Physiological and Molecular Plant Pathology最新文献

{"title":"Acetylcholinesterase Mediated Nematicidal Potential of Alkaloid-Enriched Lycopodium clavatum against Meloidogyne incognita","authors":"Himani Karakoti ,&nbsp;Ravendra Kumar ,&nbsp;Om Prakash ,&nbsp;Shilpi Rawat ,&nbsp;D.S. Rawat","doi":"10.1016/j.pmpp.2026.103173","DOIUrl":"10.1016/j.pmpp.2026.103173","url":null,"abstract":"<div><div>The increasing resistance of plant-parasitic nematodes like <em>Meloidogyne incognita</em> to synthetic nematicides necessitates the exploration of sustainable alternatives. In this study, <em>Lycopodium clavatum</em> (LC), a medicinal fern traditionally valued for its alkaloid-rich profile, was investigated for its nematicidal potential against <em>M. incognita</em> for the first time. This study aimed to assess the chemical composition, nematicidal activity, and acetylcholinesterase (AChE) inhibitory properties of various solvent extracts of LC such as hexane (LYHE), dichloromethane (LYDE), and methanol (LYME) extracts. Gas chromatography-mass spectrometry (GC-MS) revealed distinct chemical profiles: LYHE was dominated by fatty acids and hydrocarbons, with n-decanoic acid (43.71%) as the major component, while LYDE exhibited diverse bioactive compounds, including diterpenoids like thunbergol (12.20%), and alkaloids such as lycopodine (13.68%). LYME was rich in polar compounds, such as guanosine (10.54%), and also contained significant levels of lycopodine (26.72%), highlighting its versatile extraction capabilities. Nematicidal assays demonstrated LYME as the most potent extract, achieving 95.67% mortality at 1000 μg/mL after 96 h, followed by LYDE (89.33%) and LYHE (67.67%). LYDE exhibited superior egg-hatching inhibition, achieving 100% inhibition at 1000 μg/mL within 24 h. AChE inhibition assays identified LYDE as the most potent inhibitor (IC₅₀ = 49.33 μg/mL), outperforming LYME (108.37 μg/mL) and LYHE (289.78 μg/mL). LYDE was closed to the standard inhibitor, physostigmine (19.37 μg/mL). Molecular docking further supported the potential mode of action, with guanosine, α-obscurine, and stigmasterol showing strong binding affinities (−8.4 to −8.1 kcal/mol) against the homology-modeled AChE of <em>M. incognita</em>. These findings underscore the nematicidal efficacy of <em>Lycopodium clavatum</em>, particularly LYDE and LYME, and highlight their potential as eco-friendly alternatives to synthetic nematicides.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"143 ","pages":"Article 103173"},"PeriodicalIF":3.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanistic insights into Fusarium oxysporum suppression by Trichoderma cerinum Gur1 volatiles: Downregulation of trichothecene and bikaverin biosynthesis genes","authors":"Ekta Khare ,&nbsp;Kangmin Kim ,&nbsp;Govind Gupta ,&nbsp;Alok Pandey ,&nbsp;Shilpa Deshpande Kaistha ,&nbsp;Anuradha Kalani","doi":"10.1016/j.pmpp.2026.103179","DOIUrl":"10.1016/j.pmpp.2026.103179","url":null,"abstract":"<div><div>The biocontrol of phytopathogenic fungi by <em>Trichoderma</em> spp. is majorly attributed by the mycoparasitism and the production of various antagonistic compounds via mutual fungi-to-fungi interactions. However, detailed information on effect of <em>Trichoderma</em> volatile organic compounds (VOCs) in such interspecies interactions is still largely unknown. In this study, we reported that VOCs produced by <em>Trichoderma cerinum</em> Gur1 suppress <em>Fusarium oxysporum</em> f. sp. <em>lactucae</em> growth, conidiation and bikaverin (a reddish polyketide) production. Reduction in cytoplasmic content, vacuolization and shrinkage appeared in electron micrographs of <em>F. oxysporum</em>, indicating the role of n-hexadecanoic acid and 6-pentyl-α-pyrone (6PP) among several other VOCs of <em>T. cerinum</em> Gur1 detected by GC-TOF-MS analysis. To detect the effect of <em>Trichoderma</em> VOCs on pathogen, the expression of pathogenicity related genes of <em>F. oxysporum</em>, involved in trichothecenes (<em>tri1)</em> and bikaverin (<em>pks4</em>) biosynthesis pathways were examined during VOCs exposure bioassay. Noticeably, the expression of both <em>tri1</em> and <em>pks4</em> was down regulated on third day of VOCs exposure. The reduction of conidiation and bikaverin production significantly impacts the distribution, survival, and competitive ability of <em>F</em>. <em>oxysporum</em> in diverse environments. The reduction in expression of pathogenicity related genes including these factors are critical in understanding the ecology and pathogenicity of the fungus and can inform effective management and control strategies.