Areca palm velarivirus 1 (APV1) is the causative agent of yellow leaf disease (YLD), leading to severe yield losses in areca palms. However, how APV1 counteracts host immunity remains largely underexplored, and the underlying mechanisms are still poorly understood. RNA silencing is an evolutionarily conserved antiviral defense mechanism in eukaryotes. In this study, we identify the APV1-encoded capsid protein (CP) as a viral suppressor of RNA silencing (VSR) that inhibits both local and systemic silencing triggered by single-stranded RNA (ssRNA). Mechanistically, CP interacts with host Suppressor of Gene Silencing 3 (AcSGS3), a key component of the RNA silencing pathway, and promotes its degradation via autophagy. Additionally, CP disrupts the SGS3–AcRDR6 (RNA-dependent RNA polymerase 6) interaction, impairing the RNAi signaling cascade. Our findings reveal a novel dual mechanism to counteract host RNA silencing in which APV1 CP disrupts the SGS3–AcRDR6 complex and exploits the autophagic pathway to degrade AcSGS3, thereby undermining host antiviral defenses.
Starch is a principal storage component in plants, significantly influencing the yield and quality traits of major crops. Climate change, particularly drought and high temperatures, severely affects starch biosynthesis in crops, leading to reduced starch yield and quality. The composition and properties of native starch, such as its low amylose content, substantially affect its nutritional value and industrial applications. To tackle these issues, genes coding for starch synthetic enzymes or those involved in the regulation of starch biosynthesis could be targeted for site-directed mutation to improve starch traits in crops. The application of gene editing technology in crops, notably CRISPR/Cas9, has facilitated the precise manipulation of starch biosynthesis. This review summarizes current knowledge on the biosynthesis and regulation of starch and the influence of climate change on these processes. It highlights advancements in modifying starch biosynthesis in food crops using CRISPR/Cas9. We discuss the strategy of improving starch traits and stress tolerance in response to climate change challenges and propose future directions for research on starch modification in food crops. Developing climate resilient crops capable of stable starch production is crucial for ensuring food security in the face of a changing global climate and an increasing world population.
As the global warming intensifies, along with increased planting density and straw retention practices, stalk rot (SR) has become one of major diseases that negatively impacts crop yield and quality. The distribution of SR pathogens, encompassing both fungal and bacterial agents, is significantly influenced by climate and agricultural factors. Although significant researches have been conducted on identifying fungal SR in different crop plants, there remains a lack of comprehensive reviews focused on the genetic and molecular mechanisms that contribute to crop resistance against fungal and bacterial SR. This review provides a comprehensive comparison of the pathogenic mechanisms associated with fungal and bacterial SR. It emphasized recently cloned genes and molecular regulations linked to resistance against SR, highlighted the pivotal role of several smart strategies in advancing gene discovery and functional research. Furthermore, it summarized the potential molecular regulatory pathways involved in SR resistance. Ultimately, the article presents insights into several critical areas that warrant further investigation in the study of SR-resistant mechanisms and crop breeding.
Cold stress is a major environmental challenge limiting the survival and productivity of tropical aquaculture species such as Nile tilapia (Oreochromis niloticus). The brain and gill represent two key organs that orchestrate systemic and environmental responses: the brain serves as the central thermosensory integrator and neuroendocrine control center, while the gill serves as the primary interface for respiration, ion regulation, and immune defense. However, the molecular mechanisms underlying their tissue-specific and potentially coordinated responses to cold remain unclear. Here, we applied integrative ATAC-seq and RNA-seq analyses to systematically investigate chromatin accessibility and gene expression dynamics in tilapia brain and gill tissues under cold stress. We identified thousands of differentially expressed genes and accessible regions, with significant correlations between transcriptional changes. Transcription factor footprinting revealed that Fra1 and Nrf act as key tissue-specific regulators, governing immune, apoptotic, and metabolic reprogramming in the brain and gill, respectively. Notably, the Fra1 module in the brain activated signaling pathways associated with stress response, neurodevelopment, and metabolic regulation which may influence peripheral responses by coordinating systemic physiological adjustments under cold stress, while Nrf-mediated regulation in the gill supported local homeostasis through redox and transport-related mechanisms. These findings highlight the hierarchical and organ-specific transcriptional control underlying cold adaptation in ectotherms. Our study provides the first chromatin accessibility atlas of cold-responsive regulatory networks across central and peripheral organs in fish, offering mechanistic insight and molecular targets for breeding cold-tolerant aquaculture strains.
