Magnus Karlsson

Various microorganisms are constant threats to crop production on a global scale. Bacteria, fungi, oomycetes, viruses and nematodes cause yield losses and quality reduction before harvest, as well as during storage. Understanding the mechanisms of disease development is important when deciding strategies for efficient disease control in agriculture. Fungal infections on plants can be controlled by multiple approaches within an integrated pest management context. Biological control of diseases and disease-resistant crops can contribute to sustainable plant protection strategies.

The current focus of my research is to understand mechanisms that parasitic fungi use to interact with plant hosts and other microbes, and how this results in diseased or healthy plants. I also study the resistance biology of plants, i.e. what plant factors that contribute to the ability to resist pathogen attack.

Research Gate

Projects

Population genomics of the mycoparasite Clonostachys rosea

Biological control of plant diseases in agricultural production is an attractive alternative to the extensive use of chemical pesticides, and is therefore expected to be used in organic production and integrated pest management (IPM). However, biocontrol traits are complex and considered to be highly strain-specific. The objective of the proposed project is to investigate the genetic basis of biocontrol efficiency in the fungal biological control agent (BCA) Clonostachys rosea, and to identify high performing individuals for biocontrol of fusariose (caused by Fusarium spp.) on wheat. We will re-sequence the genomes of 70 C. rosea individuals, and evaluate these individuals with regards to; a) control of fusariose on wheat, and b) compatibility with the Proline fungicide used for chemical control of fusariose. A limited number of high- and low-performing individuals will be further evaluated in short field experiments, in order to confirm the results from the laboratory-based experiments. We will then correlate genotypic (gene and allele content) and phenotypic variation, and identify genes and gene families that distinguish high-performing individuals. This study will result in a better mechanistic understanding of biological control, and identify high-performing BCA individuals for control of fusariose on wheat in IPM.

Biological control of fungal diseases

Certain fungi lives as parasites on other fungi, and can be referred to as hyperparasites. We can use these hyperparasites to control plant pathogenic fungi causing diseases on our crop plants. Examples on hyperparasites used commercially today are different species from the fungal genera Trichoderma and Clonostachys. Several products are available on the market and research is done with the aim to develop more products and to make full use of their potential. A key factor for succeeding with our ambition to improve and optimize the use of hyperparasites is a deeper understanding of the mechanisms that results in efficient biological control. We study mechanisms employed by Trichoderma and Clonostachys species to interact with and antagonize plant pathogenic fungi and to improve plant growth. For this purpose, we use a variety of techniques, from field trials to genetic and molecular approaches.

Results from this work shows that the ability to control plant pathogenic fungi varies considerably between individuals of the same hyperparasite species. This means that it matters which individuals that are used for biological control of different plant diseases. New techniques for large-scale analyses of complete genomes of fungi have revolutionized our understanding of the genetics behind complex traits such as biological control. This work have the potential to result in genetic markers that can facilitate identification and selection of highly efficient individuals for biocontrol, for formulation and storage, and for combinations with other biological, chemical or physical control measures. In the long-term, breeding programs for biological control organisms are plausible.

The extensive use of chemical fungicides can result in development of fungicide resistance in fungal plant pathogen populations. Our ongoing research investigates the possibility to alternate between chemical and biological control measures during the growing season, in order to prevent development of fungicide resistance. This is currently investigated for septoria tritici blotch in wheat and grey mould on strawberry.

Breeding for root rot resistance in pea

The objective of this project is to develop new pea varieties with resistance towards root rot disease, in combination with excellent production properties. The disease is mainly caused by the oomycete Aphanomyces euteiches. Currently, neither pea varieties with resistance nor chemical pesticides are available for growers. However, a non-commercial pea variety (PI180693) is partially resistant to aphanomyces root rot, and can be used for studies of resistance trait and be the starting point for commercial breeding. We will utilize high-throughput genotyping to identify genetic markers that co-segregate with root rot resistance. These markers will then be used to speed up the plant breeding program by improving precision in the selection of resistant plants for further evaluation. Studies of the population structure and virulence of the pathogen will enable optimal choices of pea cultivars in different countries and regions. Having pea varieties with resistance towards aphanomyces root rot promises to be a very efficient plant protection strategy, which is compatible with principles of integrated pest management and organic farming.

