Fungi causing diseases on crop plants have traditionally been controlled by chemical measures. Biological control of plant disease is an attractive alternative to fungicide use for managing plant diseases and sustainable crop production which is expected to play an increasing and important role in the future both in ecologically farmed crops and in integrated pest management.
1) I am interested in working on fungal biocontrol agents Trichoderma atroviride and Clonostachys rosea and their interactions with fungal plant pathogens and host plants to understand the biocontrol mechanisms of plant diseases.
2) Small-RNA based strategies to control fungal plant pathogens
Small RNAs (sRNAs) are noncoding RNA, often ranging in size from 19–40 nucleotides, play a variety of roles, including gene regulation, chromatic modification, and genome integrity via a process called RNA interference (RNAi). Recent studies show the role of sRNAs in interspecies communication between closely interacting parasitic, pathogenic and symbiotic organisms. In addition, sRNAs can move horizontally between species and influence the biology of recipient species by regulating gene expression through targeted gene silencing. This cross-species gene silencing has recently been exploited to control certain plant pathogens by exogenous application of dsRNAs and sRNAs targeting genes in pathogens essential for disease development. Small-RNAs application in controlling plant disease is an emerging method, which can be used extensively to develop RNAi-based strategies for future crop protection
My current research is focussed on to
i) characterise the RNAi machinery and its biological functions in biocontrol fungus Clonostachys rosea,
ii) identify if, or to what extent, sRNAs are key determinant of parasitic fungus-fungua and beneficial fungus-plant interactions and if so their potential target genes in interacting organisms (Trans-species RNAi)
iii) understand sRNAs trafficking between the interacting organisms
iv) evaluate the potential application of sRNAs/dsRNA in controlling fungal plant diseases, specifically Botrytis cinerea, Fusarium graminearum and Phytophthora infestans (Spray Induced Gene Silencing)
v) sRNA functional genomics to characterise the biological function of sRNAs.
3) Secondary metabolomics
Secondary metabolites are important for ecological and evolutionary adaptation of fungi. Our recent aim is to investigate the biological functions of genes related with secondary metabolites in Clonostachys rosea, with emphasis on their role in biotic interactions with relevance for biological control of fungal plant diseases.
Peer-reviewed publications: 2012-2021
- 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. bioRxiv, 2021.02.07.430140.
- 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. https://doi.org/10.1007/s00438-020-01732-3.
- 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 C haudhary, Karl Lundén1, 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.