{"entity": "researcher", "timestamp": "2026-07-12T09:01:03.193Z", "family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "affiliations": ["Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciencesgrid.6341.0, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72"}}, "publications": [{"entity": "publication", "iuid": "04e23b32f608475991bc284705d024a8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04e23b32f608475991bc284705d024a8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04e23b32f608475991bc284705d024a8"}}, "title": "Transcriptomic and functional analyses on a Botrytis cinerea multidrug-resistant (MDR) strain provides new insights into the potential molecular mechanisms of MDR and fitness.", "authors": [{"family": "Sofianos", "given": "Georgios", "initials": "G", "orcid": "0009-0002-2678-7158", "researcher": {"href": "https://publications.scilifelab.se/researcher/6caa00e6738e4dfaa70832c456ddc6e6.json"}}, {"family": "Piombo", "given": "Edoardo", "initials": "E", "orcid": "0000-0003-2830-1967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff26b84d14643f3ae4e45a23cd2107b.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Karlsson", "given": "Magnus", "initials": "M", "orcid": "0000-0001-6098-138X", "researcher": {"href": "https://publications.scilifelab.se/researcher/34e4b8bad4e34912b011f2ead759b422.json"}}, {"family": "Karaoglanidis", "given": "George", "initials": "G", "orcid": "0000-0002-7413-2052", "researcher": {"href": "https://publications.scilifelab.se/researcher/477fa9557e904366aabb7d7b6b53e4d6.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2024-09-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "volume": "25", "issue": "9", "pages": "e70004", "issn-l": null}, "abstract": "Botrytis cinerea is a notorious pathogen causing pre- and post-harvest spoilage in many economically important crops. Excessive application of site-specific fungicides to control the pathogen has led to the selection of strains possessing target site alterations associated with resistance to these fungicides and/or strains overexpressing efflux transporters associated with multidrug resistance (MDR). MDR in B. cinerea has been correlated with the overexpression of atrB and mfsM2, encoding an ATP-binding cassette (ABC) and a major facilitator superfamily (MFS) transporter, respectively. However, it remains unknown whether other transporters may also contribute to the MDR phenotype. In the current study, the transcriptome of a B. cinerea multidrug-resistant (MDR) field strain was analysed upon exposure to the fungicide fludioxonil, and compared to the B05.10 reference strain. The transcriptome of this field strain displayed significant differences as compared to B05.10, including genes involved in sugar membrane transport, toxin production and virulence. Among the induced genes in the field strain, even before exposure to fludioxonil, were several putatively encoding ABC and MFS transmembrane transporters. Overexpression of a highly induced MFS transporter gene in the B05.10 strain led to an increased tolerance to the fungicides fluopyram and boscalid, indicating an involvement in efflux transport of these compounds. Overall, the data from this study give insights towards better understanding the molecular mechanisms involved in MDR and fitness cost, contributing to the development of more efficient control strategies against this pathogen.", "doi": "10.1111/mpp.70004", "pmid": "39244735", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11380696"}], "notes": [], "created": "2024-10-21T11:12:58.472Z", "modified": "2024-10-21T11:13:08.829Z"}, {"entity": "publication", "iuid": "656b4a9c8ec1478e9c2baa2806ac8cb5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/656b4a9c8ec1478e9c2baa2806ac8cb5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/656b4a9c8ec1478e9c2baa2806ac8cb5"}}, "title": "Verticillium longisporum phospholipase VlsPLA2 is a virulence factor that targets host nuclei and modulates plant immunity.", "authors": [{"family": "Rafiei", "given": "Vahideh", "initials": "V", "orcid": "0000-0003-0021-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c453e43d63594937aa2efd03e37bee1e.json"}}, {"family": "V\u00e9l\u00ebz", "given": "Heriberto", "initials": "H", "orcid": "0000-0003-3146-0555", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9a3146e50264c32b9074894e32892a0.json"}}, {"family": "Piombo", "given": "Edoardo", "initials": "E", "orcid": "0000-0003-2830-1967", "researcher": {"href": "https://publications.scilifelab.se/researcher/4ff26b84d14643f3ae4e45a23cd2107b.