Phytopathology最新文献

Chemical modifications are prevalent on the genomic and messenger RNAs of RNA viruses. The AlkB family proteins are a class of demethylases that have the capacity to modulate the abundance and distribution of chemical modifications on nucleic acids in a dynamic manner, thereby dictating the functional competence of viral RNAs and, ultimately, affecting viral infectivity and replication. A subset of positive-sense RNA viruses harbour an AlkB domain within their polyproteins; however, whether this domain displays enzymatic activity equivalent to that of canonical AlkB enzymes, and thus participates in virus-host interactions, remains unresolved. Here, we characterized the biological role of the AlkB domain embedded in ORF1 of citrus leaf blotch virus (CLBV). Site-directed mutagenesis of catalytic core residues within the domain did not abolish infectivity in Nicotiana benthamiana, but markedly delayed cell-to-cell movement, reduced viral accumulation in emerging leaves, and attenuated plant stunting. Moreover, m⁶A peaks in total RNA were significantly more abundant, and their distribution patterns on both host mRNAs and the viral genomic RNA were altered, in plants inoculated with the AlkB-mutated infectious clone. Collectively, these data suggest that the CLBV-encoded AlkB domain likely possesses m⁶A demethylase activity that is analogous to that of cellular AlkB proteins. The results of the present study provide the first functional characterisation of a viral AlkB domain and provide a critical reference for future mechanistic interrogation of AlkB-domain function across viral systems.

Pantoea ananatis was first reported infecting rice in the United States in 2021, causing leaf blight in research plots in Arkansas. In 2024, two breeding lines exhibited leaf blight symptoms in research plots at the Rice Research and Extension Center, Stuttgart, AR. This study aimed to recover new P. ananatis isolates and characterize their pathogenicity in rice, as well as their ability to induce plant responses in rice, tobacco, and onion. Isolates were obtained from seeds of symptomatic plants using a Pantoea genus-specific agar protocol and confirmed by PCR and sequencing of 16S rRNA and gyrB genes. P. ananatis isolates were infiltrated into tobacco and rice plants and inoculated in onion to determine their ability to elicit hypersensitive or necrotic responses. Notably, isolate PP105 consistently triggered a necrotic response in rice, tobacco and onion, suggesting distinct pathogenicity mechanisms compared with the other isolates. Overall, this study enhanced the understanding of P. ananatis characterization in rice and alternative model hosts, while highlighting challenges and raising new questions for future research.

In this study, we present novel genomic data for Xanthomonas citri pv. bilvae (Xcb), the causal agent of bacterial shot-hole disease in bael trees. Using a hybrid sequencing approach that combines short- and long-read technologies, we assembled high-quality genomes of the only two available contemporary Xcb strains. Furthermore, we reconstructed the first historical genome of Xcb from a herbarium specimen collected in 1848, thereby extending the documented presence of this overlooked disease in India by nearly 100 years. We then characterized the genomic features of these strains, with a particular emphasis on virulence factors and plasmid content, using a suite of specialized bioinformatics tools. The contemporary Xcb strains were found to carry between one and four plasmids, which varied in their mobility potential (conjugative, mobilizable, or non-mobile). A total of 30 to 32 type III effector genes were identified across chromosomes and plasmids. Notably, one of the contemporary strains harbored four plasmid-borne transcription activator-like effectors (TALEs), which showed only distant similarity to TALEs found in X. citri pv. citri, a globally major pathogen with a partially overlapping host range. Comparative genomic analysis between the contemporary and historical strains revealed a remarkable conservation of effector gene content, indicating that key pathogenic traits may have been acquired early in Xcb's evolutionary history. Collectively, these new genomic resources provide valuable insights into the biology and evolution of this underexplored bacterial pathogen.

Rice blast, caused by the ascomycete fungus Magnaporthe oryzae, is one of the most problematic diseases for rice production, threatening global food security. Genetic resistance to some M. oryzae races can be achieved using major resistance genes that recognize their corresponding fungal avirulence genes. Weedy rice, a close relative of cultivated rice that competes with the crop, has evolved unique genetic mechanisms to resist M. oryzae infections; thus, weedy rice can serve as an excellent resource for blast control. In this study, we assessed disease scores of 183 F₅ and F₆ recombinant inbred lines (RILs) derived from a weedy rice × crop biparental mapping population and their parental lines, a Black Hull Awn weedy rice strain (PI 653413, RR14) and the aus-196 rice variety, using four distinct common U.S. blast races (IB33, IG1, IE1K, and IC17) under greenhouse conditions. All the parental lines were resistant to all blast races; however, RILs showed a wide degree of variation in resistance. Genotyping-by-sequencing of the RIL population and parents generated 1,498 single-nucleotide polymorphisms, which were used to construct a linkage map, and quantitative trait locus (QTL) mapping of blast resistance was performed using r/qtl. A single major blast resistance QTL on chromosome 12 was mapped to the Pi-ta/Pi39(t)/Ptr locus. Identification of Pi-ta/Pi-39(t)/Ptr as the key contributor to blast resistance in weedy rice provides insight into the evolution and adaptation of weedy rice and can aid in the development of blast-resistant rice varieties through marker-assisted selection.