The domestication and selective breeding of horses have profoundly influenced the emergence of adaptive traits and stress resistance mechanisms, shaping modern equine populations. This comprehensive review examines the genomic foundations of these traits, emphasizing recent advancements in high-throughput sequencing technologies and bioinformatics. These tools have elucidated the genetic underpinnings of key characteristics such as endurance, speed, metabolic efficiency, and disease resistance. Importantly, the review identifies and connects gene variants associated with thermoregulation, immune function, and cellular repair mechanisms, shedding light on their synergistic roles in enabling horses to adapt to diverse environmental challenges and physiological stressors. By establishing these causal links, this review enhances the coherence between genomic findings and their implications for equine biology. Furthermore, the integration of genomic insights provides a framework for addressing contemporary challenges in horse management and conservation. Issues such as climate change, disease outbreaks, and the preservation of genetic diversity demand innovative strategies grounded in genomics. By bridging the findings on equine adaptation and stress resistance mechanisms with practical applications in breeding and management, this review highlights the potential of genomics to ensure the sustainability and resilience of equine populations in the face of evolving environmental and societal pressures. This expanded perspective underscores the critical role of genomics in both understanding the evolutionary trajectory of horses and guiding future practices in equine health and conservation.
Cryptocaryon irritans is an obligate parasitic ciliate that significantly endangers marine fish. Hypoxia suppresses the development and hatchability of C. irritans during the tomont stage, which often develops on the seafloor under hypoxic conditions. Despite this knowledge, the underlying adaptation mechanisms of tomonts remain poorly understood. We aimed to determine how hypoxia reprograms tomont metabolism and whether ferroptosis contributes to hypoxia-induced vulnerability. Herein, metabolomic profiling revealed 2,964 differential metabolites under hypoxia. Notably, there were significantly elevated glucose levels, suggesting enhanced glycolytic activity. Enzymatic and qRT-PCR analyses further confirmed hypoxia-induced metabolic reprogramming, including increased hexokinase and pyruvate kinase activities and upregulation of glycolysis-related genes. Hypoxia also induced surface depressions, disrupted cell walls, mitochondrial deformation, reduced mitochondrial membrane potential, disrupted energy homeostasis, and increased NAD⁺/NADH ratio fluctuations and lactate accumulation. To probe ferroptotic susceptibility under hypoxia, hypoxic tomonts were exposed to the ferroptosis inducer erastin, resulting in a hatchability of 13% and promoting reactive oxygen species (ROS) accumulation, lipid peroxidation, and mitochondrial damage. Fluorescence staining revealed strong PI and ROS signals in hypoxic tomonts exposed to the ferroptosis inducer erastin. Notably, mitochondrial dysfunction was accompanied by Ca2⁺ and Fe2⁺ accumulation. Ferroptosis-related genes were upregulated at 24 h post-hypoxia induction. In contrast, gpx4 and mitochondrial electron transport chain components were downregulated at 48 h post-hypoxia induction. These findings demonstrate that hypoxia triggers glycolytic reprogramming and mitochondrial dysfunction in C. irritans, whereas erastin induces ferroptosis under hypoxic stress. This study provides new insights into protozoan hypoxia adaptation and highlights ferroptosis as a potential therapeutic target for controlling parasitic infections in marine aquaculture.
Advanced genotyping technologies for understanding the genetic intricacies of fungal pathogens have broad applications in crop protection. Here, we introduce a novel genotyping-by-target sequencing (GBTS) chip, a versatile tool designed for comprehensive genetic analysis of fungal populations. This technology overcomes key limitations of traditional molecular marker-based approaches by providing a more efficient, economic, and streamlined solution while bypassing the need for labor-intensive pathogen culturing. We demonstrate its utility by applying it to profile Pucciniastriiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust. Our analysis involved 225 infected leaves collected from wheat fields in the northwest oversummering region for Pst in China. We delineated three genetic groups and revealed frequent gene flow, with closer connectivity between Qinghai and Gansu than either province with Ningxia, a pattern consistent with wind trajectory models. These findings illustrate a highly connected regional epidemic system and highlight the value of the GBTS chip for genomic epidemiology. The methodology established here provides a scalable framework for population genetic studies in other fungal pathogens, promising to enhance disease monitoring and management across agricultural systems.
