabolic targets, providing a theoretical basis for breeding climate-adaptive crops with optimized root systems.

Natural variation in OsMYB305 downregulating cytokinin‐mediated inhibition of leaf senescence contributes to regional adaptation in rice

Thu, 04 Jun 2026 22:11:37 -0700

Proposed regulatory model of OsMYB305 in leaf senescence.

Summary

Accumulating evidence has identified transcription factors (TFs) as key regulators of the onset and progression of leaf senescence. However, the regulatory role of the rice myeloblastosis (MYB) TF OsMYB305 in this process remains largely unknown. CRISPR/Cas9-mediated osmyb305 knockout mutants were used to examine senescence phenotypes. Protein–DNA interactions were analyzed using in vivo and in vitro binding assays and predicted using AlphaFold. Natural variations in OsMYB305 were investigated using the International Rice Genebank Collection Information System database. osmyb305 mutants exhibited delayed leaf senescence under both natural and dark-induced senescence conditions. OsMYB305 TF downregulated adenosine phosphate-isopentenyltransferase 8 (OsIPT8) and upregulated cytokinin oxidase/dehydrogenase 2 (OsCKX2) by directly binding to their promoters, thereby modulating cytokinin homeostasis during leaf senescence. Natural single-nucleotide polymorphisms (SNPs) in OsMYB305 were associated with phenotypic variation in leaf senescence among 3000 rice accessions, and a SNP in the cis-element of OsIPT8 promoter disrupted OsMYB305 binding affinity. These results identify OsMYB305 as a key transcriptional activator inducing leaf senescence and suggest that natural allelic variation in OsMYB305 contributes to regional adaptation in rice cultivation.

Pollinator efficiency, rather than bee decline, explains a shift to hummingbird pollination in tropical montane forests

Thu, 04 Jun 2026 08:00:46 -0700

Hummingbird pollination is a hallmark of American plant diversity and has long been thought to evolve in tropical mountains due to declining bee activity. Using sister species of Costus specialized on bees (C. kuntzei) and hummingbirds (C. wilsonii), we show that this shift is not driven by reduced bee visitation with elevation, but by greater pollination effectiveness of hummingbirds. Photographs by P. Juárez.

Summary

A longstanding but untested hypothesis proposes that reduced bee visitation in tropical montane cloud forests has repeatedly driven the evolution of hummingbird pollination. Here, we test whether recently diverged bee and hummingbird pollination syndromes in two sister species are adapted to their pollination environments, and whether this reflects declining bee activity at higher elevations. Alternatively, we ask whether higher pollen transfer efficiency drives adaptation to hummingbirds regardless of bee availability. We measured visitation and per-visit efficiency to estimate pollinator effectiveness and conducted reciprocal translocations of Costus kuntzei, with ancestral bee pollination, and Costus wilsonii, with derived hummingbird pollination, across an elevational gradient in Costa Rica, including sites within and outside each species' range and at their elevational boundary. In their ranges, the species are specialized on bees or hummingbirds. However, pollinator effectiveness was higher for hummingbird-pollinated C. wilsonii because of greater per-visit efficiency, despite bee-pollinated C. kuntzei experiencing higher visitation. In reciprocal translocations, C. kuntzei showed uniform bee visitation across habitats, whereas hummingbird visitation increased with elevation for C. wilsonii. Our results show that floral adaptation to hummingbird pollination is likely driven by higher hummingbird visitation in montane environments combined with greater per-visit efficiency, rather than declining bee visitation with elevation.

Resumen

Una hipótesis antigua, pero aún no evaluada, propone que la reducción en las visitas de abejas en los bosques nubosos tropicales de montaña ha impulsado repetidamente la evolución de la polinización por colibríes. Aquí evaluamos si los síndromes de polinización por abejas y por colibríes, recientemente divergentes en dos especies hermanas, están adaptados a sus ambientes de polinización, y si esto refleja una disminución en la actividad de las abejas a mayores elevaciones. Alternativamente, evaluamos si una mayor eficiencia en la transferencia de polen impulsa la adaptación a los colibríes independientemente de la disponibilidad de abejas. Medimos la visitación y la eficiencia por visita para estimar la efectividad de los polinizadores, y realizamos translocaciones recíprocas de Costus kuntzei, con polinización ancestral por abejas, y Costus wilsonii, con polinización derivada por colibríes, a lo largo de un gradiente elevacional en Costa Rica, incluyendo sitios dentro y fuera del rango de distribución de cada especie y en su límite elevacional. Dentro de sus rangos de distribución, las especies están especializadas en abejas o colibríes. Sin embargo, la efectividad de los polinizadores fue mayor para C. wilsonii, polinizada por colibríes, debido a una mayor eficiencia por visita, a pesar de que C. kuntzei, polinizada por abejas, recibió una mayor visitación. En las translocaciones recíprocas, C. kuntzei mostró una visitación uniforme por abejas entre hábitats, mientras que la visitación por colibríes aumentó con la elevación en C. wilsonii. Nuestros resultados muestran que la adaptación floral a la polinización por colibríes probablemente está impulsada por una mayor visitación de colibríes en ambientes montanos combinada con una mayor eficiencia por visita, más que por una disminución en la visitación de abejas con la elevación.

CNGCs in Marchantia paleacea uncouple arbuscular mycorrhizal symbiosis and rhizoid development

Anson Ho Ching Lam, Aisling Cooke, Jake Richardson, Myriam Charpentier — Thu, 04 Jun 2026 00:40:10 -0700

Rhizoid growth and AM fungal infection are uncoupled.

Summary

In Marchantia paleacea, MpaDMI1-dependent nuclear Ca²⁺ oscillations are essential for arbuscular mycorrhizal (AM) fungal colonisation, indicating that endosymbiosis-mediated nuclear Ca²⁺ signalling is a conserved feature of land plant–AM symbiosis. Despite this conservation, DOES NOT MAKE INFECTION (DMI)1 regulatory properties have diverged between bryophytes and angiosperms, suggesting lineage-specific adaptation and incomplete conservation of the Ca²⁺ oscillation machinery. In angiosperms, DMI1-dependent Ca²⁺ release requires CYCLIC NUCLEOTIDE-GATED CHANNELS (CNGC)15, but whether a comparable CNGC module operates in bryophytes, whose CNGC gene family is greatly reduced, has remained unknown. Here, we combined phylogenetic, genetic and cell biology approaches to investigate diverging land plant CNGCs function. Phylogenetic analyses across streptophytes reveal that CNGCs diversified into three ancient superclades before the terrestrialisation of plants. Functional analyses reveal that in M. paleacea, the combined activity of three MpaCNGCs spanning two superclades is required for endosymbiosis-associated nuclear Ca²⁺ oscillations and AM fungal colonisation. Although two of these MpaCNGCs redundantly regulate rhizoid elongation, AM fungi activate Ca²⁺ signalling and penetrate ventral cells lacking rhizoid growth, indicating that tip-growing cells are not strictly required for fungal entry in M. paleacea. Together, these findings link MpaCNGC function in rhizoid development and AM symbiosis to nutrient acquisition, supporting both soil exploration and AM fungal colonisation.

Gravity sensing in plants

Xiaolian Wang, Xinyue Cai, Huan Huo, Haodong Chen — Thu, 04 Jun 2026 00:38:35 -0700

Gravitropism in plants.

Summary

Gravity, a constant force on Earth, fundamentally shapes plant architecture by directing organ growth, a process known as gravitropism. Shoots typically grow upward (negative gravitropism) and roots downward (positive gravitropism). In seed plants, gravity is sensed by specialized cells, including endodermal cells in shoots and columella cells in roots, collectively termed statocytes. The gravitropic response occurs through three sequential steps: gravity sensing/perception, signal transduction, and growth response. For over a century, the starch-statolith hypothesis dominated our conceptual understanding of gravity sensing, yet its molecular mechanism remained elusive. A molecular basis was established in 2023, when sedimenting amyloplasts were shown to repolarize LAZY proteins. This discovery allows us to molecularly define one type of gravity sensing as the process from amyloplast sedimentation (physical susception) to LAZY repolarization (physiological signal conversion). Meanwhile, evidence suggests the existence of alternative gravity-sensing pathways independent of the starch-statolith model, the mechanisms of which remain largely unknown. This review summarizes current knowledge and perspectives on gravity sensing, primarily in vascular plants, while integrating key insights from nonvascular lineages to provide an evolutionary context. Potential agricultural applications of gravity-sensing mechanisms are also discussed.

概括

重力是地球上恒定存在的力，通过指引器官的生长方向从根本上塑造了植物的形态结构。植物对重力刺激产生定向生长反应的过程被称为向重力性。植物的地上部分通常表现为向上生长(负向重力性)，而根则向下生长(正向重力性)。在种子植物中，重力由特化的细胞所感知，包括茎中的内皮层细胞和根中的根冠柱细胞，它们统称为平衡细胞。向重力性反应通过三个连续步骤完成:重力感受、信号转导和生长反应。一个多世纪以来，“淀粉-平衡石”假说主导着我们对重力感受的认知，但其分子机制一直未被揭示。2023年，淀粉体沉降被证明可使LAZY蛋白重新极性化，从而为这一机制奠定了分子基础。这一发现使我们能够从分子层面将一类重力感受定义为从淀粉体沉降(物理感知)到LAZY蛋白重新极性化(生理信号转换)的过程。同时，有证据表明存在不依赖于“淀粉-平衡石”模型的其他重力感受通路，但其机制在很大程度上仍不清楚。本文综述了当前关于重力感受的研究进展与观点，主要以维管植物为对象，同时从演化视角整合了非维管植物的关键发现，并探讨了重力感受机制潜在的农业应用价值。

How ecological lifestyle rewires the architecture of photoprotection across the green lineage

EonSeon Jin — Wed, 03 Jun 2026 21:30:52 -0700

New Phytologist, Volume 251, Issue 1, Page 5-7, July 2026.

If not cold, then short days

Yanjie Song, Laura E. Dixon — Wed, 03 Jun 2026 21:30:52 -0700

New Phytologist, Volume 251, Issue 1, Page 8-10, July 2026.

The epigenetic set‐point: metabolic and redox gating of developmental transitions in plants

Latif Ahmad Peer — Wed, 03 Jun 2026 21:30:52 -0700

Epigenetic Set-Point: A biophysical integrator of plant developmental transitions. (1) Analog Inputs: Environmental cues, metabolic status, and redox signals (ROS/NO) converge to modulate the chromatin landscape. (2) Threshold Modulation: These signals regulate the kinetic barrier (ΔG‡) by governing writers (PRC2), erasers (JMJ), and readers (LHP1). Redox-mediated ‘eraser jamming’ and metabolic licensing lower this barrier. (3) Digital Outcomes: Crossing the threshold triggers a stable, bistable ‘Digital Lock,’ enabling predictive phenology and epibreeding targets. TOR, Target of Rapamycin; ROS, reactive oxygen species; NO, nitric oxide; PRC2, Polycomb Repressive Complex 2; JMJ, Jumonji demethylase; LHP1, LIKE HETEROCHROMATIN PROTEIN 1; ΔG‡, effective kinetic barrier.

Summary

Plants survive fluctuating environments by converting transient stress signals into stable developmental decisions; however, the biophysical logic that filters environmental ‘noise’ from true ‘signals’ remains elusive. I propose the epigenetic set-point paradigm, in which chromatin acts as a biophysical integrator that couples metabolic and redox inputs to establish developmental thresholds. I delineate the molecular hardware, writers that nucleate chromatin states, readers that compact chromatin, and erasers that reset marks, which convert analog environmental cues into digital, bistable switches at master regulatory loci, such as FLOWERING LOCUS C and VERNALIZATION 1. I present a testable model showing how redox gating of histone erasers mediated by nitric oxide and reactive oxygen species and metabolic gating of chromatin writers mediated by Target of Rapamycin signaling and acetyl–CoA availability collectively modulate developmental transition probabilities. This integration generates a spectrum of memory stabilities, from the Digital Set-Point of vernalization to Metastable Set-Point underlying thermomemory and rare transgenerational inheritance. Finally, I translate this framework into an epibreeding roadmap, proposing the use of single-cell epigenomic approaches for predictive phenology and tunable epigenetic engineering to design crops with ‘rheostat-like’ resilience. Together, this synthesis positions the epigenetic set-point as a dynamic, programmable logic governing plant adaptation to climate change.

Issue Information

Wed, 03 Jun 2026 21:30:52 -0700

Cover Legend Maximum projection confocal micrograph of a developing maize ear primordium expressing PIP2-CFP membrane marker (cyan) and developmental receptor BAM1D-YFP (yellow). Image courtesy of Penelope Lindsay (Lindsay et al., pp. 262–275).

Correction to ‘Shortcutting photorespiration: avenues and challenges toward realizing higher‐yielding photorespiratory bypass crops’

Wed, 03 Jun 2026 21:30:52 -0700

New Phytologist, Volume 251, Issue 1, Page 589-589, July 2026.

Photosynthetic primary production in the Mesoproterozoic

Patricia Sánchez‐Baracaldo, John A. Raven — Wed, 03 Jun 2026 21:30:52 -0700

Summary

The Mesoproterozoic atmosphere had more CO₂ and less O₂ than at present. While the upper ocean was oxygenated, the deeper ocean was euxinic or ferruginous. Primary production was performed by Chlorobia, Cyanobacteria, Proteobacteria, and Archaeplastida. Cyanobacteria and Archaeplastida presumably performed oxygenic photosynthesis above the chemocline, while photosynthesis below the chemocline involved anoxygenic photolithotrophic oxidation of S²⁻ or Fe²⁺ by Proteobacteria and S²⁻ by Chlorobia and Cyanobacteria. Photolithotrophic growth of extant Proteobacteria with Rubisco, and Chlorobia with the reverse tricarboxylic acid cycle, involves diffusive CO₂ entry; this likely also occurred under high Mesoproterozoic CO₂. By contrast, Cyanobacteria may already have possessed CO₂-concentrating mechanisms comparable to extant lineages. Here, we evaluate how differences in primary carboxylation pathways and inorganic carbon acquisition among these groups influence stable carbon isotope fractionation and assess how isotopic signatures in modern representatives inform interpretations of Mesoproterozoic carbon isotope records. Although culture-based fractionation patterns broadly overlap with Mesoproterozoic sedimentary δ¹³C values, these records are strongly biased towards continental margin settings, and direct evidence for open-ocean planktonic primary producers is lacking. The evidence reviewed highlights that physiological constraints on carbon acquisition and metabolism provide a framework for interpreting Mesoproterozoic carbon isotope signals with implications for primary production and the biological pump.