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"143 ","pages":"Article 103179"},"PeriodicalIF":3.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147386469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Organic acids produced by Solanum sisymbriifolium contribute to its resistance against nematodes","authors":"Nataniel D. Jablonski ,&nbsp;Faith M. Fishburn ,&nbsp;Lindsay L. Schulz ,&nbsp;Harpreet Kaur ,&nbsp;Joseph C. Kuhl ,&nbsp;Fangming Xiao ,&nbsp;Louise-Marie Dandurand ,&nbsp;Cynthia A. Gleason ,&nbsp;Allan B. Caplan","doi":"10.1016/j.pmpp.2026.103145","DOIUrl":"10.1016/j.pmpp.2026.103145","url":null,"abstract":"<div><div>Much of the current literature on the mechanisms of plant resistance to pathogens has focused on the role of cellular sensors that initiate a “pathogen-associated molecular-pattern triggered immunity” or PTI response. Less attention has been given to the benefits that some common metabolites may provide to plant resistance. In this study, an untargeted metabolomic analysis identified 230 metabolites that were 3-fold higher in the trap crop <em>Solanum sisymbriifolium</em> than in two nematode-susceptible potato varieties. Several of these metabolites had nematicidal activity <em>in vitro</em> against the root-knot nematodes, <em>Meloidogyne chitwoodi</em>, <em>M. incognita</em>, and <em>M. hapla</em>, at concentrations measured in <em>Solanum sisymbriifolium</em> roots. The most effective of the chemicals tested were furoic, aconitic, and quinic acids. Further studies revealed first that the 3 acids were most effective at or below their acid dissociation constant (pKa) implying that the protonated forms were better able than the charged ones to cross cell membranes and/or bind to critical targets. Second, that the effects of these chemicals were due partially to their structures and not to the creation of an acidic environment. Third, that these chemicals acted additively indicating that <em>S. sisymbriifolium</em> resistance may be partially due to a combination of metabolites rather than to any single chemical.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"143 ","pages":"Article 103145"},"PeriodicalIF":3.3,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146161848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Primary metabolomics analyses and detection of citrus “huanglongbing” disease based on UHPLC-MS/MS and machine learning","authors":"Biyun Yang ,&nbsp;Jun Tian ,&nbsp;Yayong Chen ,&nbsp;Yong Xu ,&nbsp;Wei Cheng ,&nbsp;Zhiling Yang ,&nbsp;Fenglin Zhong ,&nbsp;Dapeng Ye ,&nbsp;Haiyong Weng","doi":"10.1016/j.pmpp.2026.103110","DOIUrl":"10.1016/j.pmpp.2026.103110","url":null,"abstract":"<div><div>‘Candidatus Liberibacter asiaticus’ is the major agent associated with citrus “huanglongbing” (HLB) disease, which is the most destructive citrus disease and has caused serious losses to citrus industry worldwide. Ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS)-based nontargeted metabolomics and machine learning algorithms were developed for identifying HLB disease in different citrus varieties and growing seasons. In this study, 52 (28 up-regulated and 24 down-regulated) and 33 (26 up-regulated and 7 down-regulated) differential metabolites were screened in Navel orange (<em>Citrus sinensis</em> Osbeck) and Ponkan (<em>Citrus reticulata</em> Blanco cv. Ponkan) leaves, respectively. The variable importance in projection (VIP) algorithm was then used to select the common differential metabolites in HLB diseased samples, and a total of 19 differential metabolite variables were obtained from Navel orange and Ponkan varieties (mainly including primary metabolites such as D-ribose, D-threonate, L-ornithine). Finally, support vector machine (SVM) model based on the metabolites with significant features performed the best for the prediction of citrus HLB disease, with a classification accuracy of 100 %. The results showed that the proposed method was able to provide important and common information about citrus host-'<em>Ca. L. asiaticus</em>' interactions. They also demonstrated that combing untargeted metabolomics with machine learning can be effective tools for distinguishing citrus HLB infection (from asymptomatic to symptomatic) in different growing stages and cultivars.