Small-RNA based strategies to control fungal plant pathogens

In this project, the main focus is on a new biocontrol method based on small RNA (sRNAs) and the biological process called RNA interference (RNAi). Small RNAs play variety of roles in organisms and are key factors in interactions between hosts and their parasites, pathogens and symbionts. During interactions, sRNAs travel from one species to another and modulate regulatory machinery of host cells through targeted gene silencing. Present proposal aims 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 biocontrol interactions in C. rosea and if so their potential target genes in interacting organisms and iii) evaluate the potential application of sRNAs in controlling fungal plant diseases. We will use 1) Fusarium graminearum- wheat and 2) Botrytis cinerea- strawberry as model pathosystems to evaluate the prospect of exogenous applications of sRNAs for crop protection. Selection of pathosystems is based on the fact that Fusarium head blight and foot and root rot pose serious threats world-wide for food safety including mycotoxin contamination in cereals and maize, while B. cinerea causes a serious risk to several vegetables, fruits and flowers in their pre- and post-harvest stages by causing grey mould disease. Our findings will expand the understanding of how sRNA-based biocontrol mechanism can be exploited for future plant disease control.

105. Westergren O, Samaras A, Gunnarson A, Karlsson M, Tzelepis G (2025) Assessing the resistance of commercial oilseed rape cultivars to verticillium stem striping disease in Sweden. European Journal of Plant Pathology (in press)

104. Mamani M, Catacora L, Nina N, Daniela Tola Alarcon W, Cai F, Rydén J, Druzhinina I, Funck Jensen D, Crespo C, Karlsson M, Dubey M (2025) Diversity of Trichoderma in the unexplored Bolivian Amazon region and their potential for coffee diseases control. FEMS Microbiology Letters (in press)

103. Ramirez X, Gonzales V, Maydana R, Dubey M, Funck Jensen D, Carrasco C, Karlsson M, Crespo C (2025) Brewery spent yeast medium for Serratia sp. bio-beads improves Chenopodium quinoa Willd. growth in the northern altiplano of Bolivia. Letters in Applied Microbiology (in press)

102. Kruhler N, Shakya S, Dubey M, Sützl L, Peterbauer C, Karlsson M, Sandgren M, Atanasova L (2025) Structural insights into cellobiose dehydrogenases of a non-lignocellulolytic fungus and their transcriptional dynamics across different nutritional modes. Microbiology Spectrum (in press)

101. Chaudhary S, Piombo E, Dubey M, Funck Jensen D, Grenville-Briggs L, Karlsson M (2026) Transcriptomic analysis of two wheat genotypes in the presence of the pathogen Zymoseptoria tritici and the biological control agent Clonostachys rosea. Physiological and Molecular Plant Pathology 141:103013.

100. Rafiei V, DeGenring L, Schwister E, Elmore J, Dubey M, Karlsson M, Drott M (2025) Comparative analysis of distinct phenotyping methods for assessing wheat resistance and pathogen virulence among Fusarium species causing head blight disease. Plant Methods 21:85.

99. Chaudhary S, Zakieh M, Dubey M, Funck Jensen D, Grenville-Briggs L, Chawade A, Karlsson M (2025) Plant genotype-specific modulation of Clonostachys rosea-mediated biocontrol of septoria tritici blotch disease in wheat. BMC Plant Biology 25:576.