Colletotrichum fructicola is a significant phytopathogen in both pre- and postharvest stages of fruit development and storage. The development of environmentally friendly biological control agents has attracted increasing research interest. In this study, we characterized a fungal strain (Epicoccum layuense LQ) that strongly inhibits C. fructicola. A potato dextrose broth culture filtrate of strain LQ inhibited the vegetative growth of C. fructicola by approximately 80% at a 1:10 (vol/vol) dilution. Cytological observations revealed that the filtrate disrupted mitosis and cellular polarity during conidial germination. Furthermore, the culture filtrate effectively suppressed C. fructicola infection on both apple leaves and fruits. The fungal strain LQ was identified as E. layuense through integrated morphological characterization and multilocus phylogenetic analysis. Whole-genome sequencing of strain LQ identified 36 biosynthetic gene clusters (BGCs), and subsequent gene synteny analysis demonstrated structural conservation in three BGCs homologous to known antifungal clusters. Notably, substitution of NaNO₃ with yeast extract in a Czapek-Dox medium enhanced the antifungal activity of the strain LQ filtrate by 14.2-fold. Consistent with this finding, transcriptomic profiling revealed significant upregulation of BGCs associated with epipyrone A and burnettramic acid A biosynthesis under a yeast extract supplementation condition. In sum, our results demonstrate the antagonistic potential of E. layuense LQ and identify two candidate BGCs that may mediate this biocontrol activity, which lays a foundation for further mechanism dissection.

Glutathione (l-γ-glutamyl-l-cysteinyl-glycine) is a key molecule that regulates numerous plant processes under both biotic and abiotic stress conditions. However, its role in plant responses to soilborne pathogens, particularly the economically important root-knot nematodes (Meloidogyne spp.), remains largely unexplored. Here, we investigated the role of glutathione in Arabidopsis thaliana during M. incognita infection using a combination of genetic (glutathione biosynthetic mutants), biochemical (thiol and camalexin measurements), and pharmacological (exogenous glutathione supplementation) approaches. We found that glutathione depletion in the roots of mutants in glutathione synthesis (rax1, pad2, cad2, and nrc2) significantly reduced gall formation by up to 27% and egg mass production by up to 33% compared with the control, suggesting its important role in nematode infection. Additionally, the exogenous application of glutathione increased plant susceptibility to M. incognita, resulting in a 23% increase in gall formation and a 19% increase in egg mass production compared with the mock-treated control. Biochemical analysis revealed that reduced glutathione levels disrupted the cysteine-glutathione balance early in the infection process. However, further assays, including camalexin measurements and infection assays with gstf6 loss-of-function lines, indicated that glutathione-dependent phytoalexin camalexin does not significantly contribute to M. incognita parasitism. These findings underscore the importance of glutathione in maintaining thiol homeostasis during the early stages of M. incognita infection and suggest that manipulating glutathione levels could be a potential strategy for nematode control in agriculture.

Rice is a critical crop for global food security and economic stability. However, various diseases, including rice blast and bacterial leaf blight, pose significant threats to rice cultivation. Existing methods for detecting rice leaf diseases suffer from low efficiency and limited generalization capability. These methods are incapable of capturing variations of disease characteristics across different growth cycles. Therefore, a lightweight detection model named lightweight knowledge distillation YOLO (LWKD-YOLO) is proposed. The convolutional layers in the YOLOv8 network are replaced with the ADown module. This change significantly reduces computational load while improving detection accuracy. A lightweight detection head, termed the lightweight shared re-parameterizable convolutional detection head (LSRP-Head), was designed. It incorporates group normalization RepConv, further reducing computational complexity while enhancing multi-scale perception capabilities. Furthermore, based on the improved ADown module and LSRP-Head, the YOLOv8x model is employed as a teacher model for inter-channel correlation knowledge distillation. This effectively enhances the ability to learn complex rice leaf disease features. The effectiveness of the proposed method was verified through ablation and comparative experiments on the constructed rice leaf disease dataset. Compared with the baseline model, LWKD-YOLO increases mAP@50 by 1.4%, reduces the number of parameters by 1.3M, and lowers FLOPs by 3.1G. As a result, the proposed model enables efficient rice leaf disease detection in complex environments, demonstrating notable economic and practical significance.

