Molecular Plant-microbe Interactions最新文献

The root-lesion nematode Pratylenchus vulnus parasitizes a wide range of hosts including woody perennials such as walnut (Juglans regia) and grapevine (Vitis vinifera), significantly damaging roots and reducing yields. Here, we present a high-quality, chromosome-level genome assembly of P. vulnus (61.7 Mb across six chromosomes). Comparative genomic analysis revealed high collinearity in protein-coding genes between P. vulnus and the root-knot nematode Meloidogyne graminicola, indicating a closer evolutionary relationship with this sedentary endoparasite. Large chromosomal regions in P. vulnus lack synteny with other nematode genomes, have comparatively low GC content (<30%), and are enriched in genes with unique or lineage-specific functions. Transcriptome analysis highlighted dynamic, stage-specific expressions of genes involved in parasitism, development, and metabolism. Additionally, we identified an extensive repertoire of putative effector genes and characterized lineage-specific expansions of cell wall-degrading enzyme families. Overall, these findings provide insight into the genome organization, chromosome evolution, and parasitism-related gene repertoire in a woody-plant parasitizing nematode.

Plant-parasitic nematodes (PPNs) are a serious threat to global food security, with estimated annual losses exceeding $173 billion. Beyond their direct damage, interactions between PPNs and other phytopathogens can lead to synergistic relationships, referred to as disease complexes, which result in more severe symptoms than either pathogen alone. Disease complexes have been documented across diverse PPN species with distinct lifestyles, including migratory ectoparasites, migratory endoparasites, and sedentary endoparasites, and have been shown to involve partners spanning viruses, bacteria, oomycetes, and fungi. In this review, we discuss specific aspects of PPN life cycles that may facilitate disease complex formation. Nematode-induced wounding may provide entry points or release exudate signals that promote secondary pathogen infection. Nutrient-rich feeding sites established by endoparasitic nematodes may support proliferation of secondary parasites. Furthermore, certain PPN families can vector pathogens such as viruses directly into the plant via their stylet or by carrying bacteria on the cuticle surface. Finally, PPNs can suppress or evade host immune responses, thereby increasing plant susceptibility to other microbial pathogens. Elucidating the molecular mechanisms underlying these interactions will improve our understanding of disease complexes associated with PPN infection and may inform the development of novel management strategies to mitigate their impact on agricultural systems. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2026.

Agroathelia rolfsii causes stem rot in multiple crops, survives as sclerotia in the absence of host plants, and remains a difficult-to-manage pathogen globally. Although Trichoderma species offer a sustainable biocontrol solution, their dual roles as antagonists and plant biostimulants present a complex trade-off under stress conditions that remains underexplored. This study analyzed the pathogen suppression and plant growth promotion induced by Trichoderma virens DM5 in the context of tomato protection against A. rolfsii. Using a combination of phenotypic assays and transcriptomic analyses, we observed that T. virens DM5 suppressed A. rolfsii via both mycoparasitism and antibiosis, producing antifungal compounds that inhibited pathogen growth. Simultaneously, it enhanced host vigor by increasing seed germination by 54.5% and plant survival rates by 70% under pathogen pressure. Molecular analyses revealed that plants treated with T. virens DM5 exhibited rapid early activation of defense-associated pathways, including MAPK signaling, MYB transcription factors, and amino sugar metabolism within 24 h post inoculation, followed by attenuation of prolonged defense responses. These responses reduced the need for prolonged immune activation, suggesting an energy-saving strategy, allowing the plant to allocate resources toward development and survival. These findings highlight the multifaceted role of T. virens DM5 in sustaining tomato growth and disease suppression under A. rolfsii-conducive conditions. By combining direct antagonism with strategic modulation of plant defense, T. virens facilitates an optimized biocontrol-biostimulant trade-off. Understanding this interplay is critical for enhancing the efficacy of Trichoderma-based applications in climate-smart, sustainable agriculture. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Pathogenicity in Phytophthora species is in part underpinned by a sophisticated arsenal of RxLR effectors, which function as molecular determinants of host immune manipulation. Among these, conserved RxLR effectors (CREs) represent an evolutionarily conserved subset that is indispensable for virulence. However, the structural basis of their function remains poorly understood. Here, we conducted in silico analysis of CREs across five agriculturally significant Phytophthora species, revealing a conserved subset that integrates WY domains with embedded short linear motifs (SLiMs), a previously recognized architectural feature with functional implications. Notably, our findings indicate that despite the canonical association of SLiMs with intrinsically disordered regions, their incorporation within the structured WY domain preserves domain integrity while