{"title":"Whole genome sequencing and annotation of Pseudocercospora abelmoschi, a causal agent of black leaf mould of okra.","authors":"Shagun Sinha, Sudhir Navathe, Anjali, Shubham Vishwakarma, Priyanka Prajapati, Ramesh Chand, Ravindra Nath Kharwar","doi":"10.1007/s11274-025-04398-4","DOIUrl":"10.1007/s11274-025-04398-4","url":null,"abstract":"<p><p>Pseudocercospora abelmoschi causes black mould on the leaves of okra. The disease is prevalent post-rainy season when high moisture and warm temperatures prevail. Severe defoliation is observed during favourable environments, leading to a significant loss in productivity. Based on the importance of the pathogen agriculturally, the P. abelmoschi isolate Cer 86 - 18 (MCC:9491) was selected for genome sequencing. The genome assembly of P. abelmoschi resulted in a genome of 31.90 Mb with an overall GC content of 54.26%. Quantitative genome assessment using BUSCO (Benchmarking Universal Single-Copy Orthologs) identified 1,664 (97.53%) complete BUSCOs, reflecting a high representation of conserved genes with minimal duplication and strong orthologous uniqueness. Gene prediction analysis identified 11,325 protein-coding genes, of which 3,857 were annotated using the KEGG database. As per analyses, 410 genes were predicted to encode carbohydrate-active enzymes, whereas 369 genes were predicted to encode peptidases. Eighteen gene clusters involved in secondary metabolite biosynthesis were also identified. A total of 143 proteins were predicted to be effectors using the in-silico pipeline. This is the first report on the genome organisation of P. abelmoschi. This study was designed to address this gap by enhancing our understanding of the genome organisation of P. abelmoschi and gene annotation, thereby paving the way for functional genomics studies, such as identifying virulence genes to aid in resistance breeding. Also, this genome could be another addition to the available genomic resources of the genus Pseudocercospora and can provide valuable insights into host-pathogen interactions and evolutionary relationships.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"174"},"PeriodicalIF":4.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Xuedong Zhang, Jiabin Wang, Haoran Shi, Na Zhou, Shanshan Li, Lan Ye, Wensheng Xiang, Xiangjing Wang, Yanyan Zhang
{"title":"Overexpression of the Wbl family regulator whiD<sub>sbh</sub> modulates secondary metabolite biosynthesis in Streptomyces.","authors":"Xuedong Zhang, Jiabin Wang, Haoran Shi, Na Zhou, Shanshan Li, Lan Ye, Wensheng Xiang, Xiangjing Wang, Yanyan Zhang","doi":"10.1007/s11274-025-04400-z","DOIUrl":"10.1007/s11274-025-04400-z","url":null,"abstract":"<p><p>Streptomyces species are prolific producers of a diverse array of bioactive secondary metabolites (SMs), which constitute approximately two-thirds of natural product-based pharmaceuticals with significant clinical, agricultural, and biotechnological applications. However, the regulatory mechanisms underlying the biosynthesis of these compounds remain poorly understood, impeding the development of high-yielding strains for industrial production. Herein, we investigated the role of the WhiB-like (Wbl) family transcriptional regulator, WhiD<sub>sbh</sub>, in modulating SM production in Streptomyces bingchenggensis BC04. Overexpression of whiD<sub>sbh</sub> in BC04 significantly suppressed milbemycin production by repressing the transcription of the milbemycin biosynthetic gene cluster via the ActK/R-KelR regulatory cascade. Comparative transcriptomic analysis between the whiD<sub>sbh</sub> overexpression strain and BC04 revealed that whiD<sub>sbh</sub> overexpression not only altered the expression of multiple other biosynthetic gene clusters but also impacted genes involved in central carbon metabolism, glutathione biosynthesis, and cofactor synthesis. Furthermore, cross-species genetic analysis demonstrated that whiD<sub>sbh</sub> overexpression enhanced actinorhodin production in Streptomyces coelicolor and avermectin production in Streptomyces avermitilis, while inhibiting the biosynthesis of nemadectin and guvermectin in Streptomyces cyaneogriseus ssp. noncyanogenus and Streptomyces caniferus, respectively. These results expanded our understanding of the regulatory networks controlling SM biosynthesis in Streptomyces and provided beneficial regulatory targets for developing strategies to optimize SM yield.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"176"},"PeriodicalIF":4.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yanxin Ye, Leilei Li, Yanyan Chen, Bingbing Li, Zhenshang Xu