98. Wikström J, Chaudhary S, Persson L, Wikström M, Fatehi J, Karlsson M (2025) Distribution of plant pathogenic Aphanomyces species in Sweden, Denmark and Lithuania and its relationship with soil factors. Journal of Plant Pathology https://doi.org/10.1007/s42161-025-01835-z

97. Gonzales V, Huallpan M, Ramirez X, San Miguel Y, Dubey M, Funck Jensen D, Karlsson M, Crespo C (2024) Rhizosphere bacteria from the Bolivian highlands improve drought tolerance in quinoa (Chenopodium quinoa Willd.). Journal of Applied Microbiology 135:lxae296.

96. Chaudhary S, Ricardo R, Dubey M, Funck Jensen D, Grenville-Briggs L, Karlsson M (2024) Genotypic variation in winter wheat for fusarium foot rot and its biocontrol using Clonostachys rosea. G3: Genes|Genomes|Genetics jkae240.

95. Piombo E, Tzelepis G, Gustavsson Ruus A, Rafiei V, Funck Jensen D, Karlsson M, Dubey M (2024) Sterol regulatory element-binding proteins mediate intrinsic fungicide tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea. Microbiological Research 289:127922.

94. Piombo E, Vetukuri R, Konakalla N, Kalyandurg P, Sundararajan P, Funck Jensen D, Karlsson M, Dubey M (2024) Dicer-mediated RNA silencing is a key regulatory mechanism in the biocontrol fungus Clonostachys rosea-wheat interactions. BMC Biology 22:219.

93. Sofianos G, Piombo E, Dubey M, Karlsson M, Karaoglanidis G, Tzelepis G (2024) Transcriptomic and functional analyses on a Botrytis cinerea multidrug resistant (MDR) strain provides new insights on the potential molecular mechanisms of MDR and fitness. Molecular Plant Pathology 25:e70004.

92. Kälin C, Piombo E, Bourras S, Kolodinska Brantestam A, Dubey M, Elfstrand M, Karlsson M (2024) Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea. BMC Plant Biology 24:144.

91. Piombo E, Vetukuri R, Tzelepis G, Funck Jensen D, Karlsson M, Dubey M (2024) Small RNAs: A new paradigm in fungal-fungal interactions used for biocontrol. Fungal Biology Reviews 48:100356.

90. Bösch Y, Pold G, Saghai A, Karlsson M, Jones C, Hallin S (2023) Distribution and environmental drivers of fungal denitrifiers in global soils. Microbiology Spectrum 11:e00061-23.

89. Himmelstrand K, Brandström Durling M, Karlsson M, Stenlid J, Olson Å (2023) Multiple rearrangements and low inter and intra species mitogenome sequence variation in the Heterobasidion annosum s.l. species complex. Frontiers in Microbiology 14:1159811.

88. Stenberg J, Becher P, Jonsson M, Karlsson M, Sundh I, Viketoft M (2023) Political deafness may impede transition to biological control. Trends in Plant Science 28:498-500.

87. Kälin C, Kolodinska Brantestam A, Arvidsson A, Dubey M, Elfstrand M, Karlsson M (2023) Evaluation of pea genotype PI180693 partial resistance towards aphanomyces root rot in commercial pea breeding. Frontiers in Plant Science 14:1114408.

86. Piombo E, Guaschino M, Funck Jensen D, Karlsson M, Dubey M (2023) Insights into the ecological generalist lifestyle of Clonostachys fungi through analysis of their predicted secretomes. Frontiers in Microbiology 14:1112673.

85. Kälin C, Berlin A, Kolodinska Brantestam A, Dubey M, Arvidsson A, Riesinger P, Elfstrand M, Karlsson M (2022) Genetic diversity of the pea root pathogen Aphanomyces euteiches in Europe. Plant Pathology 71:1570–1578.

84. Piombo E, Vetukuri R, Sundararajan P, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M (2022) Comparative small RNA and degradome sequencing provide insights into antagonistic interactions in the biocontrol fungus Clonostachys rosea. Applied and Environmental Microbiology 88:e00643-22.