potentially expanding the effector's interactome within host cells. To explore the functional relevance of this domain organization, we characterized Phytophthora nicotianae RxLR6 (PpRxLR6), a representative WY-SLiM CRE identified in this study. Using Agrobacterium-mediated transient expression assays, we demonstrate that PpRxLR6 activates key immune defense networks in Nicotiana and Solanum species, suggesting a role in modulating host immune signaling. Structural predictions further reveal that PpRxLR6 harbors its SLiM within a well-ordered WY-like helical core region, suggesting that SLiM-mediated interactions may occur within structured effector domains rather than being confined to intrinsically disordered regions. These findings enhance our understanding of the effector domain architecture of PpRxLR6, illustrating how structured domains in CREs may serve as scaffolds for SLiM-mediated interactions. This structural arrangement may represent an adaptive strategy in Phytophthora evolution, potentially enhancing effector versatility in host interactions and immune modulation. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Tomato brown rugose fruit virus (ToBRFV; Tobamovirus fructirugosum) is a recently discovered new species in the genus Tobamovirus that causes an ongoing pandemic and threatens tomato production worldwide. In this study, we determined the complete genome sequences of three ToBRFV isolates collected from greenhouse tomato plants in Canada in 2019, analyzed their possible phylogenetic relationships, and developed corresponding full-length infectious cDNA clones. Using the ToBRFV infectious clone, we generated gene-specific mutants via site-directed mutagenesis, followed by an infection assay. We confirmed that both the movement protein and the coat protein (CP) are indispensable for ToBRFV long-distance movement. Moreover, we found that alanine substitution of amino acid D89 or R114, both of which are highly conserved among tobamoviral CPs, compromised ToBRFV systemic infection. Confocal and electron microscopy analyses further revealed that either D89A or R114A substitution disrupted CP self-interactions and virion assembly. Additionally, we demonstrated that the ToBRFV 126-kDa replicase has RNA silencing suppression activity. Taken together, our data contribute to a better understanding of ToBRFV-encoded proteins at the molecular level, and the ToBRFV full-length infectious cDNA clones developed from this study are a useful tool to facilitate ToBRFV research. [Formula: see text] © 2026 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food Canada. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Plasmodiophora brassicae, the obligate parasite responsible for clubroot in Brassica crops and other crucifers, poses a major challenge to sustainable disease management due to its biotrophic lifestyle and adaptability. Recent advances in genomics, transcriptomics, and bioinformatics have accelerated the identification of its effector repertoire, which underpins host colonization and symptom development. To date, more than 100 putative effectors have been described, including several that modulate key plant defense processes such as pattern-triggered immunity, programmed cell death, phytohormone signaling, and ubiquitin-mediated protein degradation. Despite the inability to culture or genetically manipulate P. brassicae, functional studies using heterologous systems and transgenic approaches have revealed important insights into effector activity and host-pathogen interactions. Notably, conserved effectors such as PbBSMT and PbZF1 play central roles in virulence, highlighting their potential as targets for resistance breeding and effector-informed management strategies. However, the majority of candidate effectors remain uncharacterized, and inconsistent naming conventions across studies complicate cross-comparison. This review provides the first comprehensive synthesis of current knowledge on P. brassicae effectors, aiming to classify them according to their roles in host manipulation. Putative effectors that are consistently expressed across life cycle stages and host systems were identified and may serve as candidates for future investigation. We also discuss methodological advances and limitations in effector discovery and functional analysis, as well as opportunities to leverage effector biology in clubroot management. Ultimately, classifying conserved versus accessory effectors and understanding their interactions with host targets will be key to developing durable resistance and innovative strategies for clubroot management. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is the most economically damaging soilborne pathogen affecting soybean, causing significant yield losses in the United States and worldwide. Current commercial cultivars rely heavily on a limited genetic resistance base, primarily from PI 88788 and Peking, which has led to the emergence of virulent SCN populations that threaten the durability of this resistance. To address this challenge, we performed a comprehensive allelic analysis of key resistance loci (rhg1, Rhg4, qSCN10 (O), and qSCN18 (G)) using whole-genome resequencing data from 1,110 diverse soybean accessions. Our study identified novel nonsynonymous single-nucleotide polymorphisms in 27 accessions, including PI 602492 (Glycine max) and two Glycine soja accessions (PI 522226, PI 522228), that display strong to moderate resistance across multiple SCN HG types (Heterodera glycines) or SCN races. Additionally, we identified two G. soja accessions, PI 507380B and PI 507752, that exhibited strong resistance to HG type 2.5.7 (race 5). Notably, accessions with genotypes similar to these five showed variable resistance phenotypes, suggesting the presence of additional, yet unidentified, genes contributing to broad-based SCN resistance. Among these, PI 602492 stands out as a valuable new resistance source with strong activity against multiple HG types (races), making it an excellent candidate for gene discovery and breeding efforts to enhance resistance independently of conventional germplasm. These findings provide important, underutilized genetic resources that can expand the resistance base and drive the development of more durable SCN-resistant soybean cultivars. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Knowledge of the factors structuring populations of pathogenic fungi is fundamental to disease management efforts and basic biology. However, this crucial information is missing for many important pathogens, including broad-host-range and drought-associated pathogens from the globally distributed Macrophomina genus. The objectives of this work were to evaluate the evidence for host specialization, geographic adaptation, and recombination using a global survey of Macrophomina isolates from diverse geographic, temporal, and host sources. We obtained high-quality short-read sequence data for 463 Macrophomina spp. isolates, representing four putative species, collected from 91 host plant species and soil in 23 countries. Analysis of bi-allelic, single-nucleotide polymorphisms revealed high diversity, admixture, and equal mating type ratios, suggesting ongoing recombination. Although most tested isolates asymptomatically colonized strawberry, only strawberry-derived isolates caused disease on this host. These isolates were all in a single lineage, suggesting that the ability to cause disease on strawberry is not widespread among M. phaseolina. Significant associations were also found between isolations from soybean plants and specific population clusters, suggesting that specialization for virulence or reproduction has also occurred for soybean. Geography × isolate genotype associations were weak, suggesting that Macrophomina spp. were frequently trafficked between regions. Reference-free whole-genome comparisons support current boundaries among four Macrophomina species, and new molecular markers were designed to specifically identify each species. Contrary to expectations, M. phaseolina should be considered a single species with both specialist and generalist populations in which meiosis can maintain genetic diversity. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Sinorhizobium meliloti forms a robust N₂-fixing root-nodule symbiosis with Medicago sativa. We are interested in identifying the minimal symbiotic genome of the model strain S. meliloti Rm1021. This gene set refers to the minimal genetic determinants required to form a robust N₂-fixing symbiosis. Many symbiotic genes are located on the 1,354-kb pSymA megaplasmid of S. meliloti Rm1021. We recently constructed a minimalized pSymA, minSymA2.1, that lacked over 90% of the pSymA genes. Relative to the wild type, minSymA2.1 showed a reduction in M. sativa shoot biomass production and nodule size with an increase in total nodule number. Here, we show that the addition of either the stachydrine (stc) or trigonelline (trc) catabolism genes from pSymA to minSymA2.1 restores nodule size and total nodule number to levels indistinguishable from the wild type but does not restore reduced shoot biomass production. In the context of the complete Rm1021 genome, removing the stc genes reduced the nodule size and increased the total nodule number, whereas removal of the trc genes alone had no apparent effect. Together, these observations implicate stachydrine catabolism as an important determinant of root nodule symbiosis between S. meliloti and M. sativa, whereas trigonelline catabolism seems to contribute in a more conditional manner, in the context of the minimized genome. These findings highlight the minimal symbiotic genome as a tool for investigating the impact of individual genetic determinants in conferring an optimal symbiosis, factors whose impact, in the context of a complete genome, may be hidden or dampened due to redundancies. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Reliable, high-throughput quantification of early fungal infection events is crucial for gene function studies, but it remains labor-intensive. We report an openly available pipeline that automates the detection of β-glucuronidase (GUS)-stained epidermal cells and the intracellular haustoria formed by powdery mildew on barley and wheat leaves. Whole-slide images are captured with a commercial scanner, focus-projected, tiled, and analyzed by deep-learning models trained on expertly annotated datasets. A You Only Look Once (YOLO) network identifies GUS-positive cells, and a companion segmentation model pinpoints haustoria within each cell; automatic focus-layer selection preserves fine structural detail. The workflow runs in minutes per slide on a single workstation and maintains near-perfect agreement with manual counts in both barley and wheat, demonstrating robust cross-species transferability. By delivering single-cell readouts with minimal user input, the pipeline enables rapid functional validation screens and supports large-scale phenotyping of cereal-powdery mildew interactions. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.