{"title":"Molecular methods for rapid detection and identification of foodborne pathogenic bacteria.","authors":"Yanxin Ye, Leilei Li, Yanyan Chen, Bingbing Li, Zhenshang Xu","doi":"10.1007/s11274-025-04396-6","DOIUrl":"10.1007/s11274-025-04396-6","url":null,"abstract":"<p><p>Foodborne pathogenic bacteria are one of the main factors causing food safety issues. The rapid and accurate detection of pathogenic bacteria using molecular techniques is an effective and powerful strategy for preventing and controlling outbreaks of foodborne diseases, thereby ensuring food safety. This article summarizes the rapid and efficient molecular diagnostic techniques for detecting pathogenic bacteria, including polymerase chain reaction and its derivatives, isothermal amplification, DNA hybridization, genomic sequencing, and Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated (CRISPR/Cas)-based detection technique. Through a comparative analysis of the technical principles, advantages, and potential limitations of these diagnostic methods, as well as an outlook on the future development directions for molecular biological detection technology, which will provide a valuable reference for developing more accurate, convenient, and sensitive methods for foodborne pathogens detection, and will help better address the challenges posed by foodborne diseases, thereby ensuring public health and safety.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"175"},"PeriodicalIF":4.0,"publicationDate":"2025-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144080792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Guojun Wu, Chenyue Yin, Jie Zheng, Mengxi Wang, Dyaaaldin Abdalmegeed, Fengmin Zhang, Shengwei Sun, Sen Sun, Yuting Shao, Zhihong Xin
{"title":"Dynamic regulation of iturin production via reconstructing the quorum-sensing system ComQXPA in Bacillus subtilis.","authors":"Guojun Wu, Chenyue Yin, Jie Zheng, Mengxi Wang, Dyaaaldin Abdalmegeed, Fengmin Zhang, Shengwei Sun, Sen Sun, Yuting Shao, Zhihong Xin","doi":"10.1007/s11274-025-04390-y","DOIUrl":"10.1007/s11274-025-04390-y","url":null,"abstract":"<p><p>Pheromone ComX is a critical element of the quorum-sensing (QS) system in Bacillus subtilis. It activates the surfactin promoter (P<sub>srf</sub>) to initiate surfactin production in a cell-density-dependent manner. In this study, the natural promoter P<sub>itu</sub> of B. subtilis 1A751 WR-itu, a lipopeptide iturin mono-producing parent strain, was replaced by the constitutive promoter P<sub>43</sub>, QS P<sub>srf,</sub> and the mutated QS P<sub>M-srf</sub>, generating dynamic regulation systems to improve iturin production. HPLC analysis revealed that the P<sub>M-srf</sub> promoter-harbouring strain significantly enhanced iturin production to 409.33 ± 16.77 mg·L<sup>- 1</sup>, 2.15 times higher than the parent strain. Further identification by UPLC-HRESI-MS/MS and GC-MS indicated that the strain could produce four new C<sub>10</sub>-C<sub>13</sub> iturins. Moreover, the ComX degrading enzymes AprE or NprE were down-regulated by the CRISPR interference (CRISPRi) system, increasing iturin production to 526.46 ± 18.43 mg·L<sup>- 1</sup> and 416.99 ± 17.02 mg·L<sup>- 1</sup>, respectively. Interestingly, iturin production was further increased to 579.85 ± 19.83 mg·L<sup>- 1</sup> under simultaneous down-regulation of AprE and NprE, 3.05 times higher than the parent strain. The reconstructed ComQXPA QS system in B. subtilis combines the inhibitory of AprE and NprE to dynamically up and down-regulate the expression of iturin operon, providing an effective pipeline for regulating other bioactive molecules.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"173"},"PeriodicalIF":4.0,"publicationDate":"2025-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021652","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Role of ammonia-oxidising bacteria in the removal of odorous gases by the use of plastic recycling waste as a biofilter.","authors":"Eglė Marčiulaitienė, Jurgita Malaiškienė, Renata Boris, Jaunius Urbonavičius, Daiva Tauraitė, Saloua Biyada","doi":"10.1007/s11274-025-04392-w","DOIUrl":"10.1007/s11274-025-04392-w","url":null,"abstract":"<p><p>Ammonia gas has emerged as a major concern for many industrial facilities. With the same degree of hazard, plastic waste after mechanical