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2023-09-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "issn-l": null, "volume": "24", "issue": "9", "pages": "1078-1092"}, "abstract": "Phospholipase A2 (PLA2 ) is a lipolytic enzyme that hydrolyses phospholipids in the cell membrane. In the present study, we investigated the role of secreted PLA2 (VlsPLA2 ) in Verticillium longisporum, a fungal phytopathogen that mostly infects plants belonging to the Brassicaceae family, causing severe annual yield loss worldwide. Expression of the VlsPLA2 gene, which encodes active PLA2 , is highly induced during the interaction of the fungus with the host plant Brassica napus. Heterologous expression of VlsPLA2 in Nicotiana benthamiana resulted in increased synthesis of certain phospholipids compared to plants in which enzymatically inactive PLA2 was expressed (VlsPLA2 \u0394CD ). Moreover, VlsPLA2 suppresses the hypersensitive response triggered by the Cf4/Avr4 complex, thereby suppressing the chitin-induced reactive oxygen species burst. VlsPLA2 -overexpressing V. longisporum strains showed increased virulence in Arabidopsis plants, and transcriptomic analysis of this fungal strain revealed that the induction of the gene contributed to increased virulence. VlsPLA2 was initially localized to the host nucleus and then translocated to the chloroplasts at later time points. In addition, VlsPLA2 bound to the vesicle-associated membrane protein A (VAMPA) and was transported to the nuclear membrane. In the nucleus, VlsPLA2 caused major alterations in the expression levels of genes encoding transcription factors and subtilisin-like proteases, which play a role in plant immunity. In conclusion, our study showed that VlsPLA2 acts as a virulence factor, possibly by hydrolysing host nuclear envelope phospholipids, which, through a signal transduction cascade, may suppress basal plant immune responses.", "doi": "10.1111/mpp.13352", "pmid": "37171182", "labels": {"Global Proteomics and Proteogenomics": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10423322"}], "notes": [], "created": "2023-08-30T07:09:49.551Z", "modified": "2025-10-17T13:03:13.547Z"}, {"entity": "publication", "iuid": "0e48aa34962e4255a1555d55c0bb4a0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e48aa34962e4255a1555d55c0bb4a0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e48aa34962e4255a1555d55c0bb4a0c"}}, "title": "Comparative Small RNA and Degradome Sequencing Provides Insights into Antagonistic Interactions in the Biocontrol Fungus Clonostachys rosea.", "authors": [{"family": "Piombo", "given": "Edoardo", "initials": "E"}, {"family": "Vetukuri", "given": "Ramesh Raju", "initials": "RR", "orcid": "0000-0001-7129-5326", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbb5fb93506a4b3a8faacc38397a741c.json"}}, {"family": "Sundararajan", "given": "Poorva", "initials": "P"}, {"family": "Kushwaha", "given": "Sandeep", "initials": "S"}, {"family": "Funck Jensen", "given": "Dan", "initials": "D"}, {"family": "Karlsson", "given": "Magnus", "initials": "M"}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}], "type": "journal article", "published": "2022-07-12", "journal": {"title": "Appl. Environ. Microbiol.", "issn": "1098-5336", "volume": "88", "issue": "13", "pages": "e0064322", "issn-l": "0099-2240"}, "abstract": "Necrotrophic mycoparasitism is an intricate process involving recognition, physical mycelial contact, and killing of host fungi (mycohosts). During such interactions, mycoparasites undergo a complex developmental process involving massive regulatory changes of gene expression to produce a range of chemical compounds and proteins that contribute to the parasitism of the mycohosts. Small RNAs (sRNAs) are vital components of posttranscriptional gene regulation, although their role in gene expression regulation during mycoparasitisms remain understudied. Here, we investigated the role of sRNA-mediated gene regulation in mycoparasitism by performing sRNA and degradome tag sequencing of the mycoparasitic fungus Clonostachys rosea interacting with the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum at two time points. The majority of differentially expressed sRNAs were downregulated during the interactions with the mycohosts compared to a C. rosea self-interaction control, thus allowing desuppression (upregulation) of mycohost-responsive genes. Degradome analysis showed a positive correlation between high degradome counts and antisense sRNA mapping and led to the identification of 201 sRNA-mediated potential gene targets for 282 differentially expressed sRNAs. Analysis of sRNA potential gene targets revealed that the regulation of genes coding for membrane proteins was a common response against both mycohosts. The regulation of genes involved in oxidative stress tolerance and cellular metabolic and biosynthetic processes was exclusive against F. graminearum, highlighting common and mycohost-specific gene regulation of C. rosea. By combining these results with transcriptome data collected during a previous study, we expand the understanding of the role of sRNA in regulating interspecific fungal interactions and