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Mukesh Dubey

Mukesh Dubey
Associate Professor (Docent) in Plant Pathology at Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden


We are interested in fungus-fungus and fungus-plant interactions for sustainable plant production. We exploit biological properties of mycoparasitic fungal species such as those belong to the genus Trichoderma and Clonostachys for sustainable plant disease control and plant health promotion. We use state-of-art technique to understand underlying mechanisms of parasitic fungus-fungus and beneficial fungus-plant interactions in relation to biological control of fungal plant diseases.

Our work is currently focussed on the following projects:

-Mycotoxins and food safety and security in Rwanda: Understanding the biology and epidemiology of maize ear rots for sustainable maize production.

-RNAi based technologies to control plant diseases.

-Small-RNAS in mycoparasitic interactions.

-Fungus-fungus interactions in relation to biolocical control of plant diseases.

-Harnessing soil–microbe-plant interactions for sustainable wheat production.

-Fungal secretome, secondary metabolome including mycotoxins.





-PhD students

-Master Students

-Bachelor students

Selected publications

Peer-reviewed publications: 2012-till date

Piombo E, Kelbessa BG, Sundararajan P, Whisson SC, Vetukuri RR and Dubey M (2023). RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents. Frontiers in Microbiology. 14:1076522. doi: 10.3389/fmicb.2023.1076522.

Kälin C, Kolodinska Brantestam A, Arvidsson A-K, Dubey M, Elfstrand M and Karlsson M (2023). Evaluation of pea genotype PI180693 partial resistance towards aphanomyces root rot in commercial pea breeding. Frontiers in Plant Science 14:1114408. doi: 10.3389/fpls.2023.1114408

Piombo E, Guaschino M, Jensen DF, Karlsson M and Dubey M (2023).  Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes. Frontiers in Microbiology, 14:1112673. doi: 10.3389/fmicb.2023.1112673.                        

Kelbessa BG, Dubey M, Catara V, Ghadamgahi F, Ortiz R, Vetukuri RV (2022). Potential of plant growth-promoting rhizobacteria to improve crop productivity and adaptation to a changing climate CABI Reviews,  

Edoardo Piombo, Micol Guaschino, Dan Funck Jensen, Magnus Karlsson and Mukesh Dubey (2023). Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes (2023). Frontiers in Microbiology, 14:1112673.
doi: 10.3389/fmicb.2023.1112673.

Bekele Gelena Kelbessa, Mukesh Dubey, Vittoria Catara, Farideh Ghadamgahi, Rodomiro Ortiz, and Ramesh Raju Vetukuri (2023). Potential of plant growth-promoting rhizobacteria to improve crop productivity and adaptation to a changing climate. CABI Reviews,

Carol Kälin, Anna Berlin, Agnese Kolodinska Brantestam, Mukesh Dubey, Anna-Kerstin Arvidsson, Paul Riesinger, Malin Elfstrand, and Magnus Karlsson (2022). Genetic diversity of the pea root pathogen Aphanomyces euteiches in Europe. Plant Pathology, 2022, 1570-1578.

Piombo E, Vetukuri RR, Sundararajan P, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M (2022). Comparative small RNA and degradome sequencing provide new insights into antagonistic interactions in the biocontrol fungus Clonostachys rosea. Applied and Environmental Microbiology, 10.1128/aem.00643-22. 

Beatriz Gomez-Munoz, Aikaterini Efthymiou, Mukesh Dubey, Jonathan Sølve,Mette Nicolaisen, Dan F. Jensen, Ole Nybroe, John Larsen )2022). Cellulose amendment promotes P solubilization by Penicillium aculeatum in non-sterilized soil. Fungal Biology, 126 (2022) 356e365.

Vahideh Rafiei, Alessandra Ruffino, Kristian Persson Hodén, Anna Tornkvist, Raimondas Mozuraitis, Mukesh Dubey, and Georgios Tzelepis (2022). A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene. Molecular Plant Pathology,  23, 291–303. h t t p s : //d o i .org/10.1111/mpp.13162.

Edoardo Piombo, Ramesh Raju Vetukuri, Anders Broberg, Pruthvi B. Kalyandurg, Sandeep Kushwaha, Dan Funck Jensen, Magnus Karlsson, and Mukesh Dubey (2021). The role of Dicer-dependent RNA interference in regulating mycoparasitic interactions. Microbiology Spectrum, 9: e01099-21.

Ramesh R. Vetukuri, Mukesh Dubey, Pruthvi B. Kalyandurg, Anders S. Carlsson, Stephen C. Whisson and Rodomiro Ortiz (2021). Spray-induced gene silencing: an innovative strategy for plant trait improvement and disease control. Crop Breeding and Applied Biotechnology, 21(S): e387921S11.

