New Phytologist最新文献

Hybridization and polyploidy are major drivers of plant diversification, often accompanied by shifts in gene expression and genome composition. Small RNAs (smRNAs) are thought to influence such genomic changes, particularly through their interactions with transposable elements (TEs). We quantified smRNAs in established sibling allopolyploids Dactylorhiza majalis and D. traunsteineri and their diploid progenitors to assess how independent allopolyploidization events shaped smRNA landscapes. Despite independent origins, the allotetraploids exhibited substantial overlap in smRNA composition, including transgressive accumulation of smRNAs near genes related to transcriptional regulation, cell division, and stress response. Consistently, TE-associated 24 nt smRNAs more closely resembled the paternal and larger genome, while shorter smRNAs typically reflected the maternal and smaller genome. Nevertheless, distinct patterns were also evident: the older D. majalis showed greater accumulation of smRNAs near genes involved in transcriptional and translational regulation, while the younger D. traunsteineri displayed stronger non-additive patterns, suggesting ongoing resolution of post-polyploid meiotic and mitotic instability. Our results reveal both convergence and divergence in smRNA landscapes among independently formed allopolyploids. Our study highlights the central role of smRNAs in resolving genomic conflict, with possible implications for functional divergence and ecological innovation during polyploid evolution.

Plant diversity is known to enhance soil resource availability and productivity through niche partitioning and facilitation; however, existing studies have predominantly examined these effects at the community level. The role of tree neighborhood diversity in alleviating nutrient limitations remains unclear. Here, using a tree diversity experiment in a subtropical forest with naturally low phosphorus (P) availability and depleted soil base cations, we evaluated how neighborhood diversity helps alleviate nutrient co-limitation. We found that greater neighborhood phylogenetic and trait dissimilarities enhanced growth rates and increased foliar P and magnesium (Mg) concentrations, as well as resorption efficiency in focal trees. Foliar Mg exhibited a more pronounced response than P and calcium (Ca), suggesting that diverse communities may prioritize alleviating Mg limitation over other nutrient limitations. Elevated foliar Mg concentration in focal trees were positively correlated with foliar transpiration, both driven by greater neighborhood phylogenetic dissimilarity. Our findings demonstrate that neighborhood diversity is essential in mitigating nutrient limitations on tree growth, highlighting the importance of phylogenetic and functional trait dissimilarities in mediating these positive effects.

The sapwood area supporting a given leaf area (Huber value, v_H) reflects the coupling between carbon uptake and water transport and loss at a whole-plant level. Geographic variation in v_H presumably reflects plant strategic adaptations, but the lack of a general explanation for such variation hinders its representation in vegetation models and assessment of its impact on the global carbon and water cycles. Here we develop a simple hydraulic trait model to predict optimal v_H by matching stem water supply and leaf water loss, and test its performance against two extensive plant hydraulic datasets. We show that our eco-evolutionary optimality-based model explains nearly 60% of global v_H variation in response to light, vapour pressure deficit, temperature and sapwood conductivity. Enhanced hydraulic efficiency with warmer temperatures reduces the sapwood area required to support a given leaf area, whereas high irradiance (supporting increased photosynthetic capacity) and drier air increase it. This study thus provides a route to modelling variation in functional traits through the coordination of carbon uptake and water transport processes.

Argonaute2 (AGO2) largely participates in maintaining viral defenses. However, its function is not understood in species that are not commonly challenged by viruses in their native habitats. The ecological model species, Nicotiana attenuata, grows in arid/desert habitats. Natural virus infections are not commonly observed in this species even when the genes essential for viral defenses, like the RdRs, are silenced. The biological function of NaAGO2 has remained elusive. Silencing NaAGO2 with inverted-repeats (irAGO2) did not alter morphology, growth, or reproductive performance of unstressed plants compared to the wild-type (WT). irAGO2 was also able to defend against herbivores or pathogens and compete with con-species neighbors. However, irAGO2 had increased tolerance to water stress, exhibiting enhanced reproductive output during drought and recovery. Water-stressed irAGO2 accumulated significantly more abscisic acid (ABA) and proline, which are critical signaling and protective metabolites. Drought-responsive miRNA accumulation patterns were largely altered in irAGO2, potentially modulating ABA and proline gene expression during water stress and recovery. The function of three such Na-miRNAs (miR156, miR172, and miR398) was examined by transient overexpression in mitigating water stress and regulating ABA and proline pathways. We infer that AGO2 functions in fine-tuning ABA and proline homeostasis that optimizes N. attenuata's growth in complex stressful environments.

Rapid environmental change reshapes both abiotic stress and biotic interactions, yet it remains unclear how these combined forces structure plants' genomic adaptation. In particular, the joint influence of temperature and pollinator identity, two ecological axes undergoing simultaneous global shifts, has rarely been quantified at genomic resolution. We resequenced Brassica rapa L. plants after a six-generation evolution experiment, combining two temperature regimes (ambient vs hot) with three pollination treatments (bumblebee, butterfly, and mixed bumblebee-butterfly), and glasshouse control, to assess how these factors shape genomic responses. Using multiple complementary statistics (allele-frequency trajectories, F_ST outliers, Cochran-Mantel-Haenszel tests, and local score analyses), we found that adaptive genomic responses differed sharply among pollinators and temperatures: warming strengthened selection in community-level pollination, yielding the clearest signals in the hot-generalised treatment; bumblebee pollination showed strong but drift-obscured genomic change; and butterfly treatments exhibited minimal genomic response. Our findings demonstrate that pollinator identity and temperature interact nonadditively to produce distinct, highly context-dependent adaptive trajectories. This work highlights the importance of accounting for demographic variation and ecological complexity when predicting evolutionary responses to climate-driven shifts in species interactions.

High concentrations of manganese (Mn) ions in the soil of facility-based cultivation significantly restrict the development of the cucumber industry. However, the genetic mechanisms governing Mn accumulation in crops are still not well comprehended. Through the comprehensive integration of molecular biology, epigenetic modification analysis combined with genetic analysis, we functionally characterized a novel regulatory module. Consisting of a long non-coding RNA (lncRNA, asCsMTP6) and its mitochondria-localized target Metal Tolerance Protein 6 (MTP6), it coordinately regulates Mn accumulation in cucumber. CRISPR-CsMTP6 or asCsMTP6-OE mimics toxicity, whereas CsMTP6-OE or asCsMTP6 knockdown enhances tolerance, confirming that asCsMTP6 negatively regulates CsMTP6 transcription. Additionally, the H3K27me3 methylation marks surrounding the CsMTP6 genome are reduced under Mn stress, and the inhibited expression of asCsMTP6 results in a lower level of H3K27me3 methylation in the CsMTP6 gene body and 3'UTR region, thereby facilitating the expression of CsMTP6 for tolerance to Mn stress. Furthermore, virus-induced silencing of histone methyltransferases SWN and CLF also reduces H3K27me3 methylation in the CsMTP6 genomic region, thus releasing the expression of CsMTP6. Taken together, this study demonstrates the epigenetic regulation of lncRNAs in response to Mn stress, providing new insights into the potential for developing cucumber varieties with improved tolerance to manganese-contaminated soils.

Forest health is critical for sustaining ecosystem services like carbon sequestration. Heart rot, a widespread disease in upland northern hardwood forests, may affect greenhouse gas (CO₂ and CH₄) fluxes, but its impacts remain poorly measured. Using non-destructive tomography and direct gas flux measurements, we quantified the effects of heart rot on sugar maple (Acer saccharum Marshall) stems and surrounding soils. Heart rot increased CH₄ emissions from stems but did not affect CO₂ fluxes from stems or soils, nor CH₄ fluxes from soils. All stems emitted CO₂ and CH₄, while soils absorbed CH₄ and emitted CO₂. Stem CH₄ fluxes strongly correlated with decay severity, but CO₂ fluxes did not. CH₄ was produced in the heartwood, CO₂ in the sapwood, and methanogens were present in all stems. Severe heart rot often caused bark fractures, enhancing CH₄ diffusion to the atmosphere and creating emission hotspots. These findings show that forest health influences carbon cycling. Capturing stem CH₄ hotspots requires direct measurement, and fungal diseases like heart rot may shift forests from CH₄ sinks to sources, with implications for atmospheric greenhouse gas dynamics.

Land plants follow an evolutionary trajectory of 'gametophyte reduction' and 'sporophyte dominance'. As a major shift in gametophyte reduction, gymnosperms have evolved a unique female gametophyte (FG) development mode, associated with their prolonged reproductive cycles. However, the genetic programs underlying this process remain largely unknown. Here, we employed anatomical, transcriptomic, and genetic approaches to investigate the female gametogenesis, focusing on the divergent coenocytic free nuclear stage in three species (Cedrus deodara, Picea smithiana, and Pinus tabuliformis) from the largest gymnosperm family Pinaceae. We obtained a comprehensive anatomical profile of FG development, correlating variations in the timing of the free nuclear stage with the diverse reproductive cycles. We also revealed the transcriptional dynamics underlying each stereotypical stage of FG development, highlighting the involvement of cyclin-dependent kinase 2a, cyclin B genes, specific MADS-box genes, and other conserved homologous transcription factors. Moreover, a focused examination of the fascinating long reproductive cycle of Pinus, the largest genus of gymnosperms, further unveiled regulatory molecules for growth-defense trade-off and summer dormancy of FG. Our study highlights the molecular mechanisms underpinning heterochronic development of FG during the free nuclear stage in Pinaceae, offering crucial insights into the evolution of plant reproductive strategies.

Generation of competent offspring is vital for the prosperity of flowering plants. The pistil not only functions as a conduit for pollen tubes to grow to the ovary but also provides a selective venue for facilitating the growth of compatible pollen tubes and discouraging invaders and incompatible pollen. This review integrates recent advances in pollen-pistil interactions on dry stigmas of the Brassicaceae in the domains of self-incompatibility (SI) and cross-compatibility. We first outline the initial recognition mechanisms that distinguish self from nonself pollen and then highlight how key stigma responses are differentially regulated during compatible and incompatible responses, including calcium signaling, exocytosis, cytoskeleton dynamics, reactive oxygen species, aquaporin activity, and cell wall permeability. By linking these discrete cellular events to their physiological outcomes, we provide a unified framework for understanding how Brassicaceae stigmas precisely control fertilization. A deeper understanding of these mechanisms also informs new strategies for improving crop breeding in economically important Brassicaceae species, which widely use SI to produce F1 hybrid seeds.