DNA barcode reference libraries provide useful tools for specimen identification, highlighting potential new species and detecting introduced ones. Here, we present a comprehensive DNA barcode library for European ants and, in order to tackle the Linnean, Wallacean and Darwinian shortfalls of this group, we provide an updated checklist, distribution data, mitochondrial genetic diversity maps and mitochondrial gene trees. The European ant fauna is here established to include 55 genera and 650 species (587 of which are native), including one species newly recorded for Europe and novel citations for 26 species from 11 countries. Our genetic dataset includes 6530 georeferenced COI sequences (62.1% de novo) for 506 species (77.8%) across all genera. On average, 12.9 sequences were obtained per species, and 209 species were sequenced for the first time. We generated intra- and interspecific genetic distance estimates, 52 genus-level trees, mitochondrial genetic diversity and specimen maps for 384 species, as well as haplotype networks for 289 species, available in the Atlas V1.0 'The Mitochondrial Genetic Diversity Maps of European Ants'. We estimate that 56.3% of European ants are monophyletic with respect to the COI gene and can be unambiguously identified by DNA barcoding, though performance varies widely among genera. We observed moderate levels of barcode sharing (19.3%) and of barcode gap presence (47.6%), as well as high levels of intraspecific divergences (up to 17.9%). These findings likely reflect both biological and operational factors and highlight the existence of potential cryptic taxa and the need for taxonomic revisions. The framework presented here aims to facilitate future research, species discovery and conservation of European ants.
The names published by Linnaeus in Species Plantarum represent the foundation of modern plant taxonomy. Despite their systematic value, very few of Linnaeus's original type specimens have been analyzed using current DNA sequencing technologies. Here, we performed high-throughput sequencing on Linnean and other type specimens of Ulva, a genus of ecological and commercial importance. Chloroplast and mitochondrial genomes were assembled for Linnaeus's U. compressa, U. intestinalis, U. lanceolata, and U. linza as well as Kützing's Phycoseris smaragdina type specimens. Phylogenetic analyses of these data showed that the names U. compressa and U. intestinalis were correctly applied, but U. linza and U. lanceolata were misapplied. Ulva linza is the earliest available name for the European species currently called U. pseudocurvata. The correct name for the globally distributed species previously known as U. "linza" is Ulva smaragdina (Kützing) comb. nov. The names Ulva lanceolata, U. crispata, and Phycoseris olivacea do not represent distinct species, instead being heterotypic synonyms of U. compressa, and P. planifolia is a heterotypic synonym of U. intestinalis. These results demonstrate that genetic characterization of type material can unequivocally resolve longstanding taxonomic debates over scientific names.
Research Highlight: Colares, L. F., Peres, C. A., Dambros, C. S. (2026). Life history induces markedly divergent insect responses to habitat loss. Journal of Animal Ecology. https://doi.org/10.1111/1365-2656.70117. Habitat loss is driving biodiversity collapse worldwide. Although this phenomenon has been extensively studied across many taxa and regions, we still lack information about whether species with distinct life histories respond differently to habitat loss. This challenge is particularly critical for tropical insects, where knowledge gaps remain large due to the Linnean (taxonomy) and Raunkiæran (traits) shortfalls. In this issue, Colares et al. (2025) address these gaps by using 236 sticky traps across the world's largest man-made tropical forest archipelago in the Central Amazon (~360,000 ha), generating a dataset of ~23,000 individual insects. They combined these surveys of insect fauna with computer vision models to assess how habitat loss affects both α- and β-diversity in insects with contrasting life histories (terrestrial vs. aquatic). The study reveals that responses diverge strongly depending on whether taxa rely on terrestrial or aquatic environments during their ontogeny. Whereas low forest amount reduced the number of terrestrial species, it increased species with aquatic life histories. Importantly, the authors also linked insect responses to body size (a proxy for dispersal ability), suggesting that larger insects, which disperse more successfully across the water matrix, may be favoured as 'winner' species in fragmented habitats. The findings of Colares et al. (2025) have broad implications for animal ecology and insect conservation. First, they highlight that insect declines in response to habitat loss are largely driven by traits that confer high or low resilience to reductions in forest cover. Second, they underscore the potential of computer vision as a powerful tool for uncovering key information about insect populations, thereby facilitating applied research such as rapid biodiversity surveys and long-term monitoring.