processing is becoming a crucial challenge for many mechanical plastics recycling plants. In this respect, the present study explored the use of plastic waste obtained from mechanical recycling plants as an adsorbent to treat ammonia gas using a biofiltration device. The physical-chemical parameters of the adsorbent used, notably moisture, ash, organic matter, pH and elemental analysis were determined. Next-generation sequencing and scanning electron microscopy analyses were carried out to detect and identify the nature of bacterial communities in the biofilters used. The results of the chemical analysis showed that the adsorbent used is appropriate for the development of the microorganisms. X-ray fluorescence analysis showed that the adsorbent belongs to the silico-aluminous materials, proving its effectiveness as an adsorbent. The efficiency of ammonia removal was over 93% using the biofilter. Next-generation sequencing revealed that bacteria belonging to ammonia oxidizers such as Nitrosomonas and Nitrosospira are among the most abundant bacteria after the biofiltration process, which explains the efficiency of ammonia removal. Scanning electron microscopy confirmed the development of a biofilm on the surface of the biofilter after filtration. Ultimately, these results offer a promising novel approach for valorisation of the plastic waste.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"172"},"PeriodicalIF":4.0,"publicationDate":"2025-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abdul Basith Akbar Aly, Balamurugan Shanmugaraj, Sathishkumar Ramalingam
{"title":"Industrial applications of Phanerochaete chrysosporium lignin-degrading enzymes: current status, production challenges, and future directions.","authors":"Abdul Basith Akbar Aly, Balamurugan Shanmugaraj, Sathishkumar Ramalingam","doi":"10.1007/s11274-025-04388-6","DOIUrl":"10.1007/s11274-025-04388-6","url":null,"abstract":"<p><p>Phanerochaete chrysosporium (Pc) is a white-rot fungus recognized for its highly efficient lignin-degrading enzymes (LDEs), including lignin peroxidase (LiP), manganese peroxidase (MnP), and laccase. These oxidative enzymes possess transformative capabilities across multiple industrial applications, such as biopulping, biofuel production, bioremediation and for the treatment of industrial wastewater. However, the commercial use of these enzymes is limited due to time-consuming scale-up procedures in native hosts, instability in industrial environments, and high production costs. The recent developments in recombinant expression systems, particularly those employing microbial and plant platforms provide promising opportunities to enhance enzyme yield, stability, and reduce the cost. Despite these advancements, significant challenges remain, which include the formation of inclusion bodies, the need for nutrient and co-factor supplementation, and the development of effective purification strategies. Modern advancements in protein engineering, such as site-directed mutation and in silico approaches, may hold significant promise in addressing the challenges posed by pH optimization, which is prominent in wild-type enzymes. This review examines the current industrial applications of P. chrysosporium ligninolytic enzymes, highlights production bottlenecks in several hosts, and discusses the strategies to enhance their commercial viability of these enzymes.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"171"},"PeriodicalIF":4.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144029694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yingjing Bi, Yun Han, Yanlan Bi, Linshang Zhang, Shangde Sun
{"title":"Bioconversion of sterol esters to steroid intermediates through Mycobacterium sp. fermentation.","authors":"Yingjing Bi, Yun Han, Yanlan Bi, Linshang Zhang, Shangde Sun","doi":"10.1007/s11274-025-04370-2","DOIUrl":"10.1007/s11274-025-04370-2","url":null,"abstract":"<p><p>Sterol esters are naturally present in the by-product of edible oil processing, which is generally converted to sterols through saponification. Steroid intermediates play a crucial role in the production of pharmaceuticals, and these intermediates are predominantly synthesized via fermentation of sterol. This research explored the direct conversion of sterol esters into steroid intermediates using Mycobacterium sp. as a fermentation agent. The results demonstrated the successful identification of four steroid intermediates: androstenedione, 