Pangenomic evolutionary possibilities for Darwin’s abominable mystery

Telomere-to-telomere pangenomes reveal a previously undersampled layer of genome evolution that may help explain rapid plant diversification vis-à-vis Darwin’s abominable mystery.

dlvr.it

From fungal detection to crop disease intelligence

As developed by Shen et al., multiple fungal pathogen detection (MFPD) enables screening of partial and full-length ITS (Internal Transcribed Spacer) datasets for reported fungal pathogens. Linking pathogen detection with crop-context interpretation can help plant science move beyond community profiling towards decision support for biovigilance, disease phenotyping, and resistance breeding.

dlvr.it

Women in plant science around the world

The article series ‘Women in plant science around the world’ marks the 30th anniversary of Trends in Plant Science, a milestone that invites us to reflect on three decades of shared discoveries, international collaborations, and the diverse voices that propel the field forward. By centring 30 of our women authors from 30 countries, we honour the global community that continues to advance plant science, and we hope to inspire the next generation of women researchers, as well as researchers from other still under-represented groups in plant science.

dlvr.it

Have we entered a ‘post-model’ era in plant biology?

Models such as arabidopsis (Arabidopsis thaliana) have underpinned genomic and physiological research in plant science. Advances in genome sequencing, pangenomics, and genome editing have prompted claims of a ‘post-model’ era, with model–crops and crops such as rice and bread wheat combining agricultural relevance with experimental tractability. We argue that the ‘simplicity-to-complexity’ approach remains valid, although model systems have evolved. Arabidopsis remains indispensable for interpreting multi-omics data, testing developmental hypotheses, and generating mechanistic insights difficult to obtain in crops. Linking these strengths to model–crops adds translational value by bridging discovery and breeding, while niche models such as Brachypodium distachyon and legumes address grass cell wall biology and nitrogen fixation. Future progress depends on diverse species with complementary strengths across fundamental and applied plant biology.

dlvr.it

Advances of N6-methyladenosine RNA methylation in tree species

N6-methyladenosine (m6A) is a pivotal post-transcriptional regulator in plants, but most mechanistic studies derive from arabidopsis (Arabidopsis thaliana) and annual crops. While core m6A machinery is conserved in plants, emerging studies in poplar, bamboo, and other tree species suggest that m6A modulates lignification and stress adaptation, likely reflecting perennial traits including long life cycle, secondary growth, seasonal developmental transitions. The major challenge of m6A research in trees is the shift from global m6A profiling to site-specific causal mechanism. New approaches like targets of RNA-binding proteins identified by editing, direct RNA sequencing, and dCas13-based programmable RNA epigenetic editors provide a practical resolution. In summary, this review extends m6A regulation from model plants to trees and highlights m6A’s potential for improving tree traits.

dlvr.it

Chloroplast sunscreen wardrobe: condensates meet protective plant metabolism

Sunlight is indispensable for photosynthesis but becomes hazardous when photon input exceeds the capacity of the photosynthetic machinery. A recent study by Shao and colleagues identifies protein condensates as a novel means of phytoprotection.

dlvr.it

From feasibility to predictability: prime editing redefines precision breeding in plants

Originally developed in mammalian systems as a genome editing strategy without double-strand breaks, prime editing (PE) has been adapted for precise genome modifications. However, its deployment revealed key limitations, including reduced efficiency, strong locus dependency, low germline transmission, and somatic chimerism. Consequently, diverse PE variants have emerged, resulting in fragmented landscape of architectures with context-dependent and inconsistent performance. This review consolidates these advances and outlines emerging design principles behind plant PE systems. It evaluates optimization strategies at multiple levels, discusses their applications in monocots and eudicots, and highlights persistent bottlenecks and future directions, including AI-guided protein engineering and improved delivery strategies. These advances position PE as a rapidly evolving platform toward enabling precision breeding in plants.

dlvr.it

Calcium in agriculture and crop production

Calcium (Ca2+) is an essential mineral for plants, functioning both as a nano- to micromolar signaling ion in gene regulation and, at millimolar levels, in nutrition—supporting structural integrity and enzyme activation. These functions depend on adequate fertilization. However, Ca2+ problems stem mainly from hydraulic access and local availability within specific tissues and compartments rather than bulk supply; thus, deficiency can occur even in Ca2+-rich soils due to soil immobilization and physiological constraints. Because Ca2+ is poorly phloem-mobile and moves mainly via transpiration-driven xylem flow, its distribution is uneven. By binding to cell walls, calcium also enhances plant stability and fruit firmness. Here we review deficiency symptoms, management strategies, developmental roles, soil interactions, detoxification, and recent fertilizer approaches.