Kalyandurg PB, Sundararajan P, Dubey M, Ghadamgahi F, Zahid AM, Whisson SC, Vetukuri RR (2021). Spray-induced gene silencing as a potential tool to control potato late blight disease. Phytopathology, In Press.

Stenberg JA, Sundh I, Becher PG, Björkman C, Dubey M, Egan PA, Friberg H, Gil JF, Jensen DF, Jonsson M, Karlsson M, Khalil S, Ninkovic V, Rehermann G, Vetukuri RR, Viketoft M (2021). When is it biological control? A framework of definitions, mechanisms, and classifications. Journal of Pest Science. 10.1007/s10340-021-01354-7

Amira MB, Faize M, Karlsson M, Dubey M, Frąc M, Panek J, Fumanal B, Gousset-Dupont A, Julien J-L, Chaar H, Auguin D, Mom R, Label P, Venisse J-S (2021). Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations. Biomolecules, 11(2):338.

Mukesh Dubey, Dan Funck Jensen and Magnus karlsson (2020) Functional characterization of the AGL1 aegerolysin in the mycoparasitic fungus Trichoderma atroviride reveals a role in conidiation and antagonism. Molecular Genetics and Genomics. 296(1):131-140.

Martin Broberg#, Mukesh Dubey#, Mudassir Iqbal, Mikael Gudmundssson, Katarina Ihrmark, Hans-Josef Schroers, Dan Funck Jensen, Mikael Brandström, Durling and Magnus Karlsson (2020) Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota,
Hypocreales). Evolutionary Applications. DOI: 10.1111/eva.13134. # joint first author.

Rajiv Chaudhary, Karl Lundén, Kerstin Dalman, Mukesh Dubey,
Miguel Nemesio‑Gorriz, Bo Karlsson, Jan Stenlid1 & Malin Elfstrand (2020) Combining transcriptomics and genetic linkage based information to identify
candidate genes associated with Heterobasidion‑resistance in Norway spruce. Scientific Reports, 10: 12711.

Iqbal M, Broberg M, Haarith D, Broberg A, Bushley KE, Viketoft M, Jensen DF, Dubey M and Karlsson M. (2020) Natural variation of root lesion nematode antagonism in the biocontrol fungus Clonostachys rosea and identification of biocontrol factors through genome-wide association mapping. Evolutionary Applications. 13;9:2264-2283.

Dubey M, Vélëz H, Broberg A Jensen DF and Karlsson M (2020) LysM proteins regulate fungal development and contribute to hyphal protection and biocontrol traits in Clonostachys rosea. Frontiers in Microbiology, 11, 679.

Iqbal M, Dubey M, Broberg A, Viketoft M, Jensen DF and Karlsson M (2019). Deletion of the Non-Ribosomal Peptide Synthetase Gene nps1 in the Fungus Clonostachys rosea Attenuates Antagonism and Biocontrol of Plant Pathogenic Fusarium and Nematodes. Phytopathology, 109(10):1698-1709.

Martin Broberg, Mukesh Dubey, Man-Hong Sun, Katarina Ihrmark, Hans-Josef Schroers, Shi-Dong Li, Dan Funck Jensen, Mikael Brandström Durling, Magnus Karlsson (2018). Out in the cold: Identification of genomic regions associated with cold tolerance in the biocontrol fungus Clonostachys rosea through genome-wide association mapping. Frontiers in Microbiology 9:2844.

Mudassir Iqbal, Mukesh Dubey, Mikael Gudmundsson, Maria Viketoft, Dan Funck Jensen, Magnus Karlsson (2018). Comparative evolutionary histories of fungal proteases reveal gene gains in the mycoparasitic and nematode-parasitic fungus Clonostachys rosea. BMC Evolutionary Biology 18:171.  

Lea Atanasova, Mukesh Dubey, Marica Grujić, Mikael Gudmundsson, Cindy Lorenz, Mats Sandgren, Christian P. Kubicek, Dan Funck Jensen and Magnus Karlsson (2018) Evolution and functional characterization of pectate lyase PEL12, a member of a highly expanded Clonostachys rosea polysaccharide lyase 1 family. BMC Microbiology 18:178.

Umma Fatema, Anders Broberg, Dan Funck Jensen, Magnus Karlsson and Mukesh Dubey (2018). Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea. Scientific Reports, 8:15009.

Ruth Schmidt, Mikael B. Durling, Victor de Jager, Riya C. Menezes,
Erik Nordkvist, Aleˇs Svatoˇs, Mukesh Dubey, Lukas Lauterbach, Jeroen
S. Dickschat, Magnus Karlsson and Paolina Garbeva (2018). Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum. FEMS Microbiology Ecology, 94, 2018, fiy078.