Leaf shape plays a crucial role in plant growth and development. Among various leaf traits, marginal lobation serves as an ideal morphological marker for breeding programs. However, the genetic mechanism underlying leaf margin lobation in Brassica juncea L. remains unclear. Through RNA sequencing and map-based cloning, we identified an incompletely dominant gene, BjA10.LL, which encodes an HD-ZIP I protein and is responsible for the formation of leaf margin lobation in B. juncea. Sequence analysis of parental alleles revealed no critical variations in the coding region but identified substantial variations in regulatory regions. Heterologous expression of BjA10.LL in Arabidopsis thaliana confirmed its sufficiency to induce lobed leaves. To functionally link the regulatory variations to the phenotype, we analyzed promoter activity and developed a co-dominant molecular marker targeting key indels in a core enhancer. The promoter activity was significantly affected by these sequence variations, and the marker exhibited perfect co-segregation with the lobed-leaf phenotype in an F₂ population, collectively establishing these regulatory polymorphisms as the causal basis for divergent BjA10.LL expression and leaf morphology. These results demonstrate that BjA10.LL positively regulates marginal lobe formation, providing insights into leaf shape regulation in B. juncea and facilitating the genetic improvement of rapeseed.
Plant viruses are among the most significant biotic stressors, posing a severe threat to crop productivity and global food security. Their success largely depends on the exploitation of host eukaryotic translation factors (eTFs), including initiation factors (eIFs) and elongation factors (eEFs), which act as molecular gatekeepers of the viral life cycle. Key members such as eIF4E, eIF(iso)4E, eIF4G, eEF1A, and eEF1B have been identified as susceptibility factors that mediate viral translation, replication, and systemic movement. Viruses have co-evolved specialized proteins and RNA elements, including VPg and IRES structures, to hijack these host factors and circumvent plant defense barriers. This review synthesizes current understanding of the mechanistic roles of eTFs in virus–host dynamics and highlights strategies to mitigate viral stress. Approaches such as natural allele mining, induced mutagenesis, TILLING/EcoTILLING, RNA interference, and precise genome editing with CRISPR/Cas systems are explored as practical tools for reducing susceptibility. Targeted manipulation of eTFs offers a promising avenue to reprogram plants for resistance while maintaining essential cellular functions. By integrating molecular biology with applied strategies, we propose an eTF-centered framework for resistance breeding within a broader stress biology perspective. Future research combining functional genomics, synthetic biology, and breeding innovation will be pivotal in delivering broad-spectrum, durable, and environmentally sustainable resistance to plant viral stress.
Indole-3-acetic acid (IAA) is a major naturally occurring auxin that shows extensive accumulation in cereal plants during the first few days of infection by the phytopathogen Fusarium graminearum. Apart from its positive effects on plant growth, empirical studies have suggested that it is a virulence factor that alters the host’s nutritional level and fine-tunes the plant’s immune responses, especially salicylic acid-mediated defenses. Plant and fungus genomic studies have predicted that their genomes carry the required genes for L-tryptophan-dependent IAA biosynthetic pathways. In recent decades, genetic and genomic studies have facilitated the description of L-tryptophan (L-TRP)-dependent IAA biosynthetic pathways in F. graminearum and its host plants. The present review illustrates and summarizes the putative and preference molecular networks related to extensive IAA accumulation in wheat heads triggered by infection with F. graminearum, based on the available knowledge about the endogenous IAA biosynthetic pathways in F. graminearum and wheat plants. Meanwhile, infection by F. graminearum could preferentially trigger L-TRP’s conversion into serotonin and even phytomelatonin via tryptamine in wheat heads as well. Lower concentrations of them have been shown to stimulate IAA accumulation or mimic IAA to promote plant growth. However, upon that hardly provides sufficient information for regarding alternative methods of controlling scab epidemics. In combination with dissecting IAA biosynthetic pathways using genetic approaches exhibits many difficulties, we thus highlight that ongoing efforts should focus more on identifying the fungal effectors involved in extensive IAA accumulation in cereals in order to understand their potential roles in wheat–F. graminearum interactions. Advancements in molecular breeding programs will further accelerate the application of these molecular targets, allowing for the development of more scab-resistant wheat cultivars and resulting in the effective and environmentally friendly suppression of scab epidemics.