Accurate species-level classification of prokaryotic 16S rRNA sequences remains difficult: existing tools rely on exact alignment, k-mer heuristics, or phylogenetic placement and are limited by incomplete reference databases. Deep learning approaches in microbial genomics have focused largely on whole-genome metagenomics, leaving 16S taxonomy under-supported. We present DeepTaxa, a hybrid CNN-BERT framework that pairs a multiscale CNN with a transformer trained from scratch on the DNABERT-2 BPE vocabulary, producing parallel rank-specific predictions across the seven Linnean ranks. On the Greengenes2 2024.09 test set, DeepTaxa achieves species-level accuracy of 92.96% and F1 of 0.9212 (3-seed mean; cross-seed standard deviation ≤ 0.0008 F1 at every rank), with F1 above 0.99 from domain through class and a species-level expected calibration error of 0.0242. DeepTaxa exceeds DADA2 (90.05%) and QIIME 2 (85.01%) at the species rank on the same held-out test set, with larger gains over the k-mer-based classifiers SINTAX and Kraken 2. Performance degrades smoothly with decreasing training-set similarity (species F1 from 0.95 to 0.45), and a dedicated V3-V4 amplicon checkpoint reaches 87.55% species accuracy from an approximately 420 bp window. Source code, trained checkpoints for full-length 16S and V3-V4 amplicons, curated datasets, and reproducible workflows are publicly available at github.com/systems-genomics-lab/deeptaxa and huggingface.co/systems-genomics-lab/deeptaxa.
One female specimen of the cetacean harbour porpoise Phocoena Phocoena (Linnaeus, 1758) was found dead on the North Sea coast of Denmark (Jutland) in May 2025. During necropsy severe pathological changes of the liver were observed (hepatic fibrosis, enlarged and thickened biliary duct walls) and when dissecting the biliary ducts six intact trematodes (total length 6.9-7.9 mm, width 1.9-2.0 mm) were recovered. Following conservation in formalin four parasites were haematoxylin stained, one specimen kept unstained but all five mounted for morphological analysis. The sixth specimen conserved in 70% ethanol was subjected to DNA purification and subsequent PCR and sequencing. All the parasites were identified as fully adult Campula oblonga (Cobbold, Trans Linnean Soc Lond 22(3):155-172, 1858). Morphometric, morphological and molecular data (NADH dehydrogenase, subunit 3 (ND3), mtDNA) are presented and indicate close relation with previous isolates from the North and Baltic Seas but a lower similarity to Pacific conspecifics.
BACKGROUND: Value-Based Healthcare (VBHC) emphasises delivering high-quality care measured by patient outcomes rather than the volume of services. Although mostly partially implemented in civilian health systems, VBHC integration within military health systems (MHS) lags behind. Given current geopolitical developments and the unique operational demands of military healthcare, this study aimed to assess the desirability and feasibility of implementing VBHC in the Dutch MHS. METHODS: A cross-sectional, descriptive survey was conducted in 2024 among active-duty personnel in the Netherlands Armed Forces. Stratified sampling targeted three stakeholder groups—care recipients, care providers, and care facilitators—followed by voluntary response recruitment. A self-administered online questionnaire assessed familiarity with VBHC, perceived desirability and feasibility of its implementation, and prioritised components for application. The survey was structured around case-based scenarios derived from the Linnean VBHC framework, adapted to the military context. Quantitative data were analysed using descriptive statistics and Likert-scale medians; open-ended responses were analysed thematically. RESULTS: Of 912 eligible participants, 290 completed the survey (32% response rate), comprised of 45% care recipients, 33% care providers, and 22% care facilitators. Most respondents (67%) had over 15 years of military service; 58% held higher education degrees. Familiarity with VBHC increased throughout the survey. Overall, 96% of respondents perceived VBHC as valuable for the Dutch MHS. Notably, 64% believed VBHC could benefit both regular and operational care. A collaborative implementation approach involving all three stakeholder groups was preferred by 82%. However, concerns were raised about feasibility in large-scale combat operations, highlighting the need to align VBHC components with military readiness and mission-critical objectives. CONCLUSION: This study provides initial evidence supporting broad acceptance of VBHC within the Dutch MHS, particularly for non-operational military healthcare contexts. While desirability was high, practical applicability raised concerns, especially regarding combat and operational care settings. These findings suggest the potential for VBHC integration, but emphasize the necessity for a military-specific adaptation. Future research should explore targeted implementation strategies that balance patient-centered outcomes with the unique operational demands of military healthcare environments.