Decoding GUN1 in plastid‐to‐nucleus signaling: what it doesn't, what it does, and why it matters

Marco Wendler, Dario Leister, Tatjana Kleine — Wed, 03 Jun 2026 21:30:52 -0700

Publication history of plant GUN1 research.

Summary

Plastid-to-nucleus retrograde signaling coordinates nuclear gene expression with the developmental and physiological state of plastids. GENOMES UNCOUPLED 1 (GUN1), a chloroplast-localized PPR-SMR protein, remains a central yet poorly understood component of this network. Its low abundance, rapid turnover and conditional phenotypes challenge functional interpretation. GUN1 has been proposed as a hub integrating stress responses, tetrapyrrole synthesis and protein homeostasis, with downstream effects mediated by factors, such as ABI4, but many of these claims are challenged by recent evidence. Here, we identify claims that have failed to replicate, highlight established consensus and outline a path toward a more grounded understanding of GUN1. Beyond its confirmed RNA-binding activity, GUN1 may act as a moonlighting checkpoint, modulating when plastid dysfunction triggers nuclear and developmental responses.

Cross‐kingdom communication between plants and parasitic nematodes

Christopher A. Bell, Lida Derevnina, Sebastian Eves‐van den Akker — Wed, 03 Jun 2026 21:30:52 -0700

Cross-kingdom communication between plants and parasitic nematodes.

Summary

Plant-parasitic nematodes and their hosts engage in a continuous exchange of signals cross-kingdom. On the one hand, parasites exploit host-derived metabolites, proteins, and RNAs to sense host identity, proximity, and condition – and as a basis for manipulating host processes to their benefit. On the other hand, hosts respond to nematode-derived pheromones, proteins, and metabolites to either subvert or accommodate parasitism. Our recent understanding is that microbes play a role mediating, at least in part, a communication, which ultimately shapes the developmental trajectories of both host and parasite, in concert. In this Tansley insight, we review the current understanding of communication between plants and parasitic nematodes, framed by the developmental timeline. We focus on notable, reciprocal signals between plant and parasite that gate key life cycle transitions in the parasite, while acknowledging that these processes are embedded within, and inseparable from, a plethora of other signals – and indeed communication with other organisms. The frequency, reciprocity, and gravity of the exchange leads us to argue that it is best described as a nuanced communication, in which parasitism succeeds or fails based on interpretation and response.

The underappreciated roles of fog and dew on vegetation and biocrusts

Lixin Wang, Yue Li, Mengyun Sun, Na Qiao — Wed, 03 Jun 2026 21:30:52 -0700

Summary

Fog and dew represent minor components of ecosystem water budgets in most ecosystems. However, fog and dew can play an essential role in ecosystem dynamics and are particularly important for water-limited systems. In addition to serving as direct water inputs, fog and dew can influence microclimate and water redistribution, thereby promoting the retention of fog and dew water near the canopy/soil surface and benefiting plants and soil microbes. In this review, we highlight recent advances in fog and dew research, emphasizing measurement approaches and the quantitative impacts of fog and dew on plant–soil functions, particularly at large scales. We focus on multiple plant functional types and biogeological soil crusts, as well as multiple spatiotemporal scales (i.e. from individual plants to the regional scale) of fog and dew research. We further highlight key knowledge gaps, including the scarcity of fog and dew-monitoring data, the quantitative role of fog and dew in mediating ecosystem water stress, the mechanisms by which they affect plant–soil processes, and their responses to a changing climate. A better understanding and quantification of the contributions of fog and dew to ecosystem functions are crucial for predicting ecosystem responses and feedback to changing climates, especially in global drylands.

摘要

在大多数生态系统中，雾水和露水仅占生态系统水分平衡的一小部分。然而，雾水和露水在生态系统尤其是干旱生态系统动态中发挥着至关重要的作用。除了作为直接的水分输入外，雾水和露水还能影响微气候和水分再分配，从而促进雾水和露水在冠层/土壤表面的滞留，使植物和土壤微生物受益。本文综述了雾水和露水研究的最新进展，重点介绍了其测量方法以及对植物-土壤功能(尤其是在大尺度上)的定量影响。我们关注多种植物功能类型和生物结皮，以及雾水和露水研究的多个时空尺度(从单个植物尺度到区域尺度)。此外，我们还指出了关键的知识空白，包括雾水和露水监测数据的匮乏、雾水和露水在调节生态系统水分胁迫中的定量作用, 它们影响植物-土壤过程的机制以及它们对气候变化的响应。更好地理解和量化雾水和露水对生态系统功能的贡献，对于预测生态系统尤其是在全球干旱区生态系统对气候变化的响应和反馈至关重要。

Mutation of the rice OsMTL gene simultaneously generates haploid, diploid, and triploid embryos

Fengyue Hu, Chaolei Liu, Tingting Sun, Yiling Lin, Kejian Wang — Wed, 03 Jun 2026 21:30:52 -0700

New Phytologist, Volume 251, Issue 1, Page 18-23, July 2026.

Generation of Brassica napus with enhanced Sclerotinia sclerotiorum resistance through CRISPR/Cas9‐mediated inhibition of the PROTEOLYSIS6 N‐degron pathway

Wed, 03 Jun 2026 21:30:52 -0700

New Phytologist, Volume 251, Issue 1, Page 24-31, July 2026.

Dual localization of translocon subunit Tic56 to chloroplasts and mitochondria modulates rRNA accumulation in both organelles

Yinjie Guo, Jiarui Zhang, Ting Cao, Jing Feng, Xiushun Wang, Wei Chi — Wed, 03 Jun 2026 21:30:52 -0700

New Phytologist, Volume 251, Issue 1, Page 11-17, July 2026.

Andrew Fleming

Wed, 03 Jun 2026 21:30:52 -0700

Andrew Fleming, University of Sheffield (UK).

Antagonistic interactions between CLAVATA receptors shape maize ear development

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Meristem activity is controlled by the CLAVATA (CLV) signaling pathway, which involves a suite of leucine-rich receptor (LRR) receptors, receptor-like proteins, and CLV-EMBRYO SURROUNDING REGION (CLE) peptide ligands. FASCIATED EAR 3 (FEA3) is a leucine-rich receptor (LRR) receptor-like protein important for meristem maintenance in maize and acts independently of canonical CLV receptors. To identify FEA3's interaction network, we used TurboID-based proximity labeling in Zea mays meristems and identified a putative co-receptor, BARELY ANY MERISTEM 1D (BAM1D). BAM1D and FEA3 proximity labeling proteomes shared over 40 proteins, including many signaling proteins, suggesting they feed into a common signaling pathway. fea3 was epistatic to bam1d in the control of inflorescence meristem (IM) size, supporting the idea that FEA3 and BAM1D interact physically. However, fea3 and bam1d act antagonistically because fea3 mutants had larger IMs, whereas bam1d mutants produced smaller IMs. This study demonstrates how in vivo TurboID-based proximity labeling clarifies complex genetic interactions between CLV receptors and expands our knowledge of downstream signaling components of CLV signaling pathways, which are largely uncharacterized. Our findings support the notion that multiple, partially overlapping CLV receptor complexes coordinately control meristem maintenance.

Tree stem methane emissions are regulated by site‐level biogeochemistry over species identity in Amazon floodplain forests

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Tree stems in Amazonian floodplains emit substantial methane (CH₄), yet controls on emission variability remain unclear. Emissions span orders of magnitude between várzea (nutrient-rich) and igapó (nutrient-poor) forests and among trees, suggesting controls beyond flooding. We tested whether site-level biogeochemistry better explains stem CH₄ variability than species identity by measuring emissions from two co-occurring species with contrasting wood densities – Eschweilera coriacea and Hevea spruceana – across várzea and igapó forests. Emissions were paired with porewater chemistry (electrical conductivity, dissolved oxygen, dissolved CH₄, and dissolved organic carbon), methane production potential (MPP), and root biomass. Stem CH₄ emissions were significantly higher in várzea than in igapó, independent of species or stem height. Várzea porewaters displayed higher conductivity, dissolved CH₄ and MPP, near-neutral pH, and lower oxygen, with fine roots concentrated in the 0- to 50-cm soil layer, indicating a shallow CH₄ supply zone. Basal stem emissions in várzea correlated with shallow porewater chemistry and fine-root biomass, whereas relationships in igapó were weak. These findings show that Amazonian floodplain stem CH₄ emissions are governed by shallow site-level biogeochemistry, rather than species identity alone and should be incorporated into basin-scale CH₄ budgets and process models to capture spatial variability.

Resumo

Troncos de árvores nas planícies alagáveis amazônicas emitem quantidades substanciais de metano (CH₄), mas os fatores que controlam essa variabilidade ainda são pouco compreendidos. As emissões variam amplamente entre florestas de várzea (ricas em nutrientes) e igapó (pobres em nutrientes), bem como entre árvores, sugerindo controles além do alagamento. Avaliamos se a biogeoquímica em nível de sítio explica melhor a variabilidade do CH₄ emitido pelos troncos do que a identidade das espécies, medindo emissões de duas espécies coocorrentes com densidades de madeira contrastantes – Eschweilera coriacea e Hevea spruceana – em várzea e igapó. As emissões foram relacionadas à química da água intersticial, ao potencial de produção de metano (MPP) e à biomassa radicular. As emissões foram maiores na várzea, independentemente da espécie ou da altura no tronco. A várzea apresentou maior condutividade, maiores concentrações de CH₄ dissolvido e maior MPP, pH próximo à neutralidade e menor oxigênio, com raízes finas concentradas nos primeiros 50 cm do solo. Emissões basais correlacionaram-se com a química superficial e a biomassa radicular na várzea, mas não no igapó. Os resultados indicam que as emissões são controladas principalmente pela biogeoquímica superficial do sítio, devendo ser incorporadas a modelos de CH₄ em escala de bacia.

Multi‐omics dissection of steviol glycoside synthesis reveals haplotype‐linked specialization of UGT76G genes in Stevia rebaudiana

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Steviol glycosides (SGs), intensely sweet diterpenoids found in Stevia rebaudiana (stevia), exhibit natural variation in composition that influences taste quality and commercial value. However, the genetic and cellular mechanisms underlying this variation remain poorly understood. We aimed to uncover how haplotype-level diversity and cell-type-specific gene expression contribute to SG profile diversity in stevia. We generated a chromosome-scale reference genome and conducted integrative multi-omics analyses combining haplotype-resolved population genomics, single-nucleus RNA sequencing, and imaging mass spectrometry. These approaches were applied to a diverse panel of breeding lines and a segregating population to associate genetic variants with SG composition and expression patterns. We identified a physically linked cluster of UGT76G glycosyltransferase genes whose structural and regulatory polymorphisms drive major differences in SG composition. Restricted expression of UGT91D4 to specific subsets of mesophyll and epidermal cells further constrained the biosynthesis of high-value SGs, such as rebaudioside D and rebaudioside M. Functional divergence among UGT76G paralogs was supported by sequence, expression, and structural modeling data. Our findings define a multi-allelic and spatially coordinated regulatory architecture underlying SG biosynthesis in stevia. These insights provide a foundation for haplotype-guided breeding and metabolic engineering strategies aimed at improving stevia sweetness quality and yield.

Inhibition of jasmonic acid‐isoleucine conjugating enzyme JAR1 shifts the local and systemic leaf signals and metabolic profiles in Arabidopsis

Ming Zeng, Axel Mithöfer — Wed, 03 Jun 2026 21:30:52 -0700

Summary

Jasmonates (JAs)-mediated pathways are central signaling hubs in plant defense responses. However, the identification of mobile and nonmobile signals involved in downstream systemic signaling is still less studied. Here, we investigate the role of the jasmonic acid-isoleucine (JA-Ile) conjugating enzyme, JAR1, in shifting wound-induced local and systemic metabolic profiles using liquid chromatography mass spectrometry (LC-MS/MS) for untargeted metabolomics, and the mobility of JA-Ile in wound-induced local and systemic defense using LC-MS/MS for targeted JAs analysis in Arabidopsis thaliana leaves. The use of jarin-1, a specific inhibitor of JA-Ile biosynthesis, suggested that JA-Ile was synthesized de novo in the particular tissues, rather than being a mobile signal. In addition, inhibition of JAR1 enzyme activity affected an array of downstream metabolic pathways, locally and systemically, such as amino acids and carbohydrate metabolism. This study suggests that the occurrence and spread of local and systemic downstream signals very likely depend on JAR1 activity, and this enzyme exclusively regulates a series of metabolic pathways under both wounding and nonwounding conditions.

Dissecting the genetic basis of drought escape across multiple traits in colonizing Arabidopsis thaliana lineages

Wed, 03 Jun 2026 21:30:52 -0700

Cape Verde Islandspopulations experience seasonal drought and high humidity during the growing season, driving drought escape strategies relative to their Moroccan outgroup.

Summary

Drought response in plants is complex, involving integration across a range of physiological processes. However, our knowledge of how different mechanisms of drought response are linked at the genetic level is limited. We investigated multi-trait adaptation in Arabidopsis thaliana from the Cape Verde Islands (CVI). Using a high-throughput phenotyping platform that minimizes spatial heterogeneity, we measured variation in rosette area, growth rate, leaf color, water use efficiency (WUE), and stomatal patterning under precisely controlled water conditions. Relative to the Moroccan outgroup, CVI populations evolved earlier flowering, a smaller rosette size with faster growth, and reduced WUE, consistent with drought escape adaptation. Genome-wide association mapping revealed evidence for pleiotropy involving MPK12 (WUE, rosette area, growth rate, and leaf color), NHL26 (WUE and leaf color), SUVH4 (stomatal patterning, rosette area, and leaf color), and FRI (flowering time, WUE, and leaf color), along with an enrichment of signals in ABA response. This study advances our knowledge of the genetic mechanisms driving plant adaptation to a novel precipitation environment. By identifying key genetic components and their contributions to multi-trait adaptation, our findings offer insights into how plants respond to environmental challenges and contribute to predicting plant responses to future climate change.

The vesicle trafficking R‐SNARE VAMP714 connects auxin responses, ROS and ion homeostasis in Arabidopsis under salt stress

Jialei Sun, Julien Agneessens, Jennifer F. Topping, Keith Lindsey — Wed, 03 Jun 2026 21:30:52 -0700

Network of VAMP714-dependent interactions during salt stress.