Sphingolipids are not only essential structural components of cellular membranes but also key signaling molecules that regulate plant growth, development, and stress responses. However, their specific roles in root development remain largely unknown. In the presented study, we demonstrate that overexpression of the GhGCS1 gene significantly enhances lateral root development in cotton. Integrated comprehensive transcriptome analysis and phytohormone quantification revealed that GhGCS1 promotes lateral root initiation and elongation primarily by suppressing cytokinin biosynthesis. Notably, GhGCS1 overexpression also markedly improved cotton resistance to Verticillium dahliae. Further molecular analyses indicated that GhGCS1 enhances cotton verticillium wilt resistance through modulation of the expression of sphingolipid-associated brassinosteroid- and pathogenesis-related genes. Collectively, these findings reveal a dual regulatory role for GhGCS1 in coordinating root architecture and immune responses in cotton, providing novel insights and potential strategies for developing crop varieties with improved yield potential and stress tolerance.
Quinoa (Chenopodium quinoa Willd.), a semi-domesticated halophyte originating in the Andean region, has emerged as a promising crop for exploiting marginal lands, valued for its exceptional nutritional profile and remarkable resilience to high salinity and drought. This review analyzes the current status and future potential of quinoa as a model halophytic crop. We begin by examining the physiological mechanisms that enable quinoa to thrive in marginal environments, which have been the subject of extensive study. Thanks to the advancement in high-throughput sequencing technology, genomic resources – including the recent development of high-quality reference genomes and a Chenopodium pangenome – are rapidly expanding. Sequence-based genetic mapping techniques hold the promise to dissect the molecular basis of complex traits in combination with the utility of functional genomics tools such as virus-induced gene silencing (VIGS) and stable genetic transformation. Ultimately, the application of modern breeding technologies, such as phenomics, genomic selection (GS), and CRISPR/Cas, will expedite the development of locally adapted, climate-resilient quinoa cultivars worldwide.
Verticillium wilt, caused by the soilborne fungus Verticillium dahliae, has resulted in high mortality of Cotinus coggygria (smoke tree) in China. Symptoms of this disease are complex, many infected smoke trees exhibit wilting or dieback on some branches but no other branches. Whether other microbial taxa act synergistically to contribute to symptom development is unknown. Here, we investigated the microbial community assembly features associated with different branches of smoke trees with or without Verticillium wilt symptoms and established linkages between symptomatic branches and putative keystone taxa. Amplicon data analyses revealed that V. dahliae significantly affected the microbiota structure within tree branches. Microbial network connectivity indicated that Verticillium wilt destabilized the network, and fungal communities were more sensitive to Verticillium wilt than the bacterial communities. Based on taxonomic level information, the fungus Botryosphaeria dothidea was significantly enriched in diseased branches and positively correlated with the abundance of V. dahliae. Through microbial isolations, pathogen co-inoculations, histopathological assays, and RNA-seq analyses, the results indicated that plants infected with V. dahliae showed significantly increased susceptibility to B. dothidea and downregulated expression of defense-related genes. Overall, the results revealed that Verticillium wilt provokes changes in the structure of the smoke tree microbiome and that these changes likely influence symptom development in some but not all tree branches. The synergistic interplay between the commensal fungus B. dothidea and the soil-borne fungus V. dahliae promotes wilt progression in smoke trees, offering new insights into developing effective control strategies through fungicides plus enhancing host vigor.