Cuscuta species, parasitic plants with minimal photosynthetic capacity, rely on light cues to locate hosts and initiate infection. Unlike nonparasitic plants, they exhibit a reversed shade response, growing towards low red:far-red (R:FR) light typical of dense vegetation. We investigated how R and FR light modulate haustorium development, gene expression, and epigenetic reprogramming in Cuscuta campestris. FR-enriched conditions promoted coiling and haustorium initiation, while red light suppressed parasitic behaviour. Phytochromes B1 and B2 displayed opposing transcriptional responses to light quality, suggesting a modified light perception mechanism. Transcriptome analyses revealed further that FR light triggered the differential expression of over 5000 genes, including those linked to auxin and cytokinin signalling, cell wall remodelling, and organogenesis. Gene co-expression networks identified phytochrome B2 and a Fhy1/Fhl regulator of phytochrome A as possible central hubs associated with chromatin remodellers, histone modifiers, and RNA-directed DNA methylation components. Small RNA profiling indicated stable global sRNA populations across treatments, with shifts in the expression of specific miRNA families, affecting a subset of light-responsive genes. Our findings demonstrate that FR light perception in C. campestris engages both transcriptional and epigenetic regulation to drive haustorium development, reflecting adaptations in light signalling cascades that underpin its parasitic lifestyle.
The fungal pathogen Magnaporthe oryzae poses a major threat to the global production of cereals such as rice, wheat, and millets. Similar to other fungal pathogens, it secretes effector proteins to manipulate host immune responses, enabling successful colonization and infection. In this study, M. oryzae strains were collected from diseased finger millet plants and wild grasses in Uganda. A candidate effector gene-Mo2928Fm-was identified from a highly virulent finger millet strain and found to be strongly induced at 2 days postinoculation, suggesting a role in the early infection process. In silico analysis indicated that Mo2928Fm is present only in a subset of M. oryzae genomes and encodes a protein with two domains connected by a serine-rich linker. Confocal microscopy confirmed its nuclear localization in host cells, and gene deletion significantly reduced fungal virulence. Transient expression of Mo2928Fm suppressed the transcription of key plant immune response genes. Further analyses also revealed a potential interaction between Mo2928Fm and the plant mitogen-activated protein kinase 3 (MAPK3) protein. Based on these findings, we propose that the Mo2928Fm-MAPK3 complex interferes with basal plant immune signaling and promotes susceptibility to blast disease. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Small interfering RNAs (siRNAs) play a crucial role in plant reproduction, yet their mobility and function remain incompletely understood. We report that a large proportion of siRNAs found in pollen of Capsella rubella relies on mobile siRNAs from maternal sporophytic tissues, highlighting the importance of non-cell-autonomous siRNAs in male gametophyte development. Unlike tapetal siRNAs, which guide DNA methylation and require CLASSY3 and DNA-dependent RNA polymerase IV (Pol IV) activity in the tapetum, we found that Pol IV-dependent mobile siRNAs (PMsiRNAs) mainly function post-transcriptionally and do not guide DNA methylation. Nevertheless, PMsiRNAs share key features with tapetal siRNAs, including Pol IV dependency, clustering and a size range of 21-24 nucleotides. Using a grafting approach, we show that sporophytic Pol IV-dependent siRNAs act as non-cell-autonomous mobile signals that trigger PMsiRNA formation through post-transcriptional gene silencing. This process parallels reproductive phased siRNA biogenesis, which is widespread across angiosperms but has been considered absent in Brassicaceae. Loss of PMsiRNAs causes pollen arrest, underscoring their essential role. Together, these findings highlight siRNAs as long-distance communication signals from maternal sporophytic tissues to the male gametophyte with critical functions in developmental regulation.
BACKGROUND: Conserving genetic diversity is crucial for effective germplasm use and crop improvement. Developing core collections with minimal redundancy and maximum diversity requires a clear understanding of population structure. However, the nationwide population structure of moso bamboo (Phyllostachys edulis) remains poorly characterized, creating a major gap for developing representative, non-redundant core collections. RESULTS: Using whole-genome resequencing data from 432 moso bamboo accessions covering a broad geographic range across the distribution of the species in China, we investigated the population genetic structure and diversity patterns. Principal component analysis and phylogenetic tree analyses identified three distinct genetic clusters together with a hybrid group. To identify the optimal strategy for core collection development, we evaluated two stratification schemes, seven sampling strategies, and five sampling intensities. Across 70 candidate cores, stratified sampling combined with expected heterozygosity optimization at 20% intensity (S-HE20) maximized genetic diversity (He = 0.3665; PIC = 0.2904; I = 0.5302) and captured broad phenotypic variation (CR = 82.32%; MD = 0%), yielding an 84-accession core spanning 15 geographic regions. CONCLUSIONS: This study revealed the population genetic structure of moso bamboo and identified the S-HE20 strategy as optimal for core collection construction. The resulting core collection offers a representative and genetically diverse resource for future gene discovery and molecular breeding efforts in moso bamboo.
Chromatin organization and histone modifications play essential roles in regulating gene expression during development. DEK is a conserved chromatin-associated protein implicated in DNA topology and transcriptional regulation, yet its in vivo function in plants has remained elusive. To uncover DEK function, we used Arabidopsis thaliana dek mutants and performed genome-wide analyses of histone modifications. Genetic and physical interactions with Polycomb Repressive Complex 2 (PRC2)-associated proteins were examined, and transcriptome comparisons were conducted among single and multiple mutants. Loss of DEK function led to a genome-wide increase in the PRC2-mediated histone modification H3K27me3. DEK genetically and physically interacts with the PRC2-associated protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), and DEK deficiency partially restores H3K27me3 levels in the lhp1 mutant. The dek multiple mutant exhibited enhanced H3K27me3 at PRC2 target genes and ectopic accumulation at pericentromeric interstitial telomeric repeats - similar to histone H1 mutants - suggesting altered chromatin accessibility. Combined dek and lhp1 mutations intensified developmental defects and disrupted expression of many PRC2 target genes, including MADS-box transcription factors. Transcriptome analyses revealed that DEK and chromatin remodeler alpha thalassemia/mental retardation syndrome X-linked chromatin remodeler have opposing effects on gene expression. Our findings uncover DEK as a novel regulator of H3K27me3 homeostasis and chromatin structure, critical for coordinated plant development.
Biomolecular condensates organize cellular processes through liquid-liquid phase separation, creating membrane-less compartments enriched in specific proteins and RNAs. Understanding their RNA composition is essential for elucidating plant stress responses, yet capturing these transiently associated RNAs remains technically challenging. We present Turbo-RIP (TurboID-based proximity labeling with RNA immunopurification), a comprehensive protocol for identifying condensate-associated RNAs in plants. Turbo-RIP employs the biotin ligase TurboID to label proximal proteins at 22 °C, followed by formaldehyde crosslinking and streptavidin-based capture of protein-RNA complexes. We provide detailed procedures for three cloning strategies, transformation of Nicotiana benthamiana and Arabidopsis thaliana, validation of TurboID activity, and RNA recovery. The protocol successfully captured processing body-associated RNAs with minimal background. Turbo-RIP enables systematic mapping of RNA populations within plant condensates under diverse conditions. The protocol requires 3-5 days from sample preparation to RNA isolation, with construct validation taking 2-4 weeks. All procedures use standard laboratory equipment, making Turbo-RIP accessible for plant molecular biology laboratories. Key features • Apply TurboID-based proximity labeling specifically for RNA capture in plant condensates. • Optimize experimental conditions for different plant species and condensate types. • Implement quality control measures and data analysis pipelines.
Here, we present a protocol for generating and selecting stable transgenic tomato lines through Agrobacterium tumefaciens-mediated transformation of cotyledon and hypocotyl explants. We describe steps for sterilizing and planting tomato seeds, cotyledon and hypocotyl excision and preculture, Agrobacterium tumefaciens preparation and co-cultivation with explants, and recovering explants and bacterial overgrowth restriction. We then detail procedures for selecting green calli; regenerating explant excision and growth in non-selective media; plant hardening, potting, and growing; and T-DNA insertion confirmation by PCR. For complete details on the use and execution of this protocol, please refer to Mountourakis et al.1,2,3.
Biomolecular condensates are membrane-less assemblies that selectively concentrate proteins, RNAs, and metabolites to integrate developmental and environmental cues. The remarkable diversity of plant condensates reflects the constraints of sessile organisms that must coordinate postembryonic organ development with continuous environmental adaptation. We review how plants employ condensates to integrate temperature, light, redox, and nutrient signals. We provide physicochemical foundations, including phase diagram behavior, critical solution temperature properties, and sticker-and-spacer models, as a framework for interpreting how environmental stimuli are transduced into condensate assembly/disassembly. We organize each biological system through a unified scaffold-client-RNA-metabolite framework, distinguishing experimentally validated conclusions from open mechanistic questions. Applying this framework across nuclear, cytoplasmic, chloroplastic, and membrane-associated condensates, we evaluate how temperature shifts, redox changes, post-translational modifications, and metabolite fluctuations drive reversible phase transitions. We highlight how saturation concentration thresholds function as nonlinear filters buffering environmental noise, how membrane-associated phase separation may nucleate cytoplasmic condensates, and where current evidence remains insufficient to distinguish bona fide liquid-liquid phase separation from alternative assembly mechanisms. By grounding plant condensate biology in physicochemical principles and comparative evidential analysis, we identify both well-supported mechanisms and critical gaps that must be addressed to translate condensate-biology into strategies for crop-resilience.
Very low-intensity selective logging can be a compromise between strict conservation and income-generating land use in tropical forests. Investigating how selective logging influences the understory environment and seedling dynamics as the forest regenerates offers insights into whether logging alters forest dynamics, influencing the composition and structure of future forests. We explored how very low-intensity logging (<2 trees ha-1) influences understory factors and seedling dynamics across a logging chronosequence (unlogged forest vs. actively logged forest and forest logged 4 and 14 years prior). To do this, we assessed (1) how canopy openness, prevalence of vegetation damage, and elephant trails differ in logged forests at different recovery stages compared to unlogged forest; (2) how these understory factors influence seedling dynamics; (3) how seedling dynamics differ across the logging chronosequence; and (4) how logging impacts liana vs. tree seedlings across the chronosequence. We observed greater canopy openness and vegetation damage in logged forests up to 4 years after logging and higher elephant trail prevalence 14 years after logging compared to unlogged forests. Seedling survival was lower in plots with higher canopy openness, more vegetation damage, and on elephant trails, while growth and recruitment were not affected by these variables. Actively logged forests initially had lower seedling survival and recruitment, but higher growth rates compared to unlogged forests. However, 14 years after logging, seedling dynamics were mostly similar to unlogged forests. Liana seedlings had a slight growth advantage over tree seedlings in all logged forests compared to unlogged forests. Results from our study suggest that very low-intensity selective logging causes temporary shifts in understory dynamics rather than long-term shifts in forest recovery trajectories. These managed areas have potential as land that can contribute to OECM targets-functioning as mixed-use corridors, connecting protected areas across a landscape and contributing to biodiversity and wildlife conservation-especially in countries with high forest cover and low deforestation.
Plants continuously emit volatile organic compounds (VOCs), which can influence the physiology and behavior of neighboring plants. While the ecological role of stress-induced VOCs is well established, the function of constitutive VOCs released by undamaged plants in mediating plant-plant interactions remains less understood. Here, we demonstrate that barley plants can detect the growth rate of undamaged conspecific neighbors through constitutive VOCs and respond by modulating their growth-defense trade-off accordingly. Exposure to volatiles from cultivars with contrasting growth (slow or fast) triggered distinct shifts in biomass accumulation and gene expression in receiver plants, whereas VOCs from cultivars with similar growth rates had negligible effects. Transcriptomic analysis revealed cultivar-specific transcriptional reprogramming of growth- and defense-related pathways, suggesting that constitutive VOCs convey information about emitter identity and competitive vigour that receiver plants use to adaptively reallocate resources and prime stress responses in anticipation of competition. These findings uncover a previously unrecognized role of constitutive VOCs as reliable cues of emitter identity and vigor, mediating adaptive responses in neighboring plants under competitive scenarios.
Organisms frequently encounter abiotic stresses such as drought, salinity, and extreme temperatures, requiring sophisticated adaptive mechanisms. Stress memory enables them to respond more efficiently to repeated environmental challenges by retaining information from prior exposures. Biomolecular condensates, dynamic, membraneless cellular assemblies formed by liquid-liquid phase separation, have emerged as crucial regulators of post-transcriptional gene expression, particularly in stress conditions. These condensates modulate RNA fate and translational repression by selectively storing and organizing key molecules in ways that may contribute to cellular memory mechanisms. Here, we explore the biophysical principles underpinning condensate formation and dynamics, with a focus on processing bodies (PBs) as potential cellular memory storage systems. We propose a framework for how PBs might integrate biochemical and biophysical signals to encode, maintain, and retrieve stress-responsive information, and discuss the evidence supporting their role in coordinated stress responses and adaptive resilience in plants.
Autophagy is a conserved intracellular catabolic process, critical for plant stress tolerance. Upon their delivery in the vacuole, how autophagic bodies containing cargo are hydrolyzed to warrant autophagy degradation remains unclear in multicellular organisms. Here, we found that two Arabidopsis phospholipases, LCAT4 and LCAT3, traffic to the vacuolar lumen and converge on autophagic bodies through fundamentally different routes. While LCAT4 directly binds ATG8 and uses autophagy as a transport system to reach the vacuole prepackaged within autophagosomes, LCAT3 traffics to the lytic compartment independently of autophagosome formation. Knocking out both genes causes an accumulation of autophagic bodies accompanied with a reduction in autophagy degradation. In vivo reconstitution demonstrated that LCAT3 can hydrolyse the membrane of autophagic bodies, enabling the activity of LCAT4 to enhance this process. Together, this work sheds light on the vacuolar stages of autophagy, showing that plants have evolved a multi-component pathway for the efficient disruption of autophagosomal membranes as a critical step for the completion of the autophagy pathway.
Grindelia mutabilis (Asteraceae, Astereae), a new species from Brazil endemic to the Espinal Ecoregion of the Río de La Plata Grasslands Bioregion and Pampa Province of the Chaco Biogeographical Domain, is proposed and illustrated. The new species is characterized by a combination of traits: small, rosette cespitose habit, linear to linear-oblanceolate leaves, light-yellow to pastel salmon ray florets, three-winged ray floret cypselae bearing a pappus of two to four elements and two-winged disc floret cypselae bearing a pappus of two elements. It has a highly restricted habitat and is known exclusively within Parque Estadual do Espinilho in Rio Grande do Sul, Brazil. Preliminary conservation assessments classify the new species as Critically Endangered. We provide illustrations and photographs, as well as a distribution map with an identification key for the South American Grindelia species with winged cypselae. The intriguing morphology of this species combines characters traditionally regarded as diagnostic for Notopappus, a genus segregated from Haplopappus and Grindelia. Previously published phylogenetic studies of related taxa indicate that the recognition of Notopappus as monophyletic is not supported and render Grindelia as non-monophyletic too. Based on this combined morphological evidence and existing phylogenetic hypotheses, we reaffirm the non-monophyly of Notopappus and formally propose its synonymization under Grindelia s.l.
Drought stress severely limits the growth of perennial trees. Xylem structure is central to water conduction; however, lignin monomer composition driving xylem remodeling for drought adaptation remains enigmatic. By integrating multi-omics analyses, genotype-environment association analysis, and metabolite-based genome-wide association studies, we identified PtoCPK3 as a key gene associated with precipitation-related traits and the aridity index in Populus tomentosa. This variation in association was linked to coniferyl alcohol and ferulic acid, two metabolites related to guaiacyl (G)-lignin monomer biosynthesis. Overexpressing PtoCPK3 enhanced drought tolerance in transgenic poplar by promoting xylem remodeling associated with a decreased lignin S/G ratio. Mechanistically, drought-induced Ca2+ signaling activates PtoCPK3 to phosphorylate PtoERF72 at Ser96, enhancing its activation of PtoWOX13b and direct repression of PtoUGT72AZ2. Synergistic repression of PtoUGT72AZ2 by PtoWOX13b reduces glycosylation of G-monomer precursors, favoring ferulic acid and coniferyl alcohol accumulation. Furthermore, natural variants in PtoCPK3 and PtoERF72 drive geographic divergence, with the PtoCPK3II_PtoERF72CC genotype conferring superior drought resilience via elevated phosphorylation efficiency. This module links drought signaling to xylem remodeling, providing genetic targets for breeding drought-resilient trees.