1,4-androstadienedione, 22-hydroxy-23,24-bisnorchol-4-ene-3-one, and 22-hydroxy-23,24-bisnorchol-1,4-dien-3-one, their individual intermediate concentrations were as follows: 144.2, 176.2, 30.8, 53.6 mg/L, with a total yield of 404.8 mg/L and a conversion rate of 29.5%. The optimized fermentation conditions included soybean oil at 3%, an initial pH of 7.0, a nitrogen source of 4.5 g/L, and hydroxypropyl-β-cyclodextrin of 15.0 g/L. Proteomic analysis revealed that sterol esters conversion pathway mirrors that of sterol, with an additional hydrolysis process. This work significantly expands our understanding of steroid intermediates production and offers valuable insights for the bioproduction industry.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"169"},"PeriodicalIF":4.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143998337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Recent advances in yeast and bacteria co-cultivation for bioprocess applications.","authors":"Anne Kathrine Clausen, Stefan Junne","doi":"10.1007/s11274-025-04385-9","DOIUrl":"10.1007/s11274-025-04385-9","url":null,"abstract":"<p><p>Yeast and bacteria co-cultures can be found in nature and have multiple advantages that can be exploited, nowadays also in a controlled bioproduction environment. Various types of co-cultivation have been used for food applications such as production of flavor compounds in dairy products and alcoholic beverages. Co-cultures can broaden the substrate spectrum for microbial food and feed production, they can increase productivity and efficiency, and the nutritional value. Workflows have been developed from plate to bioreactor scale to increase reproducibility and optimize benefits of individual co-cultivation strategies. Nonetheless, certain limitations need to be overcome for industrial application. Many interactions of microbes, in particular in suspension cultures, are not sufficiently understood or even explored. While more possibilities arose from on-line monitoring of individual populations or even single cells, off-line measurement techniques are still typically applied in order to assess growth and product formation. Promising advances have been achieved, however, by methods for single-cell at-line and on-line analysis in co-cultures which are accounted for to emphasize the current opportunities and challenges in monitoring and controlling co-cultures. This review aims to summarize the recent advances with a particular focus on cultivation procedures and process analysis in bacteria, yeast and bacteria-yeast co-cultures. The implementation of suitable monitoring methods to enable (remote) control and contribute to quality assurance will accelerate the development and optimization of industrial co-culture bioprocesses. This will support transferability and process standardization across world regions adding to the advancement of bioproduction. The applicability of some relevant technology is, however, in its infancy.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"170"},"PeriodicalIF":4.0,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Amir Mahgoub Awadelkareem, Arif Jamal Siddiqui, Mitesh Patel, Syed Amir Ashraf, Insaf Bahrini, Yazeed Albulaihed, Mohammad Saquib Ashraf, Shahida Banu Shamsuddeen, Mohd Adnan
{"title":"Curtobacterium oceanosedimentum-derived biosurfactants as eco-friendly biocontrol agent with broad-spectrum antibacterial and antifungal properties for sustainable applications.","authors":"Amir Mahgoub Awadelkareem, Arif Jamal Siddiqui, Mitesh Patel, Syed Amir Ashraf, Insaf Bahrini, Yazeed Albulaihed, Mohammad Saquib Ashraf, Shahida Banu Shamsuddeen, Mohd Adnan","doi":"10.1007/s11274-025-04382-y","DOIUrl":"10.1007/s11274-025-04382-y","url":null,"abstract":"<p><p>Biosurfactants are eco-friendly surface-active biomolecules with diverse applications in biotechnology, agriculture, and healthcare. This study identifies Curtobacterium oceanosedimentum (C. oceanosedimentum) as a novel biosurfactants producer with potent biocontrol potential against bacterial and fungal pathogens. The present study contributes to ongoing efforts in biosurfactant research by presenting the functional attributes of C. oceanosedimentum-derived biosurfactants (COBS), characterized as a complex glycolipopeptide or lipoglycoprotein containing lipid, peptide, and carbohydrate moieties. Preliminary screening through oil spreading, drop collapse, and hemolytic assays confirmed biosurfactants