Summary

Plant responses to salt stress include an altered root architecture mediated by ion imbalances, reactive oxygen species (ROS) accumulation, and altered hormonal responses. Auxin is implicated in these processes. To understand better the molecular network we investigated the role of VAMP714, an R-SNARE essential for correct trafficking of the auxin efflux carrier PIN-FORMED (PIN) proteins (implicated in the salt stress response), but also with a reported role in ROS vesicular transport in Arabidopsis. We show that under salt stress the VAMP714 gene shows a rapid transient increase in expression but subsequent perturbed localization of VAMP714 and PIN proteins and altered auxin-responsive gene expression. RNA-seq analysis revealed that pathways related to oxygen signaling, SALT OVERLY SENSITIVE (SOS) pathway activation and ROS response are influenced by salt stress in a VAMP714-dependent manner. Low levels of transgenic overexpression of VAMP714 enhanced root salt tolerance, an effect enhanced by exogenous auxin, showing that maintenance of VAMP714 expression under salt stress allows auxin-mediated maintenance of root growth. We conclude that VAMP714 contributes to the coordinated regulation of auxin signaling and the SOS pathway during salt stress via distinct roles in vesicle trafficking to the plasma membrane (for auxin) and vacuole (for SOS).

摘要

植物在响应盐胁迫时通常会发生根系结构重塑，这一过程与离子失衡、活性氧(ROS)积累以及激素响应变化密切相关，其中生长素发挥重要作用。为进一步解析相关分子调控网络，本研究考察了R-SNARE蛋白VAMP714的功能。VAMP714对生长素外排载体PIN-FORMED(PIN)蛋白的正确运输至关重要，而PIN蛋白已知参与盐胁迫响应；此外，已有研究报道VAMP714参与拟南芥中与ROS相关的囊泡运输过程。结果表明，盐胁迫可迅速诱导VAMP714基因发生短暂上调，随后导致VAMP714及PIN蛋白定位紊乱，并引发生长素响应基因表达改变。RNA-seq分析显示，在盐胁迫条件下，氧信号转导、盐超敏感(SOS)通路激活以及ROS响应等相关途径均以VAMP714依赖的方式受到影响。VAMP714的低水平转基因过表达可提高根系耐盐性，且该效应可被外源生长素进一步增强，表明在盐胁迫下维持VAMP714表达有助于保持生长素介导的根系生长。综上所述，VAMP714在盐胁迫过程中通过参与质膜(生长素相关)和液泡(SOS相关)的囊泡运输，促进生长素信号与SOS通路的协同调控。

Pseudomonas volatiles shape the root transcriptome and microbiome to promote plant growth under drought

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Volatile organic compounds (VOCs) emitted by soil bacteria influence interactions with other soil microbes and plants. While their potential as plant growth promoters is well recognized, their role in promoting plant resilience to abiotic stress and the underlying molecular mechanisms remain poorly understood. Here, we investigate the role of Pseudomonas VOCs in enhancing plant resilience to drought stress Arabidopsis seedlings were exposed to VOCs emitted by Pseudomonas strains under control and osmotic stress conditions. Plant biomass and root architecture were evaluated. Root transcriptomics analysis was performed and validated using Arabidopsis mutants and metabolomics. Volatile organic compounds effects were also tested on soil-grown Brassica oleracea and on its rhizosphere microbiome. Pseudomonas VOCs promoted plant growth under both axenic and soil conditions in A. thaliana and in B. oleracea, and under control and drought conditions. Transcriptomics, metabolomics, and functional analysis revealed interactions between Pseudomonas VOCs, glucosinolates, and ABA signalling, as well as a positive association between VOC exposure and coumarin biosynthesis. VOC treatment also reshaped the rhizosphere microbiome under drought, leading to a community composition more similar to that of well-watered plants. Overall, Pseudomonas VOCs promote plant growth under drought conditions, linked to root transcriptional reprogramming and direct or indirect microbiome modulation.

Functional divergence of a trypsin protease underpins phosphate signaling in a diatom

Wed, 03 Jun 2026 21:30:52 -0700

Gene structure of PtTryp8 in Phaeodactylum tricornutum, knockout genotypes, and growth phenotypes of mutant strains compared with KOC.

Summary

Phosphate availability constrains growth across plant and algal lineages, yet the intracellular regulatory mechanisms linking external phosphate signals to acclimation responses remain incompletely understood. Protease families are highly expanded in photosynthetic eukaryotes, but whether individual protease paralogues have evolved regulatory roles in nutrient signaling is largely unexplored. Here, we identified a trypsin protease, PtTryp8, as a key regulatory component of phosphate acclimation in the diatom Phaeodactylum tricornutum. Loss of PtTryp8 impaired growth and phosphate uptake dynamics. Transcriptome profiling revealed coordinated dysregulation of phosphate-responsive genes, including transporters, signaling components, and membrane trafficking pathways in PtTryp8 mutants. Notably, PtTryp8 disruption selectively altered Ca²⁺-dependent protein kinase expression, consistent with a role in signal integration rather than bulk proteolysis. Comparative analyses indicated that PtTryp8 has diverged functionally from other trypsin paralogues, supporting isozyme specialization within diatom protease families. Together, these findings reveal a previously unrecognized role for proteolytic signaling in phosphate sensing and acclimation and suggest that regulatory diversification of proteases represents a general strategy for nutrient adaptation in photosynthetic eukaryotes.

Alternative splicing of PeGA20ox1 impairs PeRAP2‐1‐mediated GA/ABA homeostasis leading to short internodes in the dwarf variant of Moso bamboo, Phyllostachys edulis ‘Heterocycla’

Wed, 03 Jun 2026 21:30:52 -0700

The schematic model of PeRAP2-1 regulating PeGA20ox1 and PeABA3 to participate in GA/ABA homeostasis in the culm type of Phyllostachys edulis ‘Heterocycla’.

Summary

Internode morphology critically determines bamboo wood quality. Phyllostachys edulis ‘Heterocycla’ (GJ) is a natural dwarf mutant of P. edulis (WT), yet regulatory mechanisms remain unclear. Here, we show that impaired parenchyma cell elongation is the primary cellular basis for dwarfism in GJ. This phenotype correlates with a marked reduction in gibberellin (GA) and an increase in abscisic acid (ABA) levels. Through weighted gene co-expression network analysis, we identified PeGA20ox1 as a critical regulator of internode elongation. In GJ, PeGA20ox1 undergoes alternative splicing (AS), producing a transcript, PeGA20ox1-GJ, with a premature termination codon. Moreover, we characterized that a bifunctional transcription factor PeRAP2-1 mediates GA/ABA homeostasis, which is an activator of PeABA3 and an inhibitor of PeGA20ox1 by binding to different cis-acting elements. Intriguingly, this AS event results in the loss of function of PeGA20ox1-GJ, which disrupts the PeRAP2-1-mediated hormonal balance, ultimately inhibiting internode elongation. This study suggests that the posttranscriptional regulation induced by AS may adapt to the rapid growth of bamboo plants and provides important genetic resources for the molecular breeding of bamboo with improved culm traits.

Novel Glomeromycotina–moss associations identified in California dryland biocrusts

Kian H. Kelly, Claudia Coleine, Chris Coshland, Jason E. Stajich — Wed, 03 Jun 2026 21:30:52 -0700

Summary

Drylands, which comprise c. 45% of Earth's land area, host biological soil crusts (biocrusts): symbiotic communities of cyanobacteria, fungi, algae, lichen, and bryophytes that stabilize soil and support key ecosystem functions. Moss-dominated biocrusts are particularly interesting due to their potential to illuminate ancient bryophyte–fungal interactions. To test the hypothesis that mosses in biocrusts host endophytic Mucoromycota fungi and that local climate influences the composition of these fungal communities, we conducted amplicon metabarcoding and microscopic surveys employing fungal staining across sites with varying aridity. We identified novel associations between mosses and arbuscular mycorrhizal fungi (AMF), with phylogenetic analyses revealing distinct fungal communities in moss biocrusts compared with adjacent bare soil. Intracellular branching by fungi resembling Glomeromycotina was observed within healthy Trichostomopsis australasiae (Bryophyta) cells. Moreover, shifts in AMF community composition across different aridity levels within the same moss species highlight the variation in moss-associated Glomeromycotina diversity, composition, and relative abundance. These findings provide critical insights into ancient bryophyte–fungal symbioses, potentially analogous to those enabling early land plant colonization during the Ordovician (c. 470 million years ago). They also underscore the need to understand and protect biocrust microbial communities as aridity intensifies under climate change.

GCN5‐mediated histone H3 acetylation orchestrates gene expression and plant development via H2A.Z

Wed, 03 Jun 2026 21:30:52 -0700

Genetic interactions between GCN5 and H2A.Z-related mutants affect plant development.

Summary

H2A.Z is a conserved histone variant that plays essential roles in various DNA-templated processes. Although both histone H3 acetylation and H2A.Z enrichment levels are important epigenetic marks that regulate gene expression, their functional interplay remains incompletely understood. This study integrates genetic, molecular, and genomic approaches to investigate how GCN5 – a conserved histone acetyltransferase – couples H3 acetylation with H2A.Z dynamics in Arabidopsis, and how this interplay shapes gene expression and plant development. We found that the increase in H2A.Z levels observed in the nrp1-1 nrp2-2 double mutant (defective in NAP1-RELATED PROTEIN 1 and 2) suppresses the morphological and molecular phenotypes of gcn5-7. Conversely, H2A.Z-depleted mutants aggravate these phenotypes of gcn5-7/c1. Notably, the reduction in H3 acetylation caused by GCN5 loss promotes the decrease in H2A.Z level, and this requires the function of NRPs. The integrated analysis of ChIP-Seq and RNA-Seq data revealed that the differential gene expression in the GCN5 deletion mutant is correlated with H2A.Z distribution and enrichment levels. Moreover, H2A.Z overaccumulation at genes in the nrp1-1 nrp2-2 mutant promotes increased H3 acetylation in a GCN5-dependent manner. In conclusion, our findings support a model in which GCN5-mediated H3 acetylation shapes H2A.Z occupancy, linking chromatin dynamics to precise gene expression control and proper plant development.

概括

H2A.Z是一种极其保守的组蛋白变体，在多种以DNA为模板的分子过程中发挥着关键作用。尽管组蛋白H3乙酰化修饰与H2A.Z富集水平均为重要的调控基因表达的表观遗传标记，但是二者之间的功能性互作关系仍有待阐明。本研究整合了遗传学、分子生物学与基因组学方法，研究了拟南芥组蛋白乙酰转移酶GCN5如何耦合H3乙酰化修饰与H2A.Z富集水平，以及这种表观遗传标记之间的互作如何调控基因表达与植物发育。我们发现，在nrp1-1 nrp2-2双突变体(NRPs功能缺失)中观察到的H2A.Z富集水平的上升，能够抑制gcn5-7突变体的形态与分子表型。相反，H2A.Z缺失型突变体则会加剧gcn5-7/c1的形态与分子表型。值得注意的是，GCN5缺失所导致的H3乙酰化水平下降会促进H2A.Z水平的降低，且这一过程依赖于NRPs的功能。ChIP-Seq与RNA-Seq数据的整合分析表明，GCN5缺失突变体中基因的差异表达与H2A.Z的分布和富集水平相关联。此外，nrp1-1 nrp2-2突变体中基因上H2A.Z的过度积累会以GCN5依赖的方式促进H3乙酰化水平的升高。综上所述，我们的研究结果支持以下模型:GCN5介导的H3乙酰化修饰影响H2A.Z的分布模式，从而将染色质动态变化与精确的基因表达调控以及正常的植物发育联系起来。

Provenance legacies override species effects in shaping oak rhizosphere microbiomes and metabolomes

Wed, 03 Jun 2026 21:30:52 -0700

Graphical representation of experimental setup. Quercus spp. seeds were collected at two origins: upper Rhine basin (URB) and north German lowland (NGL).

Summary

As climate change drives more frequent drought-heat extremes, selecting drought-tolerant trees is crucial for future forest resilience. However, the role of tree–microbial associations remains largely unclear. We investigated how geographic origin, species identity, and intrinsic water use efficiency (iWUE) shape the rhizosphere microbiome and root–rhizosphere metabolome of Quercus robur L. and Q. petraea (Matt.) Liebl. In a 6-yr common garden experiment, we analyzed trees from two distinct geographic origins (upper Rhine basin and north German lowland) using 16S/ITS metabarcoding and untargeted metabolomics. We found a consistent legacy effect of seed origin on the prokaryotic rhizosphere microbiome and metabolome, whereas tree species had no significant impact. The bacterial family Pseudonocardiaceae was enriched for trees from the drier origin (NGL), while Blastocatellaceae and Micromonosporaceae were associated with iWUE. Higher iWUE also correlated with lower prokaryotic diversity. Ellagic acid, a polyphenol associated with drought tolerance, was enriched in the drier origin. The rhizosphere fungal community, however, was largely unaffected by origin or species. Our findings suggest that ecotypic adaptation linked to origin can outweigh species-level traits in shaping the oak rhizosphere. These findings emphasize that provenance-driven adaptation influences plant–microbe interactions and underscore the need for provenance-aware selection to strengthen forest drought resilience.

An N‐acetyltransferase‐MAPK fusion protein modulates developmental reprogramming in Physcomitrium patens

Wed, 03 Jun 2026 21:30:52 -0700

Summary

We discovered a previously uncharacterized moss-specific protein, Rosetta NATD-MAPK 1 (RAK1) in Physcomitrium patens, which uniquely integrates MAP kinase (MAPK)-dependent signaling with N-acetyltransferase activity. Through phenotypical and biochemical analyses, we characterized RAK1 function in the regulation of the 2D-to-3D growth transition. We identified differential acetylation events associated with metabolic reprogramming in rak1 mutants and demonstrated that RAK1 has acetyltransferase activity enhanced by MAPK domain activation. Consistently, RAK1 was found to interact with proteins involved in metabolic processes. Collectively, this study uncovers a previously unknown multidomain protein and provides mechanistic insights into the interplay of post-translational modifications during developmental reprogramming.

Mycorrhizal type shifts the controls on tree root exudation from soil‐driven to carbohydrate‐driven mechanisms

Wed, 03 Jun 2026 21:30:52 -0700

Conceptual framework of root exudate release.