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103110"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145924607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomical and functional microbial community profiling in Fusarium wilt-resistant and susceptible banana plants","authors":"Shazma Gulzar ,&nbsp;Yaxing Xu ,&nbsp;Chunxia Huang ,&nbsp;Xiaoquan Li ,&nbsp;Weiyou Zou ,&nbsp;Yue Meng ,&nbsp;Rahat Sharif ,&nbsp;Zuxiang Su ,&nbsp;Chunxiang Xu","doi":"10.1016/j.pmpp.2025.103095","DOIUrl":"10.1016/j.pmpp.2025.103095","url":null,"abstract":"<div><div><em>Fusarium oxysporum</em> f. sp. <em>cubense</em>, the causal agent of Fusarium wilt, poses a significant threat to banana production. The plant microbiota plays a vital role in disease resistance. However, the relationship between the susceptible and resistant mutant associated microbiota is limited. We investigated taxonomic and functional differences in bacterial and fungal communities between a banana Fusarium wilt (<em>Foc</em> 1) susceptible cultivar ‘Guangfen 1’ (GF, ABB genome) and its resistant mutant (GFR). We used high-throughput Illumina sequencing of 16S rRNA genes and ITS_V1 regions, by sampling the rhizosphere soil, pseudostem and roots. Bacterial and fungal communities were more diverse in rhizosphere soil than plant organs. The rhizosphere of GFR exhibited lower bacterial and fungal alpha diversity (Shannon index) than GF. The dominant bacteria identified in rhizosphere of GFR included members of Acidobacteriota, Proteobacteria, Actinobacteriota and Chloroflexi. The dominant fungi in GFR were <em>Mortierellomycota</em> and <em>Basidiomycota</em>, while GF was enriched in <em>Ascomycota</em>. LEfSe identified 15 distinct bacterial biomarker taxa in rhizosphere of GF and 28 in GFR. For fungi, Agaricales was the only biomarker taxon found in the rhizosphere of GFR. KEGG pathways further revealed that xenobiotic biodegradation and metabolism, biosynthesis of other secondary metabolites, and amino acid metabolism were prominent in GFR. In a dual culture assay, strains 1–61 and 4–28 showed significant antagonistic activity against <em>Foc</em> 1 and 4, respectively. Together, these findings demonstrate that Fusarium wilt resistance in banana is associated with differences in microbial communities and functions that may contribute to enhanced disease suppression.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103095"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145839503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic insights into tomato-Fusarium relationship: Plant-pathogen interactions and virulence mechanisms","authors":"Yashoda Nandan Tripathi ,&nbsp;Richa Raghuwanshi ,&nbsp;Ram Sanmukh Upadhyay","doi":"10.1016/j.pmpp.2025.103093","DOIUrl":"10.1016/j.pmpp.2025.103093","url":null,"abstract":"<div><div><em>Fusarium oxysporum</em> is a well-known soil-borne pathogen that causes severe vascular wilting in many important crops worldwide. <em>F. oxysporum</em> f. sp. <em>lycopersici</em> (Fol) specifically affects tomatoes, leading to significant economic losses. Therefore, it is crucial to understand the molecular mechanisms underlying the pathogenesis of this pathogen. Tomato and Fol have been found to be engaged in an evolutionary arms race. Three physiological races, (1, 2 and 3) of Fol are identified based on their specific pathogenicity to different tomato cultivars. Fol employs several strategies to perceive its host and cause infection, like evading PTI by secreting proteases and also with the help of point mutations in the AVR gene. Fol's pathogenesis mechanism also involves activation of several transcription factors, secretion of toxic metabolites (e.g., fusaric acid), cell wall-degrading enzymes (e.g., polygalacturonase), and small RNAs like Fol-milR1 that impair the host immune response. In counter, the tomato plants have evolved effective defense mechanisms against the Fol attack. While no PAMP/PRR pair has been identified in tomato-Fol interactions till date, effector-triggered immunity is mediated by the recognition of the AVR effector proteins by the resistance proteins of the I locus. Moreover, as part of their defense mechanism, tomato plants secrete defense molecules like α-tomatine and chitinases to counter Fol attack, along with phytohormones like salicylic acid, which regulates susceptibility and also regulates defense genes during Fol attack by certain endogenous miRNA that targets <em>R</em> genes at the level of transcript and provides innate immunity.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103093"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145840136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sustainable cold plasma suppresses tomato brown rugose fruit virus in tomato seeds","authors":"Sahar Salami ,&nbsp;Abozar Ghorbani ,&nbsp;Mahsa Rostami ,&nbsp;Abolfazl Mazandarani ,&nbsp;Davoud Koolivand","doi":"10.1016/j.pmpp.2026.103123","DOIUrl":"10.1016/j.pmpp.2026.103123","url":null,"abstract":"<div><div>Tomato brown rugose fruit virus (ToBRFV), a highly contagious member of the <em>Tobamovirus</em> genus, poses a significant threat to global tomato production due to its seed-transmission nature and the lack of effective control measures. This study investigates the potential of cold air glow discharge plasma (CAGDP) as an effective, scalable, and environmentally sustainable method for managing ToBRFV contamination in tomato seeds. The study employed five treatment groups: untreated tomato seeds and ToBRFV-infected tomato seeds exposed to CAGDP for durations ranging from 1 to 4 min, either alone or in combination with sodium hypochlorite. The treated seeds were cultivated in greenhouse conditions, and viral detection tests were performed on the growing plants. The efficacy of each treatment was assessed through key physiological and molecular parameters, including germination rate, chlorophyll content, stem diameter, and viral accumulation, quantified via RT-qPCR. Results demonstrated that 3-min CAGDP treatment notably enhanced germination rate, chlorophyll content, and stem diameter while significantly reducing viral load, demonstrating both suppression activity at the molecular (RNA) level and growth-promoting effects. Furthermore, combined with sodium hypochlorite, CAGDP exhibited an antiviral effect at the molecular level. Molecular assays indicated that CAGDP promotes viral RNA degradation and delays virus replication, supporting its role in activating plant defense responses. Altogether, these findings highlight CAGDP as a promising alternative to chemical disinfectants, providing a dual benefit of suppression of viral replication and seedling vigor enhancement. With further optimization and field validation, CAGDP technology could serve as a valuable tool in sustainable tomato production and broader seed health management.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103123"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146187510","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salicylic acid induces disease resistance of postharvest ‘Housui’ pear fruit by modulating reactive oxygen species metabolism and activating defense-related enzymes","authors":"Jie Gao ,&nbsp;Peng-Yuan Wang ,&nbsp;Meng-Meng Wen ,&nbsp;Chen Chen ,&nbsp;Jing Zhang ,&nbsp;Chun-Lei Wang","doi":"10.1016/j.pmpp.2026.103126","DOIUrl":"10.1016/j.pmpp.2026.103126","url":null,"abstract":"<div><div>Postharvest decay caused by fungal pathogens leads to substantial economic losses in pear fruits. Salicylic acid (SA), a key plant hormone involved in defense responses, plays a vital role in enhancing disease resistance. This study aimed to evaluate the effect of postharvest SA immersion on controlling decay in pear fruit and to elucidate the underlying mechanisms. The results showed that SA application significantly inhibited the mycelial growth of five major fungal pathogens in a dose-dependent manner <em>in vitro</em> and reduced lesion diameter in inoculated fruits <em>in vivo</em>, including a newly characterized postharvest pathogen <em>Gilbertella persicaria</em>. During storage at 20 °C, SA treatment significantly reduced the decay rate. Physiological analyses indicated that SA suppressed the accumulation of reactive oxygen species (H₂O₂ and O₂⁻) and malondialdehyde, thereby alleviating oxidative damage. Moreover, SA enhanced the activities of key antioxidant enzymes (superoxide dismutase, catalase, and peroxidase) and defense-related enzymes (chitinase, β-1,3-glucanase, phenylalanine ammonia-lyase, polyphenol oxidase, and lipoxygenase). In conclusion, SA not only exhibits direct antifungal properties but also enhances systemic disease resistance in pear fruit by modulating ROS homeostasis and activating antioxidant and defense-related enzymatic pathways, demonstrating its potential as an eco-friendly strategy for managing postharvest disease.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103126"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146187511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Image processing–assisted evaluation of yeast-encapsulated clove formulations against tomato brown rugose fruit virus","authors":"Cemile Temur Çınar ,&nbsp;Kevser Karaman ,&nbsp;Şeyda Nur Türkay Rıfaioğlu ,&nbsp;Necati Çetin","doi":"10.1016/j.pmpp.2025.103025","DOIUrl":"10.1016/j.pmpp.2025.103025","url":null,"abstract":"<div><div>Tomato brown rugose fruit virus is an emerging threat to tomato and other <em>solanaceous</em> crops, demanding eco-friendly antiviral approaches. Plant-derived clove products, including essential oil and ethanolic extract, possess antiviral potential but are limited by instability and delivery challenges. In this study, clove essential oil and extract were encapsulated in plasmolysed and non-plasmolysed yeast cells (<em>Saccharomyces cerevisiae</em>) through an environmentally friendly process to enhance their stability and effectiveness. The encapsules were analysed by gas chromatography–mass spectrometry, Fourier-transform infrared spectroscopy, and scanning electron microscopy. Their antiviral activity against tomato brown rugose fruit virus infection was evaluated under greenhouse conditions, and virus presence was confirmed by reverse transcription–polymerase chain reaction. Treatment efficacy was assessed via image-based lesion quantification, including area, count, and color parameters. Image-derived results were consistent with manual measurements, validating the reliability of digital evaluation. Treated plants exhibited reduced lesion formation and color alterations associated with symptom suppression. Yeast encapsulation thus improved the antiviral performance of clove-based products, while image processing provided a non-destructive and straightforward tool for early detection and monitoring of plant virus infections.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103025"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145555209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A transparent rule-based framework using k-mer profiles for detection of cryptic infections in tomato whole-genome metagenomic data","authors":"Reza Khakvar ,&nbsp;Girish Pulinkala ,&nbsp;Maya Baghdy Sar ,&nbsp;Jan Komorowski","doi":"10.1016/j.pmpp.2025.103092","DOIUrl":"10.1016/j.pmpp.2025.103092","url":null,"abstract":"<div><div>Cryptic infections in crops—especially fresh-consumed vegetables—pose a significant threat to food safety, as low-abundance pathogens often escape conventional diagnostics. Whole-genome shotgun metagenomic sequencing (WGS) offers high-resolution detection but generates complex datasets that challenge standard bioinformatics pipelines. This study evaluates a rule-based machine learning (RBML) approach using k-mer profiles from tomato WGS metagenomic datasets. Forty-two tomato samples with varying symptoms were collected and sequenced. Infection status was determined using three independent computational tools (MetaPhlAn, Kraken2/Bracken, and CLC Genomics) and validated by PCR assays targeting known pathogens; 29 of 31 bioinformatically-positive samples were PCR-confirmed, while all 11 non-infected samples were PCR-negative. K-mer profiles (k = 10 bp) were generated using KMC3, filtered to exclude sequences with ≤15 % relative abundance variation between infected and non-infected samples, and processed through Monte Carlo Feature Selection (MCFS) and Boruta algorithms. The union of top-ranked features yielded 30 biologically validated k-mers. Biological validation included BLASTn mapping of selected k-mers to reference pathogen and endophyte. Five biologically interpretable IF-THEN rules were derived using R.ROSETTA, C5.0 and Random Forest that achieved an overall accuracy of 89 %, a precision of 0.80, and an F1-score of 0.68 under leave-one-out cross-validation. These rules capture microbial abundance shifts rather than absolute pathogen presence, offering interpretable diagnostics for precision agriculture. While limited by sample size, this proof-of-concept demonstrates RBML's potential to detect subtle infection signatures from WGS data with biological transparency and future work should validate its robustness across larger and more diverse datasets.</div></div>","PeriodicalId":20046,"journal":{"name":"Physiological and Molecular Plant Pathology","volume":"142 ","pages":"Article 103092"},"PeriodicalIF":3.3,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145796875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}