83. Bösch Y, Jones C, Finlay R, Karlsson M, Larsbo M, Keller T, Hallin S (2022) Minimizing tillage modifies fungal denitrifier communities, increases denitrification rates and enhances the genetic potential for fungal relative to bacterial denitrification. Soil Biology and Biochemistry 170:108718.

82. Funck Jensen D, Dubey M, Jensen B, Karlsson M (2022) Clonostachys rosea for the control of plant diseases. In: Köhl J, Ravensberg W (eds) Microbial bioprotectants for plant disease management. BDS Publishing, 429-471.

81. Mesny F, Miyauchi S, Thiergart T, Pickel B, Atanasova L, Karlsson M, Hüttel B, Barry K, Haridas S, Drula E, Henrissat B, Kohler A, Grigoriev I, Martin F, Hacquard S (2021) Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nature Communications 12:7227.

80. Piombo E, Vetukuri R, Broberg A, Kalyandurg P, Kushwaha S, Funck Jensen D, Karlsson M, Dubey M (2021) The role of Dicer-dependent RNA interference in regulating mycoparasitic interactions. Microbiology Spectrum 9:e01099-21.

79. Elfstrand M, Chen J, Cleary M, Halecker S, Ihrmark K, Karlsson M, Davydenko K, Stenlid J, Stadler M, Brandström Durling M (2021) Comparative analyses of the Hymenoscyphus fraxineus and Hymenoscyphus albidus genomes reveals potentially adaptive differences in secondary metabolite and transposable element repertoires. BMC Genomics 22:503.

78. Mgbeahuruike A, Ejiofor T, Ashang M, Ojiako C, Obasi C, Ezema C, Okoroafor O, Mwanza M, Karlsson M, Chah K (2021) Reduction of the adverse impacts of fungal mycotoxin on proximate composition of feed and growth performance in broilers by combined adsorbents. Toxins 13:430.

77. Broberg M, Simaan H, Shmoish M, Rabner A, Karlsson M, Horwitz B (2021) Ferulic acid, an abundant maize phenolic, regulates ABC and MFS transporter gene expression in the maize pathogen Cochliobolus heterostrophus. Journal of Plant Diseases and Protection 128:1383-1391.

76. Stenberg J, Sundh I, Becher P, Björkman C, Dubey M, Egan P, Friberg H, Gil J, Funck Jensen D, Jonsson M, Karlsson M, Khalil S, Ninkovic V, Rehermann del Rio G, Vetukuri R, Viketoft M (2021) When is it biological control? A framework of definitions, mechanisms, and classifications. Journal of Pest Science 94:665-676.

75. Ben Amira M, Faize M, Karlsson M, Dubey M, Frąc M, Panek J, Fumanal B, Gousset-Dupont A, Julien J, Chaar H, Auguin D, Mom R, Label P, Venisse J (2021) Fungal X-intrinsic protein aquaporin from Trichoderma atroviride: Structural and functional considerations. Biomolecules 11:338.

74. Zapparata A, Baroncelli R, Brandström Durling M, Kubicek C, Karlsson M, Vannacci G, Sarrocco S (2021) Fungal cross-talk: an integrated approach to study distance communication. Fungal Genetics and Biology 148:103518.

73. Ejioffor T, Mgbeahuruike A, Orjiakor C, Ushie A, Nwoko E, Remigius O, Dada T, Mwanza M, Karlsson M (2021) Saccharomyces cerevisiae, bentonite and kaolin as adsorbents for reducing the adverse impacts of mycotoxin contaminated feed on broiler histopathology and hemato-biochemical changes. Veterinary World 14:23-32.

72. Dubey M, Funck Jensen D, Karlsson M (2021) Functional characterization of the AGL1 aegerolysin in the mycoparasitic fungus Trichoderma atroviride reveals a role in conidiation and antagonism. Molecular Genetics and Genomics 296:131-140.

71. Broberg M, Dubey M, Iqbal M, Gudmundssson M, Ihrmark K, Schroers H, Funck Jensen D, Brandström Durling M, Karlsson M (2021) Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales). Evolutionary Applications 14:476-497.