Fusarium graminearum, the causal agent of Fusarium head blight (FHB), poses a major threat to global food security by contaminating cereals with the mycotoxin deoxynivalenol (DON). Although transcriptional and protein-level regulation of its stress response and virulence has been extensively studied, the functional significance of mRNA processing in these critical processes remains largely unexplored. Here, we identify Lsm8, a highly conserved core subunit of the nuclear Lsm2-8 complex, as a pivotal regulator linking RNA splicing fidelity to fungal growth, stress adaptation, and virulence. Deletion of LSM8 disrupted Lsm2-8 assembly and nuclear localization, resulting in widespread intron retention in genes essential for stress signaling (HOG1, ATF1), development (GPA1, STE12), and trichothecene biosynthesis. Consequently, osmoadaptation was impaired, sexual reproduction was abolished, and both DON production and virulence were drastically reduced. We further demonstrate that intron-retained transcripts are predominantly degraded by the RNA exosome, revealing a conserved Lsm8–exosome module that maintains splicing fidelity and RNA surveillance. Given the deep evolutionary conservation of Lsm8 across eukaryotes, these findings uncover a fundamental post-transcriptional regulatory layer governing fungal stress response, virulence, and mycotoxin biosynthesis, and highlight RNA-processing factors as universal determinants of virulence and promising antifungal targets across eukaryotic pathogens.
The allotetraploid crop quinoa (Chenopodium quinoa) accumulates red/violet betacyanins, which function as vital stress-mitigating antioxidants. We investigated the genetic basis of red/green variegation observed in the aerial organs of the P0429 accession. We demonstrated that this color mosaic is primarily localized to epidermal bladder cells (EBCs), with red EBCs accumulating betacyanin levels~50-fold higher than colorless EBCs. Cell-type-specific RNA-sequencing of EBCs identified the cytochrome P450 gene Cqu0091301 (CYP76ADα) as the dominant and rate-limiting factor, exhibiting strong upregulation in red EBCs. This high pigmentation requires a specific structural variation in the P0429 accession: a~4-kb genomic insertion that restores the full functionality of Cqu0091301, which is otherwise truncated and non-functional in common reference genomes. Genomic analysis reveals that Cqu0091301 is part of a multicopy CYP76ADα–DODA gene cluster. Notably, expression analysis revealed functional divergence between the quinoa subgenomes, with B-subgenome CYP76ADα genes highly dominant in EBCs, while A-subgenome homologs were preferentially expressed in other tissues. Our results establish a clear link between structural genomic variation and cell-type-specific betalain biosynthesis, providing molecular insight into pigment regulation and subgenome specialization in allotetraploid quinoa.
Hydrogen sulfide (H2S) is a key gaseous signaling molecule involved in plant growth and stress responses, yet its role in wheat resistance to stripe rust remains poorly understood. Here, we show that exogenous H2S enhances resistance of wheat (Triticum aestivum L.) to Puccinia striiformis f. sp. tritici (Pst), the causative agent of stripe rust. Comparative persulfidation proteomics identified the autophagy-related protein TaATG6c as a Pst-responsive H₂S target. Site-specific mass spectrometry and a modified biotin-switch assay demonstrated that Cys177 and Cys180 of TaATG6c undergo H₂S-induced persulfidation. Structural modeling based on AlphaFold predicted that these two site mutations reduced the binding activity of ATG6c to ATG14. Functional characterization using virus-induced gene silencing (VIGS) revealed that TaATG6 positively regulates wheat immunity against Pst, as silencing TaATG6 promoted fungal growth. Moreover, TaATG6 expression was markedly induced during Pst infection. Notably, the resistance-promoting effect of NaHS was compromised in TaATG6-silenced plants. Conversely, transient overexpression of TaATG6 enhanced wheat resistance to stripe rust, whereas mutation of Cys177 and Cys180 attenuated this effect. Endogenous biotin-switch assays further showed that TaATG6c persulfidation exhibits pathogen-responsive and dynamic characteristics, which were abolished in the TaATG6C177A/C180A mutant. Consistently, H₂S treatment and Pst infection stimulated the accumulation of lipidated ATG8 (ATG8–PE), indicating activation of autophagy, while this response was largely abolished in TaATG6-silenced plants. Together, these results suggest that H₂S promotes autophagy initiation through persulfidation of TaATG6c, thereby enhancing wheat resistance to stripe rust and highlighting a redox-regulated mechanism underlying plant stress adaptation.