Xylella fastidiosa is a plant-pathogenic bacterium native to the Americas. It has a wide host range and causes significant diseases in economically important crops, including grapevines, citrus, and olive trees. Since 2013, this bacterium has been detected in Europe and other countries of the Mediterranean basin, leading to the identification of several subspecies (multiplex, fastidiosa and pauca) and sequence types (STs) in various plant species in Italy, France, the Balearic Islands and mainland Spain, Portugal, Israel and Lebanon. This study focuses on genomic analyses of the subspecies pauca ST53 strains detected in France. ST53 was identified (i) on intercepted coffee plants in the Pays-de-la-Loire region in 2014 and 2015, and (ii) on two infected host plants collected in Menton in the Provence-Alpes-Côte d'Azur region in 2015 and 2019. As an efficient and promising alternative to cell culture, the targeted enrichment method developed specifically to capture X. fastidiosa gDNA was applied to obtain the whole genome. Phylogenetic and genomic comparisons were carried out to compare the ST53 genomic sequences of the samples from France with a range of X. fastidiosa subspecies pauca genomic sequences from public databases, including ST53 from Italy and Costa Rica. The results obtained from these different approaches revealed close genetic relatedness between the strains. A tip-dating analysis and transmission tree were performed, supporting the hypothesis that some ST53 strains from France may be related to the same introduction event than the Italian strains.

Mycotoxin contamination of wheat and corn grain from Fusaria is a major agricultural concern. To characterize the population of Fusarium in Michigan, 569 isolates were collected, and species composition, TRI genotype, in vitro fungicide sensitivity, and fungicide field efficacy were determined. In wheat, the Fusarium sambucinum species complex comprised 90% of isolates, of which 82.5% of all isolates were F. graminearum. In corn, the F. sambucinum species complex comprised 40%, with 37% identified as F. graminearum, whereas species from the F. fujikuroi species complex comprised 50%. Within the F. fujikuroi complex, F. awaxy (4.6%) was found and had not previously been identified in the United States. Across F. graminearum isolates, TRI genotypes were found at the following percentages: 92% 15-acetyldeoxynivalenol (15-ADON), 6% 3-ADON, 1.6% NX-2, and no NIV. In vitro mycelial growth sensitivity assays to triazole fungicides demonstrated that Fusaria were more sensitive to metconazole than to tebuconazole or prothioconazole. Species-specific differences in sensitivity were identified across the fungicides tested, with F. tricinctum species complex members significantly less sensitive than F. graminearum isolates, and the F. fujikuroi species complex was significantly more sensitive. Within F. graminearum, 10 isolates had median effective concentration (EC₅₀) values 10-fold greater than sensitive isolates. A subset of these F. graminearum isolates were chosen to investigate if reduced sensitivity in vitro would lead to practical resistance in vivo. Field plots were inoculated with spore suspensions; however, no differences in the relative fungicide efficacy were found, signaling that no demethylation inhibitor fungicide resistance was identified in our collected isolates, despite differences in vitro. Although currently, there may not be practical resistance, monitoring should continue, as there is variation in in vitro sensitivities present within and among species.

Wheat yellow mosaic virus (WYMV) is the main cause of wheat yellow mosaic disease. Although its regulation of protein translation and interactions with host proteins are well studied, independent regulation of the virus genome is poorly understood. This study performed in vitro experiments investigating replication regulation by the 5' and 3' untranslated regions of WYMV RNA2. The results confirm that the RNA-dependent RNA polymerase (nuclear inclusion protein b [NIb]) can only recognize and catalyze the synthesis of 3' 190-nt complementary chains in vitro. RNA structure probing and mutation analysis identified ³⁵⁹⁷AUU and ³⁶⁰⁷GGCU as novel interaction sites of NIb; both are essential for maintaining normal replication. Our findings provide an empirical basis for in vivo experiments on regulation of WYMV genome replication and provide a theoretical basis for the prevention and control of WYMV-related crop diseases.