Kristiina Nygren#, Mukesh Dubey#, Antonio Zapparata, Mudassir Iqbal, Georgios D. Tzelepis, Mikael Brandström Durling, Dan Funck Jensen, Magnus Karlsson (2018). The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey. Evolutionary Applications, 11:931-949. #joint first author.

Iqbal M, Dubey M, McEwan K, Menzel U, Andersson Franko M, Viketoft M, Funck Jensen D, Karlsson M. (2018). Evaluation of Clonostachys rosea for control of plant-parasitic nematodes in soil and in roots of carrot and wheat. Phytopathology, 108(1):52-59.

Dubey MK, Jensen DF and Karlsson M (2016). The ABC transporter ABCG29 is involved in H2O2 tolerance and biocontrol traits in the fungus Clonostachys rosea. Molecular Genetics and Genomics 291, 677–686.

Kamou NN, Dubey M, Tzelepis G, Menexes G, Papadakis EN, Karlsson M, Lagopodi AL, and Jensen DF (2016). Investigating the compatibility of the biocontrol agent Clonostachys rosea IK726 with prodigiosin‑producing Serratia rubidaea S55 and henazine‑producing Pseudomonas chlororaphis ToZa7. Archives of Microbiology, 198, 369–377.

Tzelepis G, Dubey, MK, Jensen DF, Karlsson M (2015). Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea. Microbiology 61,1407-1419.

Karlsson M, Durling MB, Choi J, Kosawang C, Lackner G, Tzelepis GD, Nygren K, Dubey MK, Kamou N, Levasseur A, Zapparata A, Wang J, Amby DB, Jensen B, Sarrocco S, Panteris E, Lagopodi AL, Pöggeler S, Vannacci G, Collinge DB, Hoffmeister D, Henrissat B, Lee YH, Jensen DF (2015). Insights on the Evolution of mycoparasitism from the genome of Clonostachys rosea. Genome Biology and Evolution 7, 465-480.

Tzelepis, G., Akira Hosomi, A., Hossain, T.J., Hirayama, H., Dubey, M., Jensen, D.F., Suzuki, T., Karlsson, M. (2014). Endo-b-N-acetylglucosamidases (ENGases) in the fungus Trichoderma atroviride: Possible involvement of the filamentous fungi-specific cytosolic ENGase in the ERAD process. Biochemical and Biophysical Research Communications 449, 256-261.

Dubey, M.K., Jensen, D.F. and Karlsson M. (2014). Involvement of an ATP-binding cassette pleotropic drug transporter in xenobiotic tolerance and antagonism in fungal biocontrol agent Clonostachys rosea IK726. Molecular Plant-Microbe Interaction.

Dubey, M.K., Jensen, D.F. and Karlsson M. (2014). The hydrophobins are required for conidial hydrophobicity and plant root colonization in fungal biocontrol agent Clonostachys rosea. BMC Microbiology, 14, 18.

Dubey, M.K., Broberg, A., Jensen, D.F. and Karlsson M. (2013). Role of the methylcitrate cycle in growth, antagonism and induction of systemic defence responses in the fungal biocontrol agent Trichoderma atroviride. Microbiology, 159, 2492-2500.

Dubey, M.K., Broberg, A., Sooriyaarachchi, S., Ubhayasekera, W., Jensen, D.F. and Karlsson M. (2013). The glyoxylate cycle is involved in pleotropic phenotypes, antagonism and induction of plant defence responses in the fungal biocontrol agent Trichoderma atroviride. Fungal Genetics and Biology, 58-59, 33-41.

Dubey, M.K., Ubhayasekera, W., Sandgren, M., Jensen, D.F. and Karlsson M. (2012): Disruption of the Eng18B ENGase gene in the fungal biocontrol agent Trichoderma atroviride affects growth, conidiation and antagonistic ability. PLoS ONE 7(5): e36152.

Book Chapters

Piombo, E., Dubey, M. (July 2022). Computational Analysis of HTS Data and Its Application in Plant Pathology. In: Luchi, N. (eds) Plant Pathology. Methods in Molecular Biology, vol 2536. Humana, New York, NY.

Jensen DF, Dubey M, Jensen B, and Karlsson, M (November 2021). Clonostachys rosea for the control of plant diseases, in Microbial bioprotectants for plant disease management (BDS Publishing). In: Köhl, J. and Ravensberg, W. (ed.), Microbial bioprotectants for plant disease management, Burleigh Dodds Science Publishing


Researcher at the Department of Forest Mycology and Plant Pathology; Division of Plant Pathology
Telephone: +4618-671540
Postal address:
Skoglig mykologi och växtpatologi , Box 7026
750 07 UPPSALA
Visiting address: Almas Allé 5, Uppsala