The plant cell wall provides structural support and serves as a barrier against pathogen invasion. Rice grassy stunt virus (RGSV) infection suppresses genes involved in cell wall biosynthesis, but the underlying mechanism remains unclear. To further investigate this phenomenon, we generated transgenic rice lines overexpressing the RGSV-encoded p2 protein. These transgenic lines exhibited a brittle phenotype with reduced plant height, thinner sclerenchyma cell walls, decreased cellulose and increased lignin contents. Biochemical and microscopic analyses confirmed that mechanical strength of the cell wall was significantly weakened in p2-expressing plants. Notably, immunoblotting and in situ hybridization revealed partial localization of p2 to the cell wall, suggesting potential structural association. Transcriptome analysis revealed that p2 expression significantly altered the expression of genes involved in cell wall organization, hormone signaling, and pathogen interactions, suggesting a mechanistic basis for the observed phenotypes. Additionally, p2 transgenic lines exhibited increased susceptibility to multiple viruses, but unexpectedly showed enhanced resistance to the brown planthopper (BPH, Nilaparvata lugens), a major phloem-feeding pest. These findings reveal that a single viral protein can remodel the cell wall to influence both pathogen susceptibility and insect resistance, highlighting the broader ecological impacts of virus-induced cell wall remodeling in plants.
Natural rubber is a crucial industrial raw material globally, with wide applications in industries such as automotive and healthcare. Application of ethylene promotes latex production in the Hevea rubber tree (Hevea brasiliensis). However, its potential protein-regulation mechanism remains unclear. To elucidate the role of ethylene in latex production, we employed high-resolution proteomics and phosphoproteomics to determine the global changes in protein abundance and phosphorylation during ethylene-stimulated latex production. Using latex samples collected from ethephon-treated rubber tree, we identified more than 3,700 quantifiable proteins and 2,000 phosphorylated proteins with over 6,000 phosphorylation sites. Proteins involved in the mitogen-activated protein kinase (MAPK) cascade, metabolic pathways, and vesicular trafficking, like rubber elongation factors (REFs), small rubber particle proteins (SRPPs), and 14–3-3 proteins, exhibit pronounced robust phosphorylation dynamics upon ethephon application. Interestingly, the serine/threonine–proline (S/T-P) motif, which could be recognized by MAPKs, was highly enriched in REFs, 14–3-3, and ubiquitin-associated DENN (UDENN) domain-containing proteins, suggesting a potential role of MAPKs in ethylene-induced rubber biosynthesis. Consistently, the MAPKs show altered activation in ethephon-treated Hevea rubber trees, compared to water-treated controls. Additionally, activation of UDENN domain proteins implicated Ras-related Rab GTPases in membrane trafficking and rubber particle formation. These results provide comprehensive information on global changes in protein abundance and phosphorylation upon ethephon application in latex production, and may provide valuable clues for understanding the molecular basis of ethephon-regulated natural rubber biosynthesis in Hevea rubber trees.
Metal(loid) stress is one of the key constraints limiting plant growth and productivity, thus threatening agricultural yields and ecosystem health. This review elaborates on the mechanisms through which metal(loid) stress acts on plants, with a special focus on disturbances to key physiological and biochemical aspects. Drawing on global research findings, the review then systematically discusses the interactions between various metal(loid)s and plant components, clarifying the specifity of stress responses across different plant-metal(loid) systems. A central focus of this review is the application of nanoparticles (NPs) as a mitigation strategy to enhance plant growth and improve tolerance to metal(loid) stress. Specifically, it summarizes the multifaceted roles of NPs in this context: promoting plant growth and development, inducing the activity of antioxidant enzymes, and mitigating oxidative stress. This review confirms that metal(loid) stress can strongly inhibit plant growth and physiological functions, but such adverse effects can be significantly alleviated by NPs-based interventions ultimately facilitating the cultivation of more robust and healthy plants. These findings highlight the potential of NPs-mediated strategies as a practical and effective approach to counteract metal(loid) toxicity in plants, providing valuable insights for the development of sustainable agricultural system.