dlvr.it

ISDH-seq for functional characterization of plant open chromatin

Open chromatin plays vital roles in various biological processes by fine-tuning gene transcription. Currently, a plethora of high-throughput methodologies have been utilized to profile open chromatin sites (OCSs) genome-wide, including DNase I hypersensitivity sequencing (DNase-seq), MNase hypersensitivity sequencing (MH-seq), formaldehyde-assisted isolation of regulatory elements sequencing (FAIRE-seq), and assay for transposase accessible chromatin sequencing (ATAC-seq). However, each individual technique has its own pros and cons, thus, none of the aforementioned techniques can provide a complete overview of OCSs within the plant genome.

dlvr.it

Ancient polyploidization waves as evolutionary shields for angiosperms

Chen et al. identified 132 whole-genome duplications (WGDs) clustered around environmental crises. We highlight how, over longer evolutionary timescales, ancient WGDs convergently retained MADS-box, MYB, WRKY and HSF transcription factors, building stress-adaptation networks. These insights guide climate-resilient crop improvement through comparative genomics and CRISPR engineering.

dlvr.it

Immune activation drives citrus Huanglongbing

Citrus Huanglongbing (HLB), caused by the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas) and considered the most destructive citrus disease worldwide, has long been regarded as a typical bacterial infection. However, recent compelling evidence shows that CLas drives HLB through chronic effector-triggered immunity, not via direct pathogenicity, thereby redefining HLB as an immune-mediated disease (Huang et al.).

dlvr.it

Plant Phenomics—the unrecognized rise of a scientific discipline

Plant Phenomics studies the phenotypic dynamics that form plant phenotypes by systematically measuring traits using phenotyping methods from the quantum to the ecosystem levels. It has emerged as an interdisciplinary field advancing sensing, computation, and plant biology. However, Plant Phenomics has lacked a unifying framework that integrates its community’s core concepts from the formal and life sciences. Central to this framework is the definition of the phenome as a set of phenes that govern phenotypic dynamics across all spatial and temporal scales of biological and ecological organization and in interaction with the environment. This paradigm moves beyond gene-centric views and recognizes the equal importance of all spatial and temporal scales in forming plant phenotypes, advancing Plant Phenomics as a data-driven discipline and its emerging profession, the plant phenomicist.

dlvr.it

Ubiquitin signalling redefines nutrient trade-offs in crops

Changing nutrient availability is associated with growth trade-offs in crops. Recent studies in rice and maize reveal that such constraints can be uncoupled by modifying ubiquitin-dependent proteostatic systems that integrate nutrient and stress signalling pathways. This challenges the inevitability of trade-offs and highlights new strategies for breeding nutrient-efficient, stress-resilient crops.

dlvr.it

Emerging regulatory roles of small metabolites in plant development and adaptation

Once viewed mainly as metabolic intermediates, small metabolites are increasingly recognized as spatially and temporally regulated signals that coordinate plant development and adaptation. Understanding these metabolite-based regulatory processes could reveal new strategies to improve crop resilience, productivity, and sustainability under changing environmental conditions.

dlvr.it

Decoupling developmental and physiological adaptations: a strategy to unleash nutrient use efficiency in plants?

Plants respond to spatially and temporally variable soil nutrients through root architectural plasticity, regulation of uptake and assimilation per root unit, and plant–soil–microbiome interactions. Although often viewed as complementary, these responses can also behave as compensatory strategies. Under non-optimal nutrient distributions, plants may invest either in greater root proliferation or in higher uptake capacity per root unit. We propose that this development–transport relationship should be understood as an optimization problem, rather than an additive response. Comparable morphology–physiology trade-offs occur in other resource-acquiring organs, including the gut and the lungs. Tuning or partially uncoupling these constraints could redefine crop ideotypes as dynamic combinations of root architecture, physiological elasticity, and controlled rhizosphere outsourcing, opening new routes to improve nutritional efficiencies.