Summary

Exudation is crucial for carbon and nutrient cycling in forests. However, the underlying mechanism controlling exudation in mature trees, especially its dependence on mycorrhizal type, remains unknown. Based on the control of carbon acquisition by roots, we propose an updated ‘push–trade-off–pull’ framework for exudation. We investigated three controlling categories, that is, nonstructural carbohydrates (NSCs) in branches and roots, root functional traits, and soil nutrients, as proxies for ‘push’, ‘trade-off’, and ‘pull’, respectively, over exudation for trees colonized by arbuscular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi in subtropical forests of China. The NSCs, root traits, and soil nutrients together controlled exudation of trees, particularly distinguishing AM from ECM species. Soil nutrients dominantly impacted the exudation of AM species (47%), that is, increased exudation linked with decreased soil nutrients, supporting the ‘pull’ effect. However, the NSCs mainly mediated that of ECM species (56%), that is, enhanced exudation associated with declined NSCs, which rejects the ‘push’ effect. For the ‘trade-off’, greater exudation was correlated with greater root branching for AM and with lower root tissue density for ECM species. Our findings highlight the mycorrhizal symbiosis-dependent mechanism of exuded carbon that provides a new perspective for understanding exudate-mediated belowground carbon cycling in forests.

The lineage‐specific CitmiRn23‐CitXS20 module regulates apomixis in citrus through modulation of H2O2 level

Wed, 03 Jun 2026 21:30:52 -0700

Proposed working model for CitmiRn23-CitXS20 module-mediated regulation of citrus apomixis.

Summary

Most citrus species exhibit polyembryony, a mode of sporophytic apomixis that asexual embryos develop in the nucellus. Polyembryony can propagate clonal seedlings but impedes crossbreeding. A 21-nt novel miRNA, CitmiRn23, and target gene CitXS20, encoding a XS domain protein, antagonistically express between polyembryonic and monoembryonic (sexual reproductive) ovules. CitmiRn23 overexpression and RNA interference (RNAi) of CitXS20 was conducted in minicitrus (Fortunella hindsii). The protein interacted with CitXS20 was identified, and exogenous treatments validated the effect of H₂O₂ on polyembryony. CitmiRn23 overexpression and CitXS20 RNAi both repressed nucellar embryogenesis (NE) and thus increased monoembryonic seed rate and hybrid rate. CitXS20 interacted with CitCAT2 and impaired its catalase activity. In ovaries with downregulated CitXS20, catalase activity was upregulated, while H₂O₂ level was decreased, indicating that interaction with CitXS20 might retard CitCAT2 activity in H₂O₂ scavenging. H₂O₂ preferentially accumulated in polyembryonic ovules. The treatment with H₂O₂ increased polyembryony level, whereas treatment with diphenyliodonium chloride reduced H₂O₂ level and polyembryony level, and thus increased hybrid rate. The citrus-specific CitmiRn23-CitXS20 module regulates NE through CitCAT2-mediated modulation of H₂O₂ level in ovule, which provides insights into apomixis mechanisms and promising approaches to regulate polyembryony, and thus facilitates crossbreeding in citrus.

Sex‐specific responses of flower and leaf phenology to spring warming of a dioecious tree species

Hao Wu, Mingxi Jiang, Xinzeng Wei — Wed, 03 Jun 2026 21:30:52 -0700

Differences in the days to flowering (a) and days to leaf unfolding (b) between male and female individuals of the dioecious tree species Cercidiphyllum japonicum under different treatments.

Summary

Spring phenology is closely linked to plant growth and reproduction and is highly sensitive to environmental changes. For dioecious species, the temporal overlap between female and male flowering is critical for their successful pollination. However, it remains largely unclear whether males and females respond differently to climate change and how this may influence the phenological synchrony between the sexes. By conducting twig experiments, we investigated how the flower and leaf phenology of male and female individuals of a dioecious tree species, Cercidiphyllum japonicum, responded to the changes in temperature and photoperiod. Male individuals flowered and unfolded their leaves earlier than female individuals in most cases, reflecting sexual dimorphism in spring phenology. Elevated temperature significantly advanced the flowering and leaf unfolding in both sexes, while shortened photoperiod had no significant effect on either phenophase. The time interval between flowering and leaf unfolding tended to be shortened under warming in males but not in females. Interestingly, the flowering time of females was more sensitive to temperature than that of males. These findings suggest that spring warming may paradoxically enhance reproductive fitness in this species by reducing the flowering time gap between sexes, highlighting the critical need to consider sex-specific responses when predicting population dynamics under climate change.

Despite rapid warming, seed production is not leading poleward migration in North American and European forests

Wed, 03 Jun 2026 21:30:52 -0700

Summary

To survive climate change, forest trees will have to shift seed production poleward. However, warming will not stimulate tree fecundity in the north if it is limited by other habitat variables. We evaluated the responses of tree fecundity to climate change for 292 tree species in North America and Europe, using response velocity, defined as (climate sensitivity) × (climate-change rate). The sensitivities to climate were estimated for each species and combined with rates of climate change to quantify how temperature, moisture deficits, and late freeze are influencing biogeographic shifts in tree reproduction. The results show that moisture deficit and late freeze, not annual temperature, drive changing seed production. Unlike annual temperature, which is increasing generally, change in these climate variables is not driving poleward shifts in seed production. These findings do not challenge the expectation that forests might eventually shift poleward. Rather, they show why current efforts offer divergent interpretations. The changes happening now are not consistent with annual temperature trends. As warming continues, fecundity changes can best be anticipated from temperature interactions with precipitation and extremes that impact flowering and fruiting in winter and spring.

Photosynthesis regulation impacts carbon and nitrogen assimilation in the diazotrophic cyanobacterium Anabaena sp. PCC 7120

Wed, 03 Jun 2026 21:30:52 -0700

Model of intercellular functional coordination in Anabaena.

Summary

Diazotrophic cyanobacteria fix both atmospheric carbon (C) and nitrogen (N) into biomass, but the two assimilation pathways are not compatible. Species like Anabaena sp. PCC 7120 physically separate C and N assimilation in different cell types. Even if separated, they are strongly intertwined, as N assimilation relies on the C skeletons and reducing power from photosynthesis, that in turn depends on N-rich molecules as pigments and proteins. Whereas the two pathways have been extensively studied individually, this work investigates their interaction by analysing photosynthetic properties upon exposure to changes in light, carbon dioxide (CO₂) and N availability, including the contribution of photosynthetic electron fluxes. Growth depended on the availability of both light and CO₂, whilst the N₂ fixation activity mainly relied on the C supply. Upon diazotrophic conditions, the total photosynthetic electron transport increased, with a modified contribution of different electron pathways. A mutant strain affected in the vehiculation of fixed N between cell types showed that the modulation of photosynthesis depended on the metabolic connection between assimilation pathways. Overall, data showed that the regulation of photosynthetic electron fluxes is a major component of the synergic metabolic relationship between C and N assimilation pathways upon dynamic environmental conditions.

Host‐mediated interactions between arbuscular mycorrhizal fungi and saprotrophs drive soil organic carbon dynamics

Wed, 03 Jun 2026 21:30:52 -0700

Effects of arbuscular mycorrhizal (AM) fungal hyphae on soil cumulative CO₂–C release during 30-d incubation for the host plants Leymus chinensis and Stipa grandis.

Summary

Although arbuscular mycorrhizal fungi (AMF) have been assumed to facilitate soil organic carbon (SOC) sequestration, they also regulate SOC decomposition via specific interactions with saprotrophs. We tested AMF hyphal impacts on SOC dynamics (e.g. labile C vs persistent C) under monoculture conditions with different grasses (e.g. Leymus chinensis and Stipa grandis) using an in-growth core method. Although the total SOC pool was unaffected by the presence of AM fungal hyphae, the proportional composition of labile and persistent C within SOC pools differed significantly between treatments with and without hyphal access. The presence of AM fungal hyphae from L. chinensis was associated with increased abundances of actinomycetes and Gram-positive bacteria, alongside the higher activity of polyphenol oxidase that breaks down persistent soil C, leading to a higher proportion of labile C in the SOC pool. Under S. grandis, however, hyphal presence corresponded with a greater abundance of Gram-negative bacteria that often can degrade labile soil C, resulting in a higher proportion of persistent C in the SOC pool. The influence of AM fungal hyphae on SOC depends on the identity of host plants and thus shifts in plant community composition may strongly alter SOC dynamics in grasslands.

Endophyte‐induced systemic spatial reprogramming of metabolism in Populus trichocarpa roots under drought

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Beneficial, facultative endophytes help plants thrive in challenging environments by altering their host's metabolism, but how these cellular scale metabolic changes propagate to the systems biology scale is unknown. In this work, we employed a high-resolution chemical imaging approach to map metabolic changes at the Populus trichocarpa root-zone and cell-type levels combined with machine learning (ML) models to identify root metabolites and exudates that have predictive power over treatment class. We found that a nine-strain consortium of beneficial endophytes differentially altered the metabolome of droughted root tissues in a manner specific to cell type and root zone, with endophyte abundance showing a clear correlation to individual metabolites. Our study demonstrates that integrating spatial metabolomics with ML can reveal localized metabolic patterns linked to root–microbe interactions and generate novel hypotheses about underlying biological mechanisms.

COCHLEATA controls spatial regulation of cytokinin and auxin during nodule development

Wed, 03 Jun 2026 21:30:52 -0700

Nodule development defects in the coch mutant include root-like structures, reduced colonisation, and vascular disorganisation.

Summary

Root nodules host nitrogen-fixing bacteria and likely evolved through modifications of the lateral root program. Members of the NOOT-BOP-COCH-LIKE transcriptional coregulator family suppress root identity in nodules and plant hormones play key roles in nodule organogenesis, but the interaction between these pathways is unclear. In this study, we investigate how COCH regulates nodule identity through crosstalk with plant hormones, using the Pisum sativum cochleata (Pscoch) mutant – which forms root–nodule hybrids – in combination with hormone biosensors, double mutants, hormone quantification, and RNA-seq analysis. We found that COCH suppresses cytokinin levels and response during nodule formation. By contrast, PsCOCH promotes auxin accumulation and precise auxin response patterning in nodules. Mutant coch developing nodules have gene expression profiles more similar to that of root primordia, with increased expression of defence and auxin response genes and reduced expression of cytokinin biosynthesis genes compared to wild-type. We found gibberellin is unlikely to act downstream of PsCOCH. Constitutive expression of PsCOCH also produces root–nodule hybrids and we found intriguing links between the autoregulation of nodulation pathway and PsCOCH. We show that PsCOCH is required for spatial tight regulation of auxin and cytokinin during nodule organogenesis and identify key hormone and signalling genes that act downstream of COCH.

Xylem endophytes of Salicaceae: potential role in mitigating disease symptoms from Xylella fastidiosa or Brenneria salicis

Wed, 03 Jun 2026 21:30:52 -0700

Xylem bacterial communities in Salicaceae were characterized using culture-dependent (440 isolates, 43 genera, 104 species) and independent approaches, revealing a shared core microbiome dominated by Bacillus spp. Functional screening identified 47 antagonistic strains, narrowed to 15 with plant growth–promoting and pathogen-inhibiting traits. Genome analysis and fluorescent tagging were performed on five selected strains. Co-inoculation experiments in tobacco and willow plantlets showed that selected endophytes can reduce pathogen load and disease symptoms, while also promoting plant growth, highlighting their potential for biocontrol and plant health improvement.

Summary

Increasing pressure from xylem-limited pathogens has driven the search for beneficial xylem-inhabiting endophytes that can enhance growth, stress tolerance, and disease resistance in woody plants. This study characterized the culturable xylem microbiota of Salicaceae species (willow and poplar) and evaluated their potential as biological control agents against vascular pathogens. A combination of microbial isolation, metabarcoding, and whole-genome sequencing was used to characterize xylem-associated bacteria. Functional traits were assessed through in vitro assays, while genome mining identified genes linked to plant-beneficial activities. Interactions between endophytes and pathogens were tested using fluorescently labeled strains in tobacco (Nicotiana tabacum) and in vitro-grown willow (Salix caprea). Bacterial genera (Bacillus, Pseudomonas, Erwinia) exhibited plant growth-promoting traits and strong antagonism against bacterial and fungal vascular pathogens, including Xylella fastidiosa, Brenneria salicis, Fusarium spp., and Verticillium dahliae. Genome analyses revealed functions related to nutrient acquisition, biofilm formation, and antimicrobial production. Co-inoculation assays significantly reduced pathogen load and disease symptoms in tobacco and mitigated symptoms in willow. Xylem endophytes act as context-dependent allies in woody plant defence. This study provides a functional and genomic framework supporting microbiome-based strategies to enhance resistance against vascular pathogens in long-lived woody hosts.

The Rapid Mechanically Activated channel transduces increases in plasma membrane tension into transient calcium influx

Yannick Guerringue, Sebastien Thomine, Jean‐Marc Allain, Jean‐Marie Frachisse — Wed, 03 Jun 2026 21:30:52 -0700

The activity of RMA decreases upon repetitive stimulations.

Summary

Plants respond to mechanical stimuli by a rapid increase in cytosolic calcium. The intensity and kinetics of the calcium changes define calcium signatures important for biological responses. In this study, we determine the properties of a calcium-permeable force-gated channel localized at the plasma membrane called Rapid Mechanically Activated (RMA). Using patch clamp and pressure clamp, we characterized the kinetics of the Arabidopsis thaliana RMA channel upon stimulation by pressure pulses applied onto the plasma membrane. Combining pressure pulse protocols at different frequencies with modeling, we investigated the channel's capacity to transduce high frequency mechanical stimuli. The RMA channel rapidly activates in response to membrane tension, then it inactivates during prolonged stimulation. Upon repeated stimulations, the RMA current amplitude decreases irreversibly indicating that it undergoes attenuation. The channel kinetics were modeled with four chemical states and the model predicts that it behaves as a pass band filter in the 10 Hz–1 kHz range. In conclusion, due to its activation/inactivation, the RMA channel is a candidate for mediating cytosolic calcium signaling in response to mechanostimulation. Its attenuation and filtering properties suggest its involvement in the transduction of high frequency mechanical stimulation, such as those produced by insects' vibrations.

Tree diversity–soil organic carbon relationships strengthen under colder and more arid conditions

Wed, 03 Jun 2026 21:30:52 -0700

Hypothesized relationships between tree diversity and soil organic carbon.

Summary

Soil organic carbon (SOC) plays an essential role in carbon sequestration and climate change mitigation in forest ecosystems. While experimental studies have shown that plant diversity usually increases SOC, it remains unclear whether this positive relationship holds in natural ecosystems across varying climatic conditions. Using a global dataset of 15 large and long-term monitored natural forest sites spanning a wide latitudinal range, we assess the relationship between tree diversity and SOC within and across sites in temperate, subtropical, and tropical regions. We found an overall positive relationship between tree taxonomic diversity and SOC. The relationships between tree taxonomic or functional diversity and SOC became stronger under colder and more arid conditions. Additionally, tree functional composition was linked to SOC only within a subset of sites in more arid climates. These findings suggest that warmer and more humid conditions increase decomposition, offsetting diversity-driven carbon inputs, while colder and more arid conditions enhance SOC through low decomposition and increased inputs through abiotic facilitation and biotic interactions in high-diversity communities. Our findings indicate that conserving plant diversity is critical for enhancing carbon sequestration and mitigating the effects of climatic conditions, particularly in cold climates and regions facing an increase in arid conditions.