Tardigrades, known for their extraordinary resilience to extreme environmental conditions, employ specialized stress-response proteins to maintain cellular integrity under stress. These proteins, including SAHS, CAHS, MAHS, and Dsup, play critical roles in protecting cells from dehydration, radiation, and other environmental stressors. Previous work has characterized many of these proteins in Ramazzottius varieornatus, but the taxonomic breadth, copy-number variation, and structural diversity of these families across other tardigrade lineages remain poorly understood. The recent expansion of genomic resources for additional species motivated a comprehensive multi-species analysis to map ortholog diversity and structural features across tardigrade taxa. We investigated the genetic, structural, and evolutionary features of these stress-response proteins using an integrative bioinformatics approach, analyzing gene structure, orthologous clustering, molecular phylogeny, conserved motifs, and 3D protein structures across four tardigrade species—R. varieornatus, Hypsibius exemplaris, Paramacrobiotus metropolitanus, and H. henanensis. Our results reveal significant variation in predicted gene copy numbers and sequence conservation that reflect species-specific adaptations to environmental stress. Orthologous clustering showed shared evolutionary patterns across species, and conserved motifs were identified within the SAHS, CAHS, and MAHS families. Notably, we identified a new Dsup protein (H.Henanensis.Chr5.66), a potential ortholog in H. henanensis, thereby expanding the known diversity of Dsup proteins. The Dsup protein family exhibited notable sequence diversity across species, yet structural analyses revealed conserved α-helix regions and hydrophobicity patterns, suggesting a flexible conformation that aids DNA protection during extreme stress. Phylogenetic analyses revealed patterns consistent with parallel clustering patterns among stress-response proteins. This study advances our understanding of the molecular adaptations that underpin tardigrades' resilience and offers insights into potential applications for enhancing stress tolerance in other organisms.
Indole-3-acetic acid (IAA) accumulates in host plants following infection by Xanthomonas campestris pv. campestris (Xcc), the causal agent of cruciferous black rot. How exposure to IAA affects the invading Xcc remains unclear. Here, we demonstrate that either exogenous addition of IAA or endogenous production of IAA induced turnover of the quorum sensing (QS) signal diffusible signaling factor (DSF) in a RpfB-dependent manner. IAA addition prevented the cytoplasmic and culture pH decline. Transcriptomic analyses revealed four IAA-regulated gene clusters. Specifically, IAA induced the expression of trpB-A, enhancing tryptophan biosynthesis and intracellular IAA accumulation, and thereby establishing a self-reinforcing synthesis loop. IAA upregulated F0F1 ATP synthases and a resistance-nodulation-cell division (RND)-family efflux pump HepABCD to induce a pH-dependent DSF turnover. Moreover, IAA downregulated another RND family efflux pump IaepABCDE to induce a pH-independent DSF turnover. Finally, the IAA-regulated gene clusters were transcribed during the XC1 infection of cabbage. Collectively, these findings reveal a previously unrecognized role of IAA in modulating bacterial QS, underscoring the importance of IAA in the molecular dialogue between the pathogen and its host.
The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.
Dopamine (DA) is a catecholamine that plays a role in both animals and plants. Popularly known as a neurotransmitter hormone in animals involved in motor control and reward sensing, it also has a defense-related function in the plant kingdom. In plants, DA functions as a redox-active metabolite, a signalling regulator, and a metabolic modulator, rather than a classical neurotransmitter. Accumulating evidence demonstrates that DA enhances tolerance to diverse abiotic and biotic stresses, including drought, salinity, heavy metals, nutrient imbalance, temperature extremes, and pathogen attack, by stabilizing photosynthetic machinery, optimizing root architecture, improving water and nutrient use efficiency, and activating antioxidant and detoxification systems. Mechanistically, DA operates through coordinated regulation of reactive oxygen species (ROS) signalling, calcium-mediated secondary messenger cascades, transcription factor activation (WRKY, ERF, NAC), and reprogramming of nutrient and ion transporter networks. DA also exhibits extensive crosstalk with phytohormones, fine-tuning growth defence trade-offs in a species and stress-specific manner. Collectively, these findings position DA as a central signalling hub integrating redox balance, metabolic plasticity, and transcriptional control in plants. Understanding the conserved structure yet divergent biosynthesis and signalling logic of DA across kingdoms provides critical insights into its distinct modes of action and highlights its potential as a next-generation regulator for enhancing plant resilience under changing environmental conditions.