mycoparasitism. IMPORTANCE Small RNAs (sRNAs) are emerging as key players in pathogenic and mutualistic fungus-plant interactions; however, their role in fungus-fungus interactions remains elusive. In this study, we employed the necrotrophic mycoparasite Clonostachys rosea and the plant-pathogenic mycohosts Botrytis cinerea and Fusarium graminearum and investigated the sRNA-mediated gene regulation in mycoparasitic interactions. The combined approach of sRNA and degradome tag sequencing identified 201 sRNA-mediated putative gene targets for 282 differentially expressed sRNAs, highlighting the role of sRNA-mediated regulation of mycoparasitism in C. rosea. We also identified 36 known and 13 novel microRNAs (miRNAs) and their potential gene targets at the endogenous level and at a cross-species level in B. cinerea and F. graminearum, indicating a role of cross-species RNA interference (RNAi) in mycoparasitism, representing a novel mechanism in biocontrol interactions. Furthermore, we showed that C. rosea adapts its transcriptional response, and thereby its interaction mechanisms, based on the interaction stages and identity of the mycohost.", "doi": "10.1128/aem.00643-22", "pmid": "35695572", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9275246"}], "notes": [], "created": "2022-11-09T15:52:26.203Z", "modified": "2024-01-16T13:48:35.815Z"}, {"entity": "publication", "iuid": "c7e444c1c6864297b04b31cb10b66b98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c7e444c1c6864297b04b31cb10b66b98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c7e444c1c6864297b04b31cb10b66b98"}}, "title": "A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host \u03b2-pinene monoterpene.", "authors": [{"family": "Rafiei", "given": "Vahideh", "initials": "V", "orcid": "0000-0003-0021-9734", "researcher": {"href": "https://publications.scilifelab.se/researcher/c453e43d63594937aa2efd03e37bee1e.json"}}, {"family": "Ruffino", "given": "Alessandra", "initials": "A", "orcid": "0000-0002-7039-2957", "researcher": {"href": "https://publications.scilifelab.se/researcher/acfbbc82f59b4fbc8a9ea0e6b8515e51.json"}}, {"family": "Persson Hod\u00e9n", "given": "Kristian", "initials": "K", "orcid": "0000-0003-0354-0662", "researcher": {"href": "https://publications.scilifelab.se/researcher/e8b41e8e41574ee6bcb55df3b0d145d9.json"}}, {"family": "Tornkvist", "given": "Anna", "initials": "A", "orcid": "0000-0002-6215-6727", "researcher": {"href": "https://publications.scilifelab.se/researcher/d36e5404f2a841019aa1aeac9c8c7ec9.json"}}, {"family": "Mozuraitis", "given": "Raimondas", "initials": "R", "orcid": "0000-0002-1719-2294", "researcher": {"href": "https://publications.scilifelab.se/researcher/213ecb5deb7d4d06901f461424d964cf.json"}}, {"family": "Dubey", "given": "Mukesh", "initials": "M", "orcid": "0000-0001-7393-366X", "researcher": {"href": "https://publications.scilifelab.se/researcher/da047e9540e344cc93b54a96d5c82b72.json"}}, {"family": "Tzelepis", "given": "Georgios", "initials": "G", "orcid": "0000-0001-6144-2185", "researcher": {"href": "https://publications.scilifelab.se/researcher/60b2114dba0640d3aeecba0c4e729ce0.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Mol. Plant Pathol.", "issn": "1364-3703", "volume": "23", "issue": "2", "pages": "291-303", "issn-l": null}, "abstract": "Terpenes constitute a major part of secondary metabolites secreted by plants in the rhizosphere. However, their specific functions in fungal-plant interactions have not been investigated thoroughly. In this study we investigated the role of monoterpenes in interactions between oilseed rape (Brassica napus) and the soilborne pathogen Verticillium longisporum. We identified seven monoterpenes produced by B. napus, and production of \u03b1-pinene, \u03b2-pinene, 3-carene, and camphene was significantly increased upon fungal infection. Among them, \u03b2-pinene was chosen for further analysis. Transcriptome analysis of V. longisporum on exposure to \u03b2-pinene resulted in identification of two highly expressed pleotropic drug transporters paralog genes named VlAbcG1a and VlAbcG1b. Overexpression of VlAbcG1a in Saccharomyces cerevisiae increased tolerance to \u03b2-pinene, while deletion of the VlAbcG1a homologous gene in Verticillium dahliae resulted in mutants with increased sensitivity to certain monoterpenes. Furthermore, the VlAbcG1a overexpression strain displayed an increased tolerance to \u03b2-pinene and increased virulence in tomato plants. Data from this study give new insights into the roles of terpenes in plant-fungal pathogen interactions and the mechanisms fungi deploy to cope with the toxicity of these secondary metabolites.", "doi": "10.1111/mpp.13162", "pmid": "34825755", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC8743018"}], "notes": [], "created": "2022-11-29T09:34:58.011Z", "modified": "2022-11-29T09:34:58.198Z"}]}