The telomere‐binding protein KU is required for DSB repair in rice mitosis but not in meiosis

Wed, 03 Jun 2026 21:30:52 -0700

KU70 is associated with telomeres in meiosis.

Summary

Non-homologous end joining (NHEJ) is an error-prone but efficient primary repair pathway for DNA double-strand breaks (DSBs) during mitosis. A critical unresolved question is whether NHEJ acts as a backup when homologous recombination (HR) is impaired during meiosis. Here, we integrated biochemical, cytological, and genetic approaches to dissect the biological role of KU70/KU80, the core component of the NHEJ machinery, in both mitotic and meiotic DSB repair in rice (Oryza sativa). Biochemical analysis confirmed that KU70 and KU80 form a stable heterodimer. KU deficiency caused hypersensitivity to bleomycin in somatic cells, underscoring its essential function in mitotic DSB repair. KU70 localized to meiotic telomeres but was dispensable for normal meiotic progression and DSB repair efficiency. Moreover, KU deficiency neither altered the aberrant chromosome associations in HR-defective mutants (com1, rec8, meica1, hus1, and rad1) nor genetically interacted with key HR factors (ZIP4 and MER3). Taken together, our findings establish rice meiosis operates under an HR-dominant DSB repair regime independent of KU-mediated NHEJ. This stands in striking contrast to the critical role of NHEJ in mitotic DSB repair and clearly demonstrates that KU-mediated NHEJ does not serve as a backup repair pathway for impaired HR during plant meiosis.

The unicellular green microalga Botryosphaerella sudetica links plant‐like light protection with an algal lifestyle

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Nonphotochemical quenching (NPQ) mechanisms fine-tune light utilisation in the photosynthetic antenna, for example, in response to excess light, to prevent photodamage. NPQ comprises distinct mechanisms, all contributing to photoprotection but acting on different time scales. Preferences for individual mechanisms and NPQ composition are proposed to reflect the organism's lifestyle, especially regarding sessile vs motile styles, with the latter enabling photophobic responses. We analysed photoprotection in the nonmotile, unicellular chlorophycean microalga Botryosphaerella sudetica, belonging to a genus known to form high-light-exposed floating aquatic biofilms. Growth, Chl fluorescence, its nuclear genome, and the expression of photoprotective genes were analysed in comparison with the motile chlorophycean microalga Chlamydomonas reinhardtii. These analyses revealed that B. sudetica is, in contrast to C. reinhardtii, equipped with a constitutive energy-dependent quenching (qE) mechanism based on the constitutive accumulation of protein PSBS, the thylakoid lumen pH-sensor, found throughout the green plant lineage. While qE was the predominant NPQ mechanism in B. sudetica and required zeaxanthin formation, state transitions (qT), which largely contributed to NPQ in C. reinhardtii, played a minor role. These data demonstrate that a core set of NPQ mechanisms conserved in the Viridiplantae is shuffled to meet better the adaptive requirements imposed by the habitat.

Conservation of the short‐day vernalization flowering response pathway in temperate Pooideae grasses

Wed, 03 Jun 2026 21:30:52 -0700

Summary

The attainment of flowering competency to respond to inductive spring conditions is a critical step in the development of many temperate plants, enabling timely reproduction and maximizing fitness. Chilling and short-day (SD) ‘vernalization’ trigger flowering competency in grasses and other species, but the relative importance of each in the colonization of temperate habitats remains poorly understood. We found that SD vernalization is widespread in the Pooideae subfamily of temperate grasses, which includes many of the world's most important crops. Similarities in genes that transcriptionally respond to SDs suggest this trait evolved early in the clade's history as grasses transitioned from tropical to temperate regions. Among the candidate genes underlying a conserved SD vernalization response, the 14-3-3 gene GENERAL REGULATORY FACTOR 14h (GF14h) was found to be a flowering repressor that is downregulated under SD vernalization conditions. Expression analyses in mutant gf14h lines suggest that its repressive action relies on positive regulation of two downstream flowering repressors VERNALIZATION 2 (VRN2) and FLOWERING LOCUS T-LIKE 4 (FTL4), under LDs. In summary, we found that an SD vernalization response evolved early in the history of Pooideae grass diversification, likely through the co-option of an SD flowering regulon that includes GF14h, VRN2, and FTL4.

Three closely linked X‐chromosomal genes potentially control sex determination in Cannabis sativa

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Sex determination mechanisms in dioecious plants remain poorly understood yet offer an excellent model system to study genetic changes underlying morphological evolution. We investigated the genetic basis of sex determination in Cannabis sativa, combining quantitative trait locus mapping in a segregating population, comparative transcriptomics between monoecious and dioecious cultivars, and a genomic analysis of X–Y chromosome divergence. Quantitative trait locus mapping identified Monoecy1, a locus on the X chromosome putatively controlling the monoecy–dioecy trait. This locus resides in the most ancient and diverged region of the sex chromosomes and contains three genes within 60,000 bp (CsREM16, lncREM16 and CsKAN4) with distinct sex-specific and monoecy-specific expression patterns. Monoecy1 harbors genes for male–female as well as monoecious–dioecious sex determination. We propose that the combinatorial interaction of CSREM16, lncREM16 and CsKAN4 provides a unifying genetic framework for understanding male–female and monoecious–dioecious sex determination in C. sativa.

Achoimre

Níl mórán tuisceana fós ann ar na meicníochtaí maidir le socrú gnéis i bplandaí dé-éiciacha, ach cuireann siad córas samhail den scoth ar fáil chun staidéar a dhéanamh ar athruithe géiniteacha atá mar bhunús leis an éabhlóid mhoirfeolaíoch. Rinneamar imscrúdú ar an mbonn géiniteach maidir le socrú gnéis i gCannabis sativa, ag comhcheangal mapáil QTL i ndaonra atá ag leithlisiú mar aon le tras-scríobhómaíocht comparáideach idir saothróga moinéiciach agus dé-éiciacha, agus anailís ghéanómach ar éagsúlacht crómasóim X-Y. Mar thoradh ar mhapáil QTL, aithníodh Monoecy1, lócas ar an X-chrómasóm a rialaíonn an tréith moinéiciach-dé-éiciach, go hiondúil. Tá an lócas seo suite san áit is sine agus is éagsúla de na crómasóim atá bainteach le gnéas. Tá trí ghéin ann (CsREM16, lncREM16, agus CsKAN4) laistigh de 60,000 péire bunanna (bp) a bhfuil patrúin léirithe sainghnéas agus sainmhoinéice acu. Tá géinte ag Monoecy1 a thugann socraithe gnéis fireann-baineann chomh maith le géinte aonchineálacha-déchineálacha le fios. Dar linn, soláthraíonn an t-idirghníomhú comhcheangailte idir CSREM16, lncREM16 agus CsKAN4 creat géiniteach aontaitheach chun socrú gnéis fireann-baineann agus aonchineálach-déchineálach i gCannabis sativa a thuiscint.

Riassunto

I meccanismi di determinazione del sesso nelle piante dioiche rimangono poco compresi, eppure offrono un eccellente sistema modello per studiare i cambiamenti genetici alla base dell'evoluzione morfologica. Abbiamo indagato la base genetica della determinazione del sesso nella Cannabis sativa, combinando la mappatura QTL in una popolazione in segregazione, la trascrittomica comparativa tra cultivar monoiche e dioiche, e un'analisi genomica della divergenza dei cromosomi X e Y. La mappatura QTL ha identificato Monoecy1, un locus sul cromosoma X che presumibilmente controlla il carattere monoicismo-dioicismo. Questo locus risiede nella regione più antica e divergente dei cromosomi sessuali e contiene tre geni nello spazio di 60.000 bp (CsREM16, lncREM16 e CsKAN4) con pattern di espressione distinti, specifici per il sesso e specifici per la monoecia. Monoecy1 ospita geni per la determinazione del sesso maschio-femmina e per quella monoecio-dioecio. Proponiamo che l'interazione combinatoria di CsREM16, lncREM16 e CsKAN4 fornisca un modello genetico unificante per comprendere la determinazione del sesso maschio-femmina e monoico-dioico nellla Cannabis sativa.

Résumé

Les mécanismes de détermination du sexe chez les plantes dioïques demeurent très mal compris alors qu’ils constituent un excellent modèle pour étudier l’évolution morphologique. Nous avons étudié les bases génétiques du déterminisme du sexe chez Canabis sativa, en combinant cartographie QTL dans une population en ségrégation, transcriptomique comparative entre cultivars monoïque et dioïque, et analyse de la divergence des chromosomes X-Y La cartographie QTL a révélé le locus Monoecy1, contenant trois gènes (CsREM16, lncREM16, et CsKAN4) dans un intervalle de 60,000 bp, apparaît comme un bon candidat au contrôle du caractère monoïque-dioïque, avec une forte divergence X-Y, et des profils d’expression spécifique du sexe et de la monœcie versus dioiécie. Monoecy1 pourrait contrôler à la fois le déterminisme mâle–femelle et les caractères monoécie–dioécie, via l’interaction combinée des gènes CsREM16, lncREM16, et CsKAN4.

Resumen

Los mecanismos de determinación del sexo en plantas dioicas siguen siendo poco comprendidos, pero representan un modelo excepcional para estudiar los cambios genéticos subyacentes a la evolución morfológica. En este estudio, investigamos las bases genéticas de la determinación del sexo en Cannabis sativa combinando mapeo de QTL en poblaciones segregantes, transcriptómica comparativa entre cultivares monoicos y dioicos, y análisis genómicos de la divergencia entre los cromosomas X e Y. El mapeo de QTL identificó Monoecy1, un locus en el cromosoma X que al parecer regula los rasgos de monoicidad/dioicidad. Este locus se localiza en la región más antigua y divergente de los cromosomas sexuales y contiene tres genes en un intervalo de 60,000 pb (CsREM16, lncREM16 y CsKAN4), los cuales presentan patrones de expresión específicos según el sexo y la condición de floración (monoicidad o dioicidad). El locus Monoecy1 contiene genes que determinan tanto la identidad masculino-femenina como los caracteres monoico o dioico. Proponemos que los patrones de expresión diferencial de CsREM16, lncREM16 y CsKAN4 constituyen un marco unificador para comprender la determinación de las identidades monoica-dioica y masculino-femenina de Cannabis sativa.

Zusammenfassung

Die Mechanismen der Geschlechtsfestlegung in zweihäusigen Pflanzen sind relativ schlecht verstanden, bieten aber ein hervorragendes Modell, um genetische Änderungen zu studieren, welche die morphologische Evolution bedingen. Wir untersuchten die genetischen Grundlagen der Geschlechtsbestimmung in Cannabis sativa. Dabei haben wir QTL-Kartierung, vergleichende Transkriptomik zwischen einhäusigen und zweihäusigen Varietäten und eine genomische Analyse der Unterschiede zwischen X- und Y-Chromosom kombiniert. Durch QTL-Kartierung konnten wir Monoecy1 identifizieren, einen Genort auf dem X-Chromosom der möglicherweise die Merkmalsausprägung einhäusig-zweihäusig kontrolliert. Dieser Genort befindet sich in der ältesten und am stärksten veränderten Region des Geschlechtschromosoms und beinhaltet drei Gene innerhalb eines Abstandes von 60.000 Basenpaaren (CsREM16, lncREM16, and CsKAN4). Diese Gene haben geschlechtsspezifische und einhäusig-spezifische Expressionsmuster. Monoecy1 beinhaltet Gene für männliche-weibliche als auch einhäusige-zweihäusige Geschlechtsbestimmung. Wir schlagen vor, dass die kombinatorische Interaktion von CSREM16, lncREM16 und CsKAN4 die genetische Geschlechtsbestimmung in Cannabis sativa steuert.

Ocean warming indirectly affects seagrass performance through effects on sediment microbial communities

Renske Jongen, Paul E. Gribben, Katherine R. Erickson, Ezequiel M. Marzinelli — Wed, 03 Jun 2026 21:30:52 -0700

Summary

Belowground microbes are increasingly recognised as mediators of plant responses to stress, but it remains unclear whether the thermal histories of marine plants and their associated belowground microbes influence plant performance under ocean warming. We conducted a common-garden field experiment at a long-term warmed site in Lake Macquarie (NSW, Australia, > 30 yr, 1–3°C warming), to test the effects of sediment origin (ambient vs warm-origin), plant origin (ambient vs warm-origin) and microbial disruption (intact vs disrupted rhizosphere and bulk sediment microbial communities) on seagrass (Zostera muelleri) performance. Both plant origins had lower aboveground biomass in intact warm-origin sediments, but warm-origin plants recovered when bulk sediment microbial communities were disrupted, indicating that warming-altered sediment microbial communities can suppress seagrass performance. Disrupted warm-origin sediments were enriched in sulphide-oxidising bacteria, which likely contributed to enhanced performance. In warm-origin sediments, rhizosphere bacterial communities were similar across plant origins, indicating that sediments shape rhizosphere bacterial assembly. Rhizosphere microbial disruption had no effect on plant performance. We show that ocean warming can shape sediment microbial communities in ways that suppress seagrass performance, suggesting that sediment microbial communities can override plant thermal history and act as hidden constraints on seagrass tolerance to warming.

Continuous monitoring of plant water potential: sensor‐based approaches and best practices

Wed, 03 Jun 2026 21:30:52 -0700

Summary

Plant water potential is a central integrator of plant water status, linking hydraulic function with physiological performance and ecosystem water dynamics across species and systems. This review is motivated by the need to capture these dynamics under rapidly changing environmental conditions, which are often missed by discrete measurements. We evaluate the main approaches for continuous monitoring of plant water potential, including direct in situ sensors, indirect methods based on plant water content, and remote-sensing proxies. We discuss the principles, measurement mechanisms, practical constraints, and environmental sensitivities of each approach. Relative to traditional methods, such as pressure chambers, continuous measurements offer major advantages by resolving rapid variation in water status and strengthening inference on plant–soil–atmosphere interactions. These approaches are especially valuable under dynamic field conditions, where temporal variability in vapor pressure deficit, soil moisture, temperature, and radiation strongly shapes hydraulic behavior. We conclude that continuous monitoring has substantial potential to advance plant and ecosystem science, but wider application will depend on careful interpretation and greater harmonization across comparable methodologies. By synthesizing core principles, methodological challenges and best practices, this review provides a practical framework for researchers and practitioners applying continuous water potential measurements.

Modelling belowground plant acclimation to low soil nitrogen – a heuristic optimality‐based approach

Arjun Chakrawal, Sacha J. Mooney, Tino Colombi — Wed, 03 Jun 2026 21:30:52 -0700

Summary

Increased root growth to access greater soil mineral nitrogen resources, and increased root exudation to stimulate microbial mineralisation of soil organic nitrogen, are widely observed plant acclimations to nitrogen limitation. However, the quantitative contribution of these belowground acclimations to whole plant growth and ecosystem productivity remains largely elusive. Here, we present a novel heuristic optimality-based eco-evolutionary nitrogen foraging model in which plants dynamically regulate carbon partitioning between root growth and exudation to maximise their aboveground growth. Our simulations indicated that the dynamic availability of soil mineral and organic nitrogen, as well as plant nitrogen demand and nitrogen uptake capacity, shape optimal carbon partitioning between root growth and exudation. The simulated carbon allocation patterns aligned with empirical studies on belowground plant responses to varying nitrogen resources in soil. These findings demonstrated the potential and versatility of our model to capture the quantitative importance of root and whole plant physiological acclimations for plant growth and productivity under fluctuating soil nitrogen availability. Our optimality-based approach represents a paradigmatic change in modelling plant nitrogen foraging, which is essential to generate hypotheses on optimal plant acclimations in future soil environments characterised by more erratic nitrogen availability.

The genetic architecture of leaf vein density and its importance for photosynthesis in maize

Tue, 02 Jun 2026 22:46:22 -0700

Vein types in maize leaves.

Summary

Leaf venation density has significantly increased during plant evolution. Higher densities are observed in angiosperms compared with early land plants, and among angiosperms, recently diverged C4 species have the highest values. This enabled leaves to increase water conductance, transpiration and possibly photosynthesis. Despite its importance, the genetic architecture of this trait is not well-characterized, and its relationship with photosynthesis has not been clearly established. Using native Mexican varieties of maize (Zea mays) adapted to a wide range of environmental conditions, we show vein density is variable and plastic. We leverage this variation to perform correlation analyses with photosynthetic rates and to map genetic regions associated with vein patterning traits using a Multiparent Advanced Generation Inter Cross population. Our results show that higher vein densities are correlated with higher photosynthetic rates, but only for small intermediate veins. Varieties adapted to drier environments can substantially increase vein density in response to heat, suggesting a role in water use efficiency. We further detected 12 quantitative trait loci (QTLs) associated with vein patterning and identified candidate genes related to small intermediate vein development. These findings have implications for understanding vein architecture evolution, particularly that of C4 plants, which have significantly higher photosynthetic efficiency and productivity under warm and dry conditions.

Pollen longevity and viability dataset: an integrated resource for plant research and conservation

Louise Winther, Conny Bruun Asmussen Lange, Sergey Rosbakh — Tue, 02 Jun 2026 22:02:59 -0700

The most common methods to estimate pollen viability.

Summary

Pollen viability and longevity are key traits in plant reproduction, with implications for gene flow, crop breeding, and ex situ plant conservation. However, published data on these traits remain dispersed across disciplines, languages, and methods, limiting their accessibility and reuse. Here, we present a curated, taxonomically broad dataset compiling pollen viability over time for 274 vascular plant species extracted from 320 primary publications published between 1962 and 2023. The dataset includes germination- and staining-based viability estimates under defined storage conditions, along with metadata on species identity, experimental design, and pollen traits. To facilitate data exploration and application, the full dataset is openly available via an online repository and accompanied by an interactive Shiny App that allows users to filter, visualize, and download customized subsets. This resource provides a structured foundation for comparative analyses of pollen longevity and viability within well-represented clades and experimental contexts. It supports trait-based and applied research when combined with external data sources, while also serving as a starting point for future syntheses.

Autophagy in plant male reproduction: conserved machinery, divergent functions

He Yan, Jianxing Li, Yuner Zheng, Hao Wang — Tue, 02 Jun 2026 20:07:13 -0700

Schematic illustration of autophagy-mediated regulation of male reproduction in angiosperms.

Summary

Autophagy is an evolutionarily conserved catabolic process essential for maintaining cellular homeostasis, mediating defense responses and supporting development and reproduction in eukaryotes. Despite substantial differences in reproductive strategies between plants and animals, the biogenesis of functional male gametes and the completion of fertilization in both systems rely on tightly regulated cellular degradation mechanisms. Disruption of autophagy typically causes severe defects in spermatogenesis and impairs sperm motility and fertility in animals. By contrast, autophagy is generally considered non-essential for sexual reproduction in many angiosperms as most autophagy-deficient mutants remain fertile and produce viable progeny. However, emerging evidence challenges this perspective by revealing that autophagy actually plays active yet divergent roles in pollen development, germination and pollen tube growth. A key unanswered question is how exactly autophagy contributes to male fertility and reproduction in flowering plants. In this review, we synthesize recent advances in understanding autophagy during male gametogenesis and fertilization, focusing on comparative insights between plant and animal systems to highlight mechanistic distinctions and identify essential unique questions for future plant research. We further discuss the potential involvement of alternative catabolic pathways that may act alongside canonical autophagy to regulate male gametophyte development and fertility in angiosperms.

Trimerous magnoliid flowers with a unique set of floral and pollen traits from the Late Cretaceous of Southern Bohemia (Czech Republic)

Tue, 02 Jun 2026 00:00:00 -0700

Morphospace position and phylogenetic placements of Trimeriantha monopolyada.

Summary

Floral structure is a key aspect of angiosperm diversity. Recent research revealed that significant floral disparity was already present in the Cretaceous. However, our understanding of early floral diversity remains limited, as it is directly dependent on the fossil record. We describe a new, exceptionally well-preserved flower with in situ pollen from the Klikov Formation (late Turonian - Santonian). Our phylogenetic analyses support relationships with the magnoliid order Piperales. Based on a morphospace analysis, we show that the new fossil is among the most morphologically divergent angiosperm flowers. Trimeriantha monopolyada gen. et sp. nov. represents the first unequivocal evidence of piperalean flowers from the Late Cretaceous and exhibits a unique combination of floral traits, including a single whorl of tepals, three whorls of stamens, anthers with a single pollen polyad per pollen sac and valvate dehiscence, a fusion of androecium and gynoecium, and an extragynoecial compitum. This trait combination distinguishes it from other extant and fossil angiosperms and further expands our understanding of Cretaceous flower diversity. Our study adds to the extraordinary morphological diversity known from the Late Cretaceous record of flowers, and we discuss some of the floral traits of T. monopolyada with respect to their phylogenetic significance and potential function in pollination biology.

Spatial inference of ancestor locations suggests northern refugia for canopy‐forming kelps in the Pacific Northwest

Mon, 01 Jun 2026 21:51:34 -0700

Population genetic structure in the Pacific Northwest for (a–c) Nereocystis and (d–f) Macrocystis.

Summary

Pockets of the formerly glaciated Pacific coastline of North America likely remained ice-free throughout the Last Glacial Maximum (LGM). These areas may have served as refugia for terrestrial species, but less is known about their role in the persistence of marine plants and other coastal species. We examined genetic diversity from > 1000 newly and previously sequenced whole genomes of canopy-forming kelps of the genera Nereocystis and Macrocystis and built simple ecological niche models. We then reconstructed ancestral recombination graphs and modeled the geographic locations of genetic ancestors through time. We detected high genetic diversity in both species in north-central British Columbia, in a region where suitable LGM habitat is plausible. Ancestor locations spatially converged backward in time toward this region, with multiple refugia inferred between northern Vancouver Island and southern Haida Gwaii. An expanded set of global samples for Macrocystis confirmed pre-LGM divergence with California but hinted at the possibility of subsequent gene flow. Nereocystis and Macrocystis survived glaciation in northern refugia. The northern persistence of these foundation species raises the possibility that biodiverse kelp forest ecosystems could have continuously occupied portions of the northern Pacific coastline since the LGM.

When solids become fluid to sustain life

Hardy Rolletschek, Ljudmilla Borisjuk — Mon, 01 Jun 2026 21:50:38 -0700

New Phytologist, EarlyView.

Arabidopsis DNA repair mutants can integrate Agrobacterium T‐DNA into the plant genome

Mon, 01 Jun 2026 21:46:51 -0700

Transient (a) and stable (b) transformation of Arabidopsis thaliana DNA repair/recombination mutants grown under normal light conditions.

Summary

Agrobacterium transfer DNA (T-DNA) integration is mediated by plant DNA repair proteins of various nonhomologous end-joining (NHEJ) pathways. However, the relative importance of these proteins for stable transformation of Arabidopsis thaliana is controversial. Using quantitative transient and stable transformation assays and droplet digital PCR analyses, we characterized single and higher order Arabidopsis NHEJ mutants to determine the importance of numerous NHEJ proteins in transformation and T-DNA integration. Simultaneous mutation of genes important for several DNA repair/recombination pathways may only partially inhibit stable Agrobacterium-mediated transformation. Some of these mutations may also inhibit transient transformation. These observations support the hypothesis that no individual NHEJ protein is essential for T-DNA integration.

FaCPK19–FaTT1 axis decodes heat‐induced Ca2+ signals and enhances thermotolerance in tall fescue

Mon, 01 Jun 2026 02:21:19 -0700

FaCPK19-mediated FaTT1^T172 phosphorylation controls FaTT1 function.

Summary

Ca²⁺ signals play a crucial role in heat stress (HS) resistance. However, how Ca²⁺ signals are decoded and regulate the downstream targets of HS signaling remains unclear in plants. Cool-season grasses are sensitive to high-temperature conditions and should evolve distinctive heat stress response mechanisms. Here, we identified the calcium-dependent protein kinase 19 (FaCPK19), which decoded the unique Ca²⁺ signal triggered by HS in cool-season grass tall fescue (Festuca arundinacea Schreb.). The FaCPK19 was activated upon HS and positively regulated thermotolerance in tall fescue. FaCPK19 interacted with the thermo-tolerance 1 (FaTT1), which encodes an α2 subunit of the 26S proteasome, and phosphorylated its Thr172 (T172) residue. Under HS, overexpressing FaTT1 ^T172A (FaTT1 ^T172A -OE, phospho-deficient) grasses resulted in significantly lower 20S and 26S proteasome activity and reduced expression of downstream HS-responsive genes compared to gain-function transgenic grasses (FaTT1-OE). The Facpk19 mutant was weakened in 20S and 26S proteasome activity under HS. Loss of T172 phosphorylation in FaTT1 ^T172A -OE showed a weakened heat-tolerance phenotype than FaTT1-OE. T172 residue at TT1 is evolutionarily conserved from plants to animals, indicating it could be widely used for thermotolerance breeding in grasses and crops. Our findings reveal a Ca²⁺-FaCPK19–FaTT1 axis by which an HS-induced Ca²⁺ signal is decoded with enhanced thermotolerance in tall fescue.

A C2H2 zinc finger transcription factor links a GWAS locus to linear growth in Gracilariopsis lemaneiformis via MCM helicase activation

Youtao Huang, Xinran Wang, Mengxing Cao, Zhenghong Sui — Sun, 31 May 2026 20:39:46 -0700

This study integrated genome-wide association studies and multiomics to identify a C₂H₂ zinc finger transcription factor linked to linear growth in Gracilariopsis lemaneiformis. Structural and functional analyses, plus binding site validation, revealed it regulates growth by activating minichromosome maintenance helicase genes, bridging genetic variation to phenotypic traits in macroalgae.

Summary

The genetic basis of linear growth rate in the red alga Gracilariopsis lemaneiformis remains poorly characterized. This study functionally characterized the gene LXC001294, a prior genome-wide association studies (GWAS) candidate associated with growth variation, to elucidate its molecular role. We employed phylogenetic analysis, yeast assays, and subcellular localization to characterize LXC001294. Its genome-wide binding sites were identified by ChIP-seq, and transcriptomic profiles of fast- (YT13) and slow-growing (QHD9) strains were compared via RNA-seq. Direct regulation of key targets was validated using yeast one-hybrid and dual-luciferase assays. LXC001294 was confirmed as a nuclear-localized C₂H₂ zinc finger transcription factor. Integrated multi-omics analysis revealed its direct targeting and upregulation of five minichromosome maintenance (MCM) genes, core components of the DNA replication machinery, in the fast-growing strain. We demonstrate that LXC001294 promotes algal growth by activating the MCM complex, thereby enhancing DNA replication. This study provides a mechanistic link from a GWAS signal to a growth phenotype in a macroalga and establishes the transcriptional regulation of replication licensing as a key node controlling growth rate in nonmodel species.

Paralogous LRR receptor kinases confer symbiosis specificity between arbuscular mycorrhizal and root nodule symbioses in Lotus japonicus

Zhiqiong Zheng, Min Cai, Jing Liu, Ning Zhou, Fanjiang Kong, Fang Xie — Sun, 31 May 2026 20:35:25 -0700

AMK2, an AMF-induced LRR-RLK, is a key regulator of arbuscule development whose kinase domain confers symbiosis specificity.

Summary

Arbuscular mycorrhizal (AM) and root nodule (RN) symbiosis play essential roles in plant nutrient acquisition and share a common symbiotic signal transduction pathway, yet they produce distinct developmental outcomes. Here, we identify arbuscular mycorrhiza-induced kinase 2 (AMK2), a leucine-rich repeat receptor-like kinase (LRR-RLK) in Lotus japonicus, as a key regulator of AM symbiosis. AMK2 is a paralog of the rhizobial infection receptor Rhizobial Infection Receptor-like Kinase 1 (RinRK1), highlighting an evolutionary link between receptors controlling different symbiotic programs. AMK2 expression is strongly induced following AM fungal (AMF) inoculation and is directly activated by the AM-specific transcription factor CBX1 through conserved CTTC cis-regulatory motifs. The AMK2 protein localizes specifically to arbuscule-containing cells, and amk2 mutants exhibit severely reduced arbuscule formation. Domain-swapping experiments between RinRK1 and AMK2 demonstrate that symbiosis specificity is determined by their intracellular kinase domains, whereas their extracellular domains are functionally interchangeable. Together, our findings show that two evolutionarily related LRR-RLK receptors have been differentially recruited to regulate AM and RN symbioses, providing mechanistic insights into how shared signaling components have diversified to control distinct mutualistic interactions between plants and microbes.