production, while emulsification index assays demonstrated strong emulsifying activity, particularly with olive oil (60%), indicating broad applicability. Advanced characterization using HPTLC, FTIR, and HR-LCMS revealed the presence of amino acids, peptides, and fatty acid amides, further validating its structural complexity. Antimicrobial assays demonstrated superior efficacy of COBS, exhibiting significant antibacterial activity against Chromobacterium violaceum (24 mm) and Acinetobacter calcoaceticus (22 mm), alongside pronounced antifungal effects against Candida albicans, Fusarium proliferatum, and Penicillium purpurogenum. These findings establish COBS as a unique biosurfactants with dual antibacterial and antifungal properties, distinguishing it from previously reported biosurfactants. Its eco-friendly nature and broad-spectrum antimicrobial potential make it a promising candidate for sustainable applications in biocontrol, healthcare, and environmental remediation. Further studies on large-scale production and stability optimization will be essential for commercial applications.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"168"},"PeriodicalIF":4.0,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144021228","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gutha Venkata Ramesh, Jaspal Kaur, Deepak Singla, Parveen Chhuneja, Anurag Saharan, O P Gangwar, Ritu Bala, Reyazul Rouf Mir, Parminder Singh Tak
{"title":"Use of Field pathogenomics approach for Puccinia striiformis f. sp. tritici race identification and phylogenomic delineation in North India.","authors":"Gutha Venkata Ramesh, Jaspal Kaur, Deepak Singla, Parveen Chhuneja, Anurag Saharan, O P Gangwar, Ritu Bala, Reyazul Rouf Mir, Parminder Singh Tak","doi":"10.1007/s11274-025-04391-x","DOIUrl":"10.1007/s11274-025-04391-x","url":null,"abstract":"<p><p>Stripe rust of wheat caused by Puccinia striiformis f. sp. tritici (Pst) is among the top 10 most important fungal phytopathogens in the world, threatening the global wheat production. Continuous pathogen evolution and air borne nature of the pathogen, increased the importance of pathogen population structure studies in case of wheat-Puccinia pathosystem. The current study aimed to characterize the Pst pathotype distribution in North India. A total of 61 stripe rust infected samples were collected from sub-mountainous areas of Punjab (50), Himachal Pradesh (HP) (8) and Jammu & Kashmir (J&K) (3) during 2021-24. Virulence profiling results of 58 samples using Indian stripe rust differentials revealed the prevalence of five pathotypes (238S119, 110S119, 46S119, 47S103 and 6S0) in North India. Among which 238S119 was the most predominant (51.72%) one followed by 110S119 (27.59%) and 46S119 (17.24%). No virulence was found against stripe rust resistant Yr5, Yr10, Yr15, Yr24 and YrSP genes indicating these genes are the most effective resistant genes in North India providing complete resistance till date. A total of 23 field infected samples were used for transcriptome analysis (RNA-seq) generating an average of 31.77 million raw reads. The clustered assembly generated mean assembly size of ∼ 45.10 Mb containing 7,587-2,49,571 contigs with 47.99% GC content, N50 value of 749.87 with 7.48-94.90% BUSCO score. Phylogenomic analysis of farmer's field samples revealed the existence of three different Pst lineages in North India i.e., Punjab lineage, Himachal lineage and Kashmir lineage, where Himachal lineage exhibited highest genetic diversity. A total of three (3) SSR and 14 KASP markers developed in previous studies were tested on farmer's field isolates for pathotype identification. Eight KASP markers showed reproducible polymorphism for pathotype specific detection. Correlating the KASP assay with results of virulence profiling revealed that these markers have the ability to detect the virulence change from five established pathotypes under field conditions. The findings of present study provided better understanding in Pst pathotype distribution in North India and pathotype detection using consistent polymorphic markers along with deciphering the behaviour of Pst under field conditions and deducing their evolutionary relationship in North India.</p>","PeriodicalId":23703,"journal":{"name":"World journal of microbiology & biotechnology","volume":"41 5","pages":"166"},"PeriodicalIF":4.0,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144037260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}