dlvr.it

Decoding dialog: the auxin–calcium signaling crosstalk in plants

Auxin and calcium (Ca2+) are central plant signals that coordinate growth, development, and responses to environmental cues. Typically studied as largely parallel pathways, they are now increasingly recognized as interconnected networks whose activities converge at multiple regulatory levels. Recent advances in live imaging, biosensors, optogenetics, and structural approaches have revealed that auxin can rapidly trigger Ca2+ influx from the apoplast via TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB)-dependent signaling mechanisms and Ca2+ channels, presumably involving cyclic nucleotides produced by TIR1/AFB auxin receptors. Conversely, Ca2+ signals arising from mechanosensing, wounding, and environmental stress can modulate auxin transport, signaling, and transcriptional outputs. Together, these discoveries highlight a dynamic, reciprocal signaling axis where Ca2+ acts both downstream and upstream of auxin to shape growth, development, tropisms, and regeneration.

dlvr.it

Painting new pathways: Castilleja enters the genomic era

Castilleja (Orobanchaceae), commonly known as Indian paintbrush, is a genus of approximately 200 hemiparasitic species found primarily across the Americas. Long studied for its taxonomic complexity, vibrant floral displays, and ecological interactions with host plants, Castilleja has recently emerged as a versatile research system spanning parasitic biology, specialized metabolism, conservation genetics, and pharmacology. The availability of whole-genome sequencing is transforming the field, revealing expanded gene families involved in host recognition, enabling genomic species delimitation of cryptic taxa, and providing frameworks for mapping biosynthetic pathways of bioactive compounds, including iridoid glycosides and phenylethanoid glycosides. This review synthesizes advances across these disciplines and highlights how genomics serves as an integrative force connecting taxonomy, ecology, phytochemistry, and parasitic biology in this genus.

dlvr.it

Hydroactive stomata: a key innovation underpinning angiosperm ecological dominance

Angiosperms rose to ecological dominance through innovations that enhanced photosynthetic capacity and water-use efficiency. We propose that a pivotal, yet underappreciated, contributor was the hydroactive stomatal mechanism, an abscisic acid-mediated, metabolically driven control of guard-cell turgor. Unlike passive hydraulic responses to changes in water status, hydroactive regulation enables rapid, multisignal integration and minute-scale adjustment of stomatal aperture, synchronising carbon gain with hydraulic safety under fluctuating light, CO2, and evaporative demand. We argue that this water-status control module complemented other stomatal signalling pathways responsive to light, CO2, and metabolism, improving physiological coordination in dynamic environments. This perspective reframes stomata as decision-making nodes linking leaf anatomical evolution, physiological plasticity, and angiosperm diversification and offers a foundation for engineering climate-resilient crops under climate change.

dlvr.it

A new sustainability paradigm beyond the organic brand

Producing enough food to feed the world in an environmentally sustainable way represents a major challenge for humanity. It requires a bold paradigm that maximises options for the future. In contrast, organic farming has serious limitations, as it is based on an oversimplified assumption that natural substances are safe and artificial substances are unsafe. This approach severely constrains options for using synthetic inputs or new breeding techniques (NBTs) because they are perceived as ‘unnatural’. In this opinion article, we encourage a more objective evaluation of the contribution of synthetic inputs and NBTs to sustainability. We argue that crop production per se is not a natural situation and that it is important to keep options open for the future.

dlvr.it

Hydrogen sulfide as a potential translational hub for crop salinity tolerance

Hydrogen sulfide (H2S) is widely implicated in plants’ adaptive responses to salinity, regulating processes ranging from ionic homeostasis to antioxidant defense and is often described as a central signaling hub due to its interaction with core signaling pathways, such as Ca2+, reactive oxygen species, nitric oxide, and phytohormones. However, most evidence remains correlative and relies heavily on pharmacological interventions. This review critically examines the mechanistic gaps, causality, and specificity of H2S-mediated signaling in regulating salinity adaptive responses in plants. We argue that moving from phenomenological observations to causal mechanisms requires a strategic shift towards advanced genetic tools, in vivo dynamic imaging, synthetic biology, and systems-level interrogation. Addressing these challenges is essential to harness the translational potential of H2S signaling for improving crop resilience in saline environments.

dlvr.it

Arbuscular mycorrhizal fungi orchestrate belowground microbiomes in plant holobionts

The traditional model of plant–arbuscular mycorrhizal (AM) fungal coevolution, based solely on interactions between plants and AM fungi, became obsolete with the discovery of the critical roles that belowground microbiomes play in the function of mycorrhizal symbiosis. Based on insights into hyphosphere microbiota, we expand the plant–AM fungus–bacterium continuum into a multipartite AM fungal-orchestrated holobiont (H-AMF) framework, where AM fungi integrate plant roots with soil microbiota into a cross-kingdom ecological unit. A division of labor exists among plants, AM fungi, and hyphosphere microbes in the mycocentric H-AMF perspective. We summarize mechanisms by which AM fungi sustain cooperative relationships with plants and hyphosphere microbiota and propose holobiont-scale methodologies to advance understanding of plant–fungal–microbial interactions and their ecological functions.

dlvr.it

Satellite fluorescence: seeing drought before plants turn brown

Solar-induced chlorophyll fluorescence (SIF) is a valuable proxy for ecosystem photosynthesis but is influenced by structural effects. Tang et al. show that normalizing SIF by absorbed photosynthetically active radiation reveals early drought-induced physiological declines before visible canopy changes, improving ecosystem drought monitoring.

dlvr.it

AI-designed crop populations for sustainable intensification

Meeting food-security targets within environmental limits requires integrating genetic advances with data-driven design and adaptive management of crop populations as engineered systems. Herein, we propose a framework for AI-designed crop populations, in which AI-enabled approaches coordinate above- and belowground architecture with management to improve productivity, resource-use efficiency, and climate resilience. AI can act as an architect by coupling phenomics with process-based crop models to optimize multiobjective population designs and identify locally tailored configurations. It can also act as a regulator by integrating sensing, model-based prediction, and environmental feedback to guide in-season adaptation under climate variability. By linking trait innovation with population-level interactions and adaptive regulation, this framework offers a potentially transferable route for shifting the yield-efficiency frontier for sustainable intensification.

dlvr.it

Emerging roles of biomolecular condensation in plant membrane biology

Plants require dynamic mechanisms of cellular organization to continuously adapt to fluctuating environmental conditions. Biomolecular condensation, which refers to nonstoichiometric assembly of macromolecules into membraneless compartments via phase separation, emerges as an essential regulatory strategy for plant development and stress responses. Unlike membrane-bound organelles, condensates can dynamically assemble/disassemble in response to different environmental cues. Increasing evidence indicates that versatile plant condensates associate with cellular membranes to regulate processes such as signal transduction, intracellular trafficking, organelle biogenesis, and gene expression. In this review, we summarize recent progress on representative condensates in association with the plant endomembrane system. We also highlight methodological advances, from multiscale in vivo characterization to in vitro reconstitution, which enable quantitative dissection of membrane–condensate interactions, with an emphasis on the biophysical principles governing them.

dlvr.it

Women in plant science around the world

The article series ‘Women in plant science around the world’ marks the 30th anniversary of Trends in Plant Science, a milestone that invites us to reflect on three decades of shared discoveries, international collaborations, and the diverse voices that propel the field forward. By centring 30 of our women authors from 30 countries, we honour the global community that continues to advance plant science, and we hope to inspire the next generation of women researchers, as well as researchers from other still underrepresented groups in plant science.

dlvr.it

Plant–cyanobacterial symbioses: mutualism with emerging translational possibilities

Engineering rhizobial–plant nitrogen fixation in crops is a major goal in plant synthetic biology. We propose expanding efforts to plant–cyanobacterial symbioses as an alternative path. Targeting the earliest step of this partnership—likely conserved across its independent evolutionary origins—may offer a comparatively simple and promising strategy for enabling nitrogen-fixing crops.

dlvr.it

Nitric oxide–melatonin crosstalk as a stress-state-dependent signaling module in plants

Nitric oxide (NO) and melatonin (MT) are ubiquitous plant stress signals, yet their interplay is often reduced to simple antioxidant additivity or fixed synergy. In this review, we synthesize current evidence into an evidence-supported working framework in which NO–MT crosstalk functions as a reversible, stress-state-dependent signaling module governed by NO set-point control, redox-encoded post-translational modifications, and phase-, tissue-, and network-gated feedback. We distinguish three operational states: feed-forward activation, buffering restraint, and network integration. We further define minimum diagnostic criteria for state assignment, including NO kinetics, blockability, turnover/denitrosation capacity, and target-selective S-nitrosation. This framework clarifies when NO–MT coupling is causal, when it is buffered, and when it is redirected by broader reactive oxygen species/calcium/hormone/hydrogen sulfide.

dlvr.it

Supramolecular agriculture: host–guest chemistry for controlled plant signaling

Modern agriculture depends extensively on chemical inputs to optimize global food production. Supramolecular host–guest chemistry allows precise regulation of the delivery, stability, and spatiotemporal release of signaling molecules, thereby enabling crop improvement. Consequently, supramolecular agriculture has the potential to transform agrochemicals into targeted and efficient tools for sustainable farming.

dlvr.it