Genome‐wide comparative diversity uncovers population structure, global distribution, and targets of selection in hexaploid oat

Fri, 29 May 2026 21:49:56 -0700

Impact of chromosome rearrangements on the population structure of oat landraces.

Summary

Here, we performed comprehensive genomic analyses aimed at elucidating the population structure, worldwide phylogeography, and breeding selection in cultivated oat. We utilized 73 261 single-nucleotide polymorphisms from a diverse collection of 920 oat accessions, encompassing 487 landraces and 433 modern cultivars. Through an examination of spatial and genetic patterns, we identified six genetic groups among landraces. Geographical isolation, founder effects, and chromosomal structural variations were responsible for the observed genetic structure. Phylogeographic reconstruction traced modern cultivars primarily back to the European gene pool, while highlighting the genetic distinctiveness of the East Asian hulless oats and Mediterranean landraces, which represent underutilized reservoirs of diversity. A comparative scan for selection signatures across major breeding regions demonstrated that modern breeding efforts have tapped into only a fraction of the diversity present in landraces, revealing both shared and region-specific selection targets. This study provides a comprehensive variation map and offers insights into the distribution of genetic diversity in oats. The findings emphasize the importance of leveraging landrace germplasm, particularly from East Asian and Mediterranean origins, to broaden the genetic base of modern oats and guide the development of cultivars with enhanced yield and adaptability.

Thioredoxin system modulates metabolic and stomatal responses to elevated CO2 in Arabidopsis

Fri, 29 May 2026 21:46:38 -0700

Integrative model of extraplastidial NADPH-dependent thioredoxin reductase/thioredoxin system-mediated regulation of stomatal function, redox homeostasis, and metabolic responses under ambient and elevated CO₂ in Arabidopsis thaliana.

Summary

The NADPH-dependent thioredoxin reductase/thioredoxin (NTR/TRX) system plays a central role in maintaining redox homeostasis of the cell by transferring electrons from NADPH to target proteins though NTR and TRX, thereby modulating cysteine redox states and regulating enzyme activity. However, the specific contribution of the extraplastidial NTR/TRX system to plant acclimation to elevated CO₂ (eCO₂) remains poorly understood. Here, we investigated the physiological and metabolic responses of Arabidopsis mutants deficient in mitochondrial TRXo1 (trxo1) or in the cytosolic/mitochondrial/nuclear thioredoxin reductases NTRA/NTRB (ntrantrb) alongside the wild-type (WT), grown under ambient (aCO₂; 400 ppm) and eCO₂ (800 ppm) CO₂ conditions. The stomatal closure induced by abscisic acid or eCO₂ was partially compromised in ntrantrb double mutant. The stomatal density decreased in WT and ntrantrb plants under eCO₂, while did not change in trxo1 lines. The mutants showed much higher increases in rosette biomass under eCO₂ compared to WT. This was associated with alterations in both primary and secondary metabolisms, but not to the level of NAD(P)(H), and reduced glutathione/oxidized glutathione (GSH : GSSG) ratio. Our results indicate that TRXo1 and NTRA/B play key roles in regulating stomatal development/movement and both primary and secondary metabolisms, thereby impacting plant acclimation to eCO₂.

Potential unlocked: an atlas of cloned wheat genes for genome engineering and breeding

Fri, 29 May 2026 21:36:17 -0700

Strategies for introducing genome edits into a wheat breeding program and their effects on cultivar longevity.

Summary

Bread wheat (Triticum aestivum) production is increasingly threatened by biotic and abiotic stresses. Developing varieties with improved stress tolerance and desirable end-use qualities is crucial for meeting growing global demand. Genome-editing technologies, particularly Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins (CRISPR/Cas)-derived systems, represent powerful tools to accelerate trait discovery and crop improvement. Here, we present a comprehensive atlas of cloned wheat genes and discuss examples and strategies for using it to identify candidate targets for CRISPR/Cas-mediated improvement. Finally, we recommend ways to integrate gene editing into breeding timelines and accelerate the incorporation of desirable alleles.

Neglected seed dispersers and research compartmentalisation: how much do we know about what we don't know?

Thu, 28 May 2026 21:26:02 -0700

Geographic distribution of seed dispersal studies by disperser guild.

Summary

Seed dispersal is critical for long-term ecosystem resilience. However, excessive compartmentalisation of research into particular disperser guilds (e.g. birds) hampers our understanding of their relative contributions to overall seed dispersal, risking erroneous conclusions and overlooking key information gaps. Here, we evaluate how information about over 11 000 interactions between 1902 plant and 455 animal species in Europe accumulated over 400 years, and estimate information completeness across disperser guilds, plant types, and dispersal mechanisms (endozoochory, epizoochory, synzoochory, and myrmecochory). Information regarding the plants dispersed by each group of animals ranges from 27% to 79% sample coverage, with birds of prey (27%), ants (28%), and rodents (31%) particularly understudied. Most research focussed on fleshy-fruited plants rather than dry-fruited plants, and most on internal dispersal as the mechanism (endozoochory). Interestingly, scientists' perceptions of what are the most neglected disperser guilds do not correlate with our sample coverage estimates, showing an inability of the scientific community to identify information gaps. We urge researchers to bridge research silos and to study overlooked guilds, mechanisms, and plant types. Implementing community-level synthesis studies that integrate data across guilds is essential for accurately predicting ecosystem responses to global change and developing effective conservation strategies.

OsMYB94 functions as a master regulator of metabolic pathways associated with rice caryopsis maturation and quality formation

Thu, 28 May 2026 20:51:27 -0700

A proposed model for OsMYB94-mediated regulation of metabolic pathways associated with caryopsis maturation and quality formation.

Summary

Rice (Oryza sativa) caryopses supply essential carbohydrates, energy, and protein to over half the world's population. Caryopsis quality depends on the biosynthesis, modification, and accumulation of primary and secondary metabolites during maturation. Yet, the regulatory and biochemical pathways remain poorly understood. Emerging evidence implicates transcription factors, particularly MYB family members, in this regulation. In this study, the function of R2R3 MYB transcription factor OsMYB94 in regulating metabolic pathways underlying rice caryopsis maturation and quality formation was characterized using integrative approaches. OsMYB94 orchestrates secondary metabolism (for protection), reserve accumulation (for energy storage), reactive oxygen species homeostasis (for antioxidant defense), and hormonal signaling (for desiccation and dormancy) to ensure proper maturation and high-quality formation of rice caryopses. osmyb94 caryopses exhibit poor appearance quality, milling quality, and eating and cooking quality, correlating with incomplete caryopsis filling, thinner aleurone and coat layers, reduced starch and triglyceride accumulation, disrupted lipid metabolism, and downregulation of genes associated with ripening-related metabolic pathways. Furthermore, the OsMYB94-OsLTPL12 module is a key regulator of rice caryopsis glossiness. This study highlights that OsMYB94 is a master regulator of metabolic pathways associated with rice caryopsis maturation and quality formation, offering a genetic target for improvement.

Kinetic parameter prediction using neural networks identifies limitations to C4 photosynthesis

Thu, 28 May 2026 20:50:22 -0700

Schematic overview of the generation of artificial training data and training of neural networks in C4TUNE.

Summary

Kinetic models of photosynthesis enable time-resolved predictions of traits related to this key process and provide the means to identify factors limiting photosynthesis. However, the use of large-scale models is currently limited by the lack of efficient approaches to estimate the hundreds of genotype-specific kinetic parameters. Here, we present C4TUNE, an artificial neural network that can efficiently predict parameters of a large-scale photosynthesis model from photosynthesis response curves. C4TUNE was trained on a biologically relevant synthetic dataset comprising matched samples of parameters and response curves obtained using a C₄ photosynthesis kinetic model. To speed up the training of C4TUNE, we devised a surrogate neural network to predict photosynthesis response curves directly from the model parameters and environmental inputs. Given response curves as input, we showed that over 99% of the parameter vectors predicted by C4TUNE could be used directly in simulation of the kinetic model and resulted in excellent fits. Finally, we applied C4TUNE to predict parameters for a population of 68 maize genotypes across two seasons. The predicted genotype-specific parameters allowed pinpointing factors that limit photosynthetic efficiency, validated using simulations. Therefore, the use of C4TUNE presents a fast and precise approach for parameter prediction based on minimal datasets.

Zusammenfassung

Kinetische Photosynthesemodelle ermöglichen zeitlich aufgelöste Vorhersagen von Merkmalen, die mit diesem Schlüsselprozess zusammenhängen. Weiterhin bieten sie die Möglichkeit, Faktoren zu identifizieren, die Photosynthese limitieren. Der Einsatz großskaliger Modelle wird derzeit jedoch durch den Mangel an effizienten Ansätzen zur Schätzung der Hunderten von genotypspezifischen kinetischen Parametern eingeschränkt. Hier stellen wir C4TUNE vor, ein künstliches neuronales Netzwerk, das Parameter eines Photosynthesemodells anhand von Photosynthese-Reaktionskurven effizient vorhersagen kann. C4TUNE wurde auf einem biologisch relevanten synthetischen Datensatz trainiert, der zusammengehöhrende Parameter und Reaktionskurven enthält, die mithilfe eines kinetischen C₄-Photosynthesemodells simuliert wurden. Um das Training von C4TUNE zu beschleunigen, haben wir ein Surrogat-Modell entwickelt, welches die Photosynthese-Reaktionskurven direkt aus den Modellparametern und experimentellen Bedingungen vorhersagt. Anhand der als Eingabe verwendeten Reaktionskurven konnten wir zeigen, dass über 99% der von C4TUNE vorhergesagten Parametervektoren direkt für Simulationen mithilfe des kinetischen Modells verwendet werden konnten und zu hervorragenden Übereinstimmungen führten. Schließlich wandten wir C4TUNE an, um Parameter für eine Population von 68 Mais-Genotypen für zwei Vegetationsperioden vorherzusagen. Die vorhergesagten genotypspezifischen Parameter ermöglichten es, Faktoren zu identifizieren, die die Photosyntheseeffizienz limitieren; diese wurden durch Simulationen bestätigt. Somit bietet C4TUNE einen schnellen und präzisen Ansatz für die Parametervorhersage auf der Grundlage minimaler Datensätze.

EMF2 deficiency disrupts epigenetic and chromatin organization landscapes, blocking root regeneration competence in Arabidopsis

Zhidan Wang, May Avraham, Tali Mandel, Leor Eshed Williams, Chang Liu — Thu, 28 May 2026 20:45:19 -0700

EMF2 mutation alters transcriptomic profiles in Arabidopsis calli while retaining responsiveness during root induction.

Summary

Plant de novo organogenesis depends on callus formation, yet the epigenetic mechanisms governing organ regeneration remain poorly understood. EMBRYONIC FLOWER 2 (EMF2), a core component of Polycomb Repressive Complex 2, mediates transcriptional repression through H3K27me3 and is essential for root regeneration in Arabidopsis. Here, we investigate how EMF2-mediated H3K27me3 shapes chromatin architecture and gene expression during root regeneration. We combined time-course transcriptome profiling, H3K27me3 chromatin immunoprecipitation, in situ Hi-C, and a probe hybridization-based Capture Hi-C approach to analyze chromatin organization and gene expression dynamics in wild-type and emf2 calli during root induction. Although emf2 calli lost root regeneration capacity, they retained responsiveness to root induction signals. Despite large-scale reduction of H3K27me3 across the emf2 genome, many genes remained transcriptionally inactive, coinciding with the formation of new long-range chromatin interactions and weakened intra- and peri-domain contacts. Genes with low basal transcription were preferentially derepressed following extensive H3K27me3 loss. Our results demonstrate that large-scale reduction of H3K27me3 in emf2 drives dynamic reorganization of chromatin architecture in Arabidopsis callus, providing new insights into how histone modification and three-dimensional chromatin topology coordinately regulate gene expression during plant regeneration.

Promoter methylation of MdRNS3a contributes to Alternaria leaf spot resistance in apple (Malus × domestica)

Qiulei Zhang, Qingqing Guo, Jinqi Tang, Xiaokun Zhao, Tianzhong Li — Wed, 27 May 2026 19:59:58 -0700

A model in which MdbHLH3 functions as a transcriptional activator of MdRNS3a by binding to its promoter in a methylation-sensitive manner. Fungal infestation induced the accumulation of MdRNS3a in apples, and MdRNS3a cleaves tRNAs to produce 5′ tsRVal, 5′ tsRVal cleaved the target genes MdTIR-1, making apples susceptible to the fungal disease. By contrast, in the resistant cultivar Han Fu (HF), promoter methylation following ALT1 exposure blocks MdbHLH3 binding, preventing MdRNS3a activation and tsRVal biogenesis, thereby sustaining MdTIR-1 levels and conferring resistance.

Summary

Apple leaf spot severely threatens global apple production, and with chemical control posing environmental and health risks, resistance breeding necessitates exploration of a previously unknown regulatory mechanism that distinguishes ALT1-susceptible from -resistant apple cultivars. Small RNA sequencing of Alternaria alternata f. sp. mali (ALT1)-infected susceptible apple ‘Golden Delicious’ revealed a novel tRNA-Val-derived tsRNA (tsRVal) that negatively regulates MdTIR-1 expression to modulate ALT1 resistance. Our findings revealed that tsRVal biosynthesis required cleavage by the ribonuclease T2 family member MdRNS3a. Interestingly, we found that DNA methylation of the MdRNS3a promoter negatively regulates its expression in the resistant apple cultivar Han Fu, which in turn abrogates tsRVal biogenesis and maintains resistance to ALT1. Conversely, ALT1 inoculation induced promoter hypomethylation in GD, leading to robust MdRNS3a activation, significant tsRVal accumulation, and the subsequent development of pathogenic phenotypes. Our findings further support a regulatory model wherein MdbHLH3 functions as a methylation-sensitive transcriptional activator of MdRNS3a via promoter binding, thereby determining tsRVal biosynthesis and the resultant leaf spot sensitivity. Our study demonstrates that the methylation status of the MdRNS3a promoter can serve as a reliable epigenetic marker for distinguishing resistant and susceptible apple varieties, thus providing a valuable tool to facilitate disease-resistant apple breeding programs.

Environmental influences on the maximum quantum yield of terrestrial primary production

David Sandoval, Victor Flo, Catherine Morfopoulos, Iain Colin Prentice — Wed, 27 May 2026 19:59:05 -0700

Temperature and aridity effects on terrestrial ecosystems' intrinsic quantum yield.

Summary

Historically, terrestrial biosphere models (TBMs) have assigned the intrinsic (maximum) quantum yield of photosynthesis (ϕ0)$$ {\phi}_0\Big) $$ a constant value for each plant functional type. However, experimental studies have shown that ϕ0$$ {\phi}_0 $$ – when measured on light-adapted leaves – depends on temperature. It is unclear whether this dependence is universal or biome-specific; how it is manifested at the ecosystem level; and how it should be represented in TBMs. By fitting empirical light-response curves to a global set of eddy-covariance CO₂ flux measurements and correcting for photorespiration, we inferred apparent, ecosystem-level ϕ0$$ {\phi}_0 $$ values and their temperature responses across a wide range of environments. The temperature response of the apparent ecosystem-level ϕ0$$ {\phi}_0 $$ follows a universal bell-shaped curve. The shape of this curve does not markedly differ among biomes, but the maximum value of ϕ0$$ {\phi}_0 $$ decreases with increasing aridity, its temperature optimum increases with increasing growth temperature, and its sensitivity to temperature increases as growth temperature declines. Our model for ϕ0T$$ {\phi}_0(T) $$ aligns with recent theory highlighting the role of cytochrome b ₆ f in regulating the light reactions of photosynthesis. If implemented in TBMs, this model should allow better predictions of the responses of terrestrial ecosystem function to a warming climate.

Barley HvBODYGUARD1 controls cuticular specialisations regulated by SHINE transcription factors

Wed, 27 May 2026 19:57:32 -0700

Cuticle defects result from defective HvBDG1 alleles.

Summary

Land plants secrete a protective outer cuticular layer with diverse functions. Barley (Hordeum vulgare L.) develops two cuticular specialisations: the β-diketone rich wax bloom on vegetative tissues and an adherent grain surface which sticks to the hulls, leading to barley's distinctive ‘covered’ grain phenotype. Two barley SHINE transcription factors, HvWIN1 and NUD, promote the wax bloom and covered grain phenotypes, respectively, yet we know little about other genes involved. We investigated a barley mutant showing defects in both cuticular specialisations to better understand the networks and processes underlying these traits. We identified the barley BODYGUARD1 (HvBDG1) gene encoding an α/β hydrolase as crucial for leaf cuticular integrity and wax-bloom deposition. Mining tetraploid wheat (Triticum turgidum ssp. durum) mutant populations demonstrated that BDG1 and WIN1 orthologues also control the wax bloom in wheat. We further reveal that NUD and HvWIN1 retain functional, independent overlap in leaf cuticle integrity and hull adhesion in barley, functions which involve upregulation of HvBDG1 and other direct or indirect targets, shared and distinct, depending on the stage and tissue. Our work greatly expands our knowledge of genetic and developmental mechanisms underlying shared and distinctive cuticular features in plants.

Endogenous RALF peptide function is required for powdery mildew host colonization

Wed, 27 May 2026 19:55:55 -0700

Model of RALF-FER-dependent effects on powdery mildew sporulation.

Summary

The receptor kinase FERONIA (FER) is a susceptibility factor for biotrophic powdery mildew fungal pathogens in Arabidopsis thaliana, but the underlying molecular mechanisms remain largely unknown. FER is required for the perception of endogenous RAPID ALKALINIZATION FACTOR (RALF) peptides to control various aspects of plant growth, development and immunity. RALFs are either perceived by FER/LORELEI-LIKE GPI-ANCHORED PROTEIN (LLG) heterocomplexes to induce cellular responses or bind to LEUCINE-RICH REPEAT EXTENSIN (LRX) proteins as cell wall structural components. Combining genetics, cell biology and biochemistry, we found that FER's endogenous RALF ligands are necessary for full colonization success of the powdery mildew-species Erysiphe cruciferarum. We reveal that LLGs and LRXs are also powdery mildew susceptibility factors. We show that cell wall remodeling and apoplastic pH homeostasis, hallmark features of RALF function, support powdery mildew reproductive success. We provide data that RALF-dependent powdery mildew pathogenesis is partially independent of FER. Powdery mildew fungi likely do not produce RALF peptide mimics, suggesting their reliance on endogenous RALFs for successful host colonization. We propose that powdery mildew fungi require RALF-mediated modulation of apoplastic pH and pectin remodeling for successful host colonization, highlighting a new susceptibility mechanism by obligate biotrophic fungi.

Investigating GERMs: how genotype, environment, and rhizosphere microbiome interactions underlie heat response in maize and sorghum

Tue, 26 May 2026 22:15:19 -0700

Three genotypes – a heat-resistant maize (Zea mays), a heat-susceptible maize, and a sorghum (Sorghum bicolor) variety – were grown to the V4 stage in growth chambers under optimal conditions or subjected to heat stress. Plants were grown in soil containing a complex microbial community, or in the same soil with a depleted microbiome. Total RNA from roots and root-associated microbes was sequenced, along with the 16S rRNA amplicon from both DNA and RNA. Plants were assigned a qualitative heat stress score based on size and leaf senescence (bottom right), as well as quantitative metrics, including biomass and root architecture.

Summary

Plant responses to heat stress emerge from interactions among host genotype, environment, and the rhizosphere microbiome, yet most studies examine these components in isolation. We applied the Genotype × Environment × Rhizosphere Microbiomes (GERMs) framework to test how host–microbe coordination contributes to heat tolerance in cereal crops Zea mays and Sorghum bicolor. We analyzed maize and sorghum grown under optimal and heat-stressed conditions across contrasting soil treatments using integrated plant–microbial metatranscriptomics. Host and microbial gene expression profiles were jointly analyzed alongside microbiome composition and plant phenotypes and compared with amplicon-based profiling. Metatranscriptomics captured microbial community structure comparable to amplicon sequencing while providing enhanced functional and taxonomic resolution. Host genotype and temperature jointly shaped microbial functional profiles. Conserved plant orthologs across maize and sorghum were linked to microbial pathways, specifically microbial d-amino acid metabolism was associated with plant heat tolerance. These findings indicate the rhizosphere microbiome actively participates in plant heat stress responses through coordinated transcriptional interactions with the host. Integrating host and microbial transcriptomes reveals mechanistic insights into plant adaptation and establishes a framework for dissecting plant–microbiome interactions under environmental stress.

Making fish oils in plants: from alpha to omega

Johnathan A. Napier — Tue, 26 May 2026 22:11:30 -0700

Schematic representation of the biosynthetic pathway for the synthesis of omega-3 long-chain polyunsaturated fatty acids. The sequential transgene-encoded activities required to convert endogenous fatty acids to the longer chain polyunsaturated forms of eicosapentaenoic acid and docosahexaenoic acid are shown in red. The metabolic bottleneck (‘substrate dichotomy’) arising from the different substrate preferences of desaturases and elongases is also represented. Transgene-encoded activities are predominantly sourced from marine microalgae but also from oomycetes and bryophytes.

Summary

The transgenic accumulation of omega-3 long-chain polyunsaturated fatty acids represents one of the most complex assemblies of heterologous sequences in a plant host. Through the combined efforts of multiple research teams from public and private sectors, GM crops synthesising these important fatty acids have progressed from the initial proof-of-principle stage to fully regulated and approved products. That this has taken over 25 years should not be surprising, but equally, there are several aspects of the sophisticated metabolic engineering which remain unresolved. The aim of this short review is to shine a light on some of the less familiar aspects of these efforts and to maybe prompt renewed consideration of the associated issues. In particular, the oft-ignored topic of transgene silencing in plant biotechnology is considered, as is the potential of multicistronic polyprotein fusions to reduce construct complexity and sequence repetition. Collectively, it is hoped that focussing on these important but neglected topics will inspire a new wave of research activity, underpinning a further shift to a fully sustainable bioeconomy.

ERF transcription factor StPti5 is a regulator of endophyte community maintenance in potato

Sun, 24 May 2026 22:35:17 -0700

Summary

We have recently identified an ethylene response factor, StPti5, as a susceptibility factor that negatively regulates immune responses to diverse pathogens. Here, we investigated the role of StPti5 in the processes involved in the colonization of potato with beneficial organisms. RNA-seq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and a complex transcriptional network was triggered, with ethylene signaling being a central module and StPti5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains. While StPti5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in shoots of StPti5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the StPti5-silenced plants. To decipher the mechanistic basis of StPti5 function, we performed a DAP-seq experiment and showed that StRIN13, a regulator of plant immune signaling, is a direct target of StPti5. StPti5 is involved both in suppressing defense against harmful and limiting colonization by beneficial microbes. Such a mechanistic understanding of plant–microbe interaction paves the way for sustainable crop management.

Polyphenol oxidase depletion in Nicotiana benthamiana enhances recombinant protein purification and preserves native protein integrity

Sun, 24 May 2026 21:25:56 -0700

Polyphenol oxidases (PPOs) depletion preserves endogenous proteins at their predicted molecular weights and enhances detectable enzymatic activities. (a) Less RbcL crosslinking in ppo mutant of Nicotiana benthamiana. Leaf extracts were incubated for 1 h, separated on protein gels, stained with Coomassie or analyzed by Western blot with the anti-RbcL antibody on n = 3 replicates.

Summary

Agroinfiltration of Nicotiana benthamiana is widely used for recombinant protein production in plant science and molecular pharming, but enzymatic browning and native protein crosslinking during extraction may limit protein integrity and purification efficiency. We generated genome-edited N. benthamiana lines lacking two polyphenol oxidases (PPOs) and analyzed protein integrity, enzymatic activity profiles, and recombinant protein purification under non-denaturing extraction conditions. PPO-deficient plants showed reduced browning and native protein crosslinking, preserved endogenous proteins at their predicted molecular weights, displayed increased detectable enzyme activities, and achieved a significantly higher recovery and improved purity of a transiently expressed recombinant protein. These findings identify PPO-mediated oxidation as a major bottleneck during protein extraction and demonstrate that PPO depletion enhances recombinant protein purification while preserving native protein integrity.

概括

在本氏烟草中进行农杆菌瞬时侵染是植物科学和分子医药农业中广泛使用的重组蛋白生产方法，但提取过程中发生的酶促褐变和内源蛋白交联可能会限制蛋白的完整性和纯化效率。我们构建了敲除两个多酚氧化酶基因的本氏烟草株系，并在非变性提取条件下分析了蛋白质完整性、酶活性谱以及重组蛋白的纯化情况。 PPO缺失突变体表现出褐化和内源蛋白交联程度的降低，内源蛋白在其预测分子量处得到保留，并且检测到更高的酶活性，此外在瞬时表达重组蛋白时实现了显著更高的回收率和更优的纯度。这些结果表明，PPO介导的氧化是蛋白质提取过程中的一个主要瓶颈，同时表明去除PPO可以在保持内源蛋白完整性的同时，提高重组蛋白的纯化效果。

In situ submitochondrial mapping in living plants via Hessian Structured Illumination Microscopy

Hailian Hu, Huiting Chen, Haohong Gan, Zhihang Feng, Baohai Li — Fri, 22 May 2026 20:52:50 -0700

In situ sub-mitochondrial compartments illumination in living Arabidopsis roots via HIS-SIM.

OsWRKY18 attenuates proteasomal degradation of OsbZIP48 to orchestrate zinc homeostasis in rice

Fri, 22 May 2026 20:47:32 -0700

OsWRKY18–OsbZIP48 regulatory module in rice Zn homeostasis.

Summary

Zinc (Zn) is an essential micronutrient for plants, and its deficiency in soils severely limits crop yield and grain nutritional quality. While the F-bZIP transcription factor OsbZIP48 is known to play a central role in maintaining Zn homeostasis in rice, the post-translational mechanisms that regulate its activity remain elusive. Here, we identify the WRKY transcription factor OsWRKY18 as a key post-translational regulator of OsbZIP48. Through a combination of molecular, genetic, biochemical, and physiological approaches, we characterized the function of OsWRKY18 and its role in modulating the OsbZIP48 protein stability to regulate Zn homeostasis. We show that OsWRKY18 expression is specifically induced under Zn-limiting conditions. Loss-of-function mutants (oswrky18) exhibited heightened sensitivity to Zn deficiency and a significant reduction in Zn accumulation in the shoots. Mechanistically, OsWRKY18 directly interacts with OsbZIP48. This physical interaction protects OsbZIP48 from proteasome-mediated degradation, thereby enhancing its protein stability. Consequently, OsWRKY18 potentiates the transcriptional activation of key Zn transporter genes, including OsZIP4 and OsZIP8, which are crucial for Zn translocation and distribution to developing tissues. Our findings reveal a novel regulatory module wherein OsWRKY18 stabilizes OsbZIP48 to orchestrate the expression of Zn transporters, providing significant insights into the post-translational regulatory mechanisms of micronutrient homeostasis in plants.

Invasive plants have stronger root recognition capabilities than native plants

Fri, 22 May 2026 20:46:07 -0700

Schematic diagram illustrating the design of the two experiments. The first experiment used a split-root design with the target plant positioned on the ridge between two adjacent pots and its roots initially equally distributed in the two pots. In each pot, a nylon mesh partition (position indicated in blue) was installed to divide each pot in half. In the pots with target and neighbor plants, this avoided root mixing. The second experiment involved conspecific pairs grown in pots containing a mixture of sterilized and preconditioned soils from the first experiment.

Summary

Root-mediated conspecific recognition and avoidance could alleviate intraspecific competition and promote interspecific competitive abilities. This could result in communities dominated by few species. However, it remains unclear whether invasive plants, which frequently become dominant, possess higher capabilities of root recognition and segregation than natives. We compared root-recognition and segregation capabilities between five congeneric pairs of invasive and native plants using a split-root assay and an intraspecific root-distribution experiment. We also assessed the roles of soil microbial legacies in root-segregation capabilities. The split-root assay showed that invasive plants exhibited stronger root-recognition capacities than natives by reducing root allocation toward conspecifics. The intraspecific root-distribution experiment showed that both invasives and natives exhibited root segregation when grown on unconditioned soils. However, when grown on soils conditioned by either invasive or native plants, root segregation of natives disappeared, whereas invasives remained unaffected. Changes in root segregation of natives were associated with changes in the composition of soil fungal and bacterial communities. Invasive plants possess mechanisms of avoiding intensive intraspecific competition irrespective of soil microbial legacies, whereas for native plants, these mechanisms can be disrupted by soil microbial legacies. This could contribute to the competitive superiority of invasive plants.

New biomolecular signatures of thermal stress in coral algal symbionts: a pathway to understanding coral resilience and adaptation

Katherina Petrou, Daniel Aagren Nielsen — Fri, 22 May 2026 05:05:50 -0700

New Phytologist, EarlyView.