70. Tzelepis G, Karlsson M (2021) The fungal chitinases. In: Zaragoza O, Casadevall A (eds) Encyclopedia of Mycology. Elsevier, 1:23-31.

69. Iqbal M, Broberg M, Haarith D, Broberg A, Bushley K, Brandström Durling M, Viketoft M, Funck Jensen D, Dubey M, 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 13:2264-2283.

68. Kadoon A, Mgbeahuruike A, Karlsson M, Chah K (2020) Identification, antifungal susceptibility and phylogenetic comparison of fungal community in a poultry environment in Nigeria. International Journal of Poultry Science 19:548-556.

67. Dubey M, Broberg M, Funck Jensen D, Karlsson M (2020) LysM proteins regulate fungal development and contribute to hyphal protection and biocontrol traits in Clonostachys rosea. Frontiers in Microbiology 11:679.

66. Iqbal M, Dubey M, Broberg A, Viketoft M, Funck Jensen D, 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 109:1698-1709.

65. Tzelepis G, Karlsson M (2019) Killer toxin-like chitinases in filamentous fungi: Structure, regulation and potential roles in fungal biology. Fungal Biology Reviews 33:123-132.

64. Broberg M, Dubey M, Sun M, Ihrmark K, Schroers H, Li S, Funck Jensen D, Brandström Durling M, Karlsson M (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.

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

62. Atanasova L, Dubey M, Grujić M, Gudmundsson M, Lorenz C, Sandgren M, Kubicek C, Funck Jensen D, Karlsson M (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.

61. Fatema U, Broberg A, Funck Jensen D, Karlsson M, Dubey M (2018) Functional analysis of polyketide synthase genes in the biocontrol fungus Clonostachys rosea. Scientific Reports 8:15009.

60. Mgbeahuruike A, Ejioffor T, Christian O, Shoyinka V, Karlsson M, Nordkvist E (2018) Detoxification of aflatoxin-contaminated poultry feeds by three adsorbents, bentonite, activated charcoal and fuller’s earth. Journal of Applied Poultry Research 27:461–471.

59. Schmidt R, Brandström Durling M, de Jager V, Menezes R, Nordkvist E, Svatoš A, Dubey M, Lauterbach L, Dickschat J, Karlsson M, Garbeva P (2018) Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum. FEMS Microbiology Ecology 94:fiy078.

58. Nygren K, Dubey M, Zapparata A, Iqbal M, Tzelepis G, Brandström Durling M, Funck Jensen D, Karlsson M (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.

57. Borisova A, Eneyskaya E, Jana S, Badino S, Kari J, Amore A, Karlsson M, Hansson H, Sandgren M, Himmel M, Westh P, Payne C, Kulminskaya A, Ståhlberg J (2018) Correlation of structure, function and protein dynamics in GH7 cellobiohydrolases from Trichoderma atroviride, T. reesei and T. harzianum. Biotechnology for Biofuels 11:5.

56. 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 108:52-59.

55. Karlsson M, Atanasova L, Funck Jensen D, Zeilinger S (2018) Necrotrophic mycoparasites and their genomes. In: Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (eds) The Fungal Kingdom. ASM Press, Washington DC, 1005-1026. Selected for rapid publication in Microbiology Spectrum 5:FUNK-0016-2016.

54. Tzelepis G, Karlsson M, Suzuki T (2017) Deglycosylating enzymes acting on N-glycans in fungi; Insights from a genome survey. Biochimika et Biophysica Acta – General Subjects 1861:2551-2558.

53. Stenlid J, Elfstrand M, Cleary M, Ihrmark K, Karlsson M, Davydenko K, Brandström Durling M (2017) Genomes of Hymenoscyphus fraxineus and Hymenoscyphus albida encode surprisingly large cell wall degrading potential, balancing saprotrophic and necrotrophic signatures. Baltic Forestry 23:41-51.

52. Funck Jensen D, Karlsson M, Lindahl B (2017) Fungal-fungal interactions: From natural ecosystems to managed plant production with emphasis on biological control of plant diseases. In: Dighton J, White J (eds) The Fungal Community: Its Organization and Role in the Ecosystem. CRC Press, Taylor & Francis Group, Boca Raton, 549-562.

51. Karlsson M, Stenlid J, Lindahl B (2016) Functional differentiation of chitinases in the white-rot fungus Phanerochaete chrysosporium. Fungal Ecology 22:52-60.

50. Kamou N, Dubey M, Tzelepis G, Menexes G, Papadakis E, Karlsson M, Lagopodi L, Funck Jensen D (2016) Investigating the compatibility of the biocontrol agent Clonostachys rosea IK726 with prodigiosin-producing Serratia rubidaea S55 and phenazine-producing Pseudomonas chlororaphis ToZa7. Archives of Microbiology 198:369–377.

49. Funck Jensen D, Karlsson M, Sarrocco S, Vannacci G (2016) Biological control using microorganisms as an alternative to disease resistance. In: Collinge DB (ed) Plant Pathogen Resistance Biotechnology. Wiley, New York and London, 341-363. 

48. Dubey M, Funck Jensen D, 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.

47. de Vries S, Nemesio-Gorriz M, Blair P, Karlsson M, Mukhtar S, Elfstrand M (2015) Heterotrimeric G-proteins in Picea abies and their regulation in response to Heterobasidion annosum s.l. infection. BMC Plant Biology 15:287.

46. Hosseini S, Elfstrand M, Heyman F, Funck Jensen D, Karlsson M (2015) Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi. BMC Genomics 16:627.

45. Schwelm A, Fogelqvist J, Knaust A, Jülke S, Lilja T, Dhandapani V, Bonilla-Rosso G, Karlsson M, Shevchenko A, Choi S, Kim H, Park J, Lim Y, Ludwig-Müller J, Dixelius C (2015) The genome sequence of the plant pathogenic rhizarian Plasmodiophora brassicae reveals insights in its biotrophic life cycle and the origin of chitin synthesis. Scientific Reports 5:11153.

44. Tzelepis G, Dubey M, Funck Jensen D, Karlsson M (2015) Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea. Microbiology 161:1407-1419.

43. Abd El Daim I, Häggblom P, Karlsson M, Stenström E, Timmusk S (2015) Paenibacillus polymyxa A26 sfp-type phosphopantetheinyl transferase inactivation limits bacterial antagonism against Fusarium graminearum but not of F. culmorum. Frontiers in Plant Science 6:368.

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

41. Hosseini S, Resjö S, Liu Y, Brandström-Durling M, Heyman F, Levander F, Liu Y, Elfstrand M, Funck Jensen D, Andreasson E, Karlsson M (2015) Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae. Journal of Proteomics 117:24-40.

40. Van der Nest M, Olson Å, Karlsson M, Lind M, Dalman K, Brandström-Durling M, Elfstrand M, Wingfield B, Stenlid J (2014) Gene expression associated with intersterility in Heterobasidion. Fungal Genetics and Biology 73:104-119.

39. Hansson D, Wubshet S, Olson Å, Karlsson M, Staerk D, Broberg A (2014) Secondary metabolite comparison of the species within the Heterobasidion annosum s.l. complex. Phytochemistry 108:243-251.

38. Himmelstrand K, Olson Å, Brandström-Durling M, Karlsson M, Stenlid J (2014) Intronic and plasmid derived regions contribute to the large mitochondrial genome sizes in Agaricomycetes. Current Genetics 60:303-313.

37. Tzelepis G, Hosomi A, Hossain T, Hirayama H, Dubey M, Funck Jensen D, Suzuki T, Karlsson M (2014) Endo-β-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.

36. Dubey M, Funck Jensen D, Karlsson M (2014) An ATP-binding cassette pleiotropic drug transporter protein is required for xenobiotic tolerance and antagonism in the fungal biocontrol agent Clonostachys rosea. Molecular Plant-Microbe Interactions 27:725–732.

35. Dubey M, Funck Jensen D, Karlsson M (2014) Hydrophobins are required for conidial hydrophobicity and plant root colonization in the fungal biocontrol agent Clonostachys rosea. BMC Microbiology 14:18.

34. Kosawang C, Karlsson M, Vélëz H, Have Rasmussen P, Collinge DB, Jensen B, Funck Jensen D (2014) Zearalenone detoxification by zearalenone hydrolase is important for the antagonistic ability of Clonostachys rosea against mycotoxigenic Fusarium graminearum. Fungal Biology 118:364-373.

33. Kosawang C, Karlsson M, Funck Jensen D, Dilokpimol A, Collinge DB (2014) Transcriptomic profiling to identify genes involved in Fusarium mycotoxin deoxynivalenol and zearalenone tolerance in the mycoparasitic fungus Clonostachys rosea. BMC Genomics 15:55.

32. Van der Nest M, Olson Å, Lind M, Vélëz H, Dalman K, Brandström-Durling M, Karlsson M, Stenlid J (2014) Distribution and evolution of het gene homologs in the basidiomycota. Fungal Genetics and Biology 64:45-57.

31. Tzelepis G, Melin P, Stenlid J, Funck Jensen D, Karlsson M (2014) Functional analysis of the C-II subgroup killer toxin-like chitinases in the filamentous ascomycete Aspergillus nidulans. Fungal Genetics and Biology 64:58-66.

30. Seidl-Seiboth V, Ihrmark K, Druzhinina IS, Karlsson M (2014) Molecular evolution of Trichoderma chitinases. In: Gupta V, Schmoll M, Herrera-Estrella A, Druzhinina IS, Upadhyay R, Tuohy M (eds) Biotechnology and Biology of Trichoderma. Elsevier 67-78.

29. Hosseini S, Heyman F, Olsson U, Broberg A, Funck Jensen D, Karlsson M (2014) Zoospore chemotaxis of closely related legume-root infecting Phytophthora species towards host isoflavones. Plant Pathology 63:708-714.

28. Dubey M, Broberg A, Funck Jensen D, 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.

27. Strandberg R, Tzelepis G, Johannesson H, Karlsson M (2013) Coexistence and expression profiles of two alternative splice variants of the pheromone receptor gene pre-1 in Neurospora crassa. Archives of Microbiology 195:773-780.

26. Dubey M, Broberg A, Sooriyaarachchi S, Ubhayasekera W, Funck Jensen D, 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.

25. Samils N, Gioti A, Karlsson M, Sun Y, Kasuga T, Bastiaans E, Wang Z, Li N, Townsend JP, Johannesson H (2013) Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings of the Royal Society B 280:20130862.

24. Nygren K, Wallberg A, Samils N, Stajich JE, Townsend JP, Karlsson M, Johannesson H (2012) Analyses of expressed sequence tags in Neurospora reveal rapid evolution of genes associated with the early stages of sexual reproduction in fungi. BMC Evolutionary Biology 12:229.

23. Nygren K, Strandberg R, Gioti A, Karlsson M, Johannesson H (2012) Deciphering the relationship between mating system and the molecular evolution of the pheromone and receptor genes in Neurospora. Molecular Biology and Evolution 29:3827-3842.

22. Ubhayasekera W, Karlsson M (2012) Bacterial and fungal chitinase chiJ orthologs evolve under different selective constraints following horizontal gene transfer. BMC Research Notes 5:581.

21. Hansson D, Menkis A, Olson Å, Stenlid J, Broberg A, Karlsson M (2012) Biosynthesis of fomannoxin in the root rotting pathogen Heterobasidion occidentale. Phytochemistry 84:31-39.

20. Hansson D, Menkis A, Himmelstrand K, Thelander M, Olson Å, Stenlid J, Karlsson M, Broberg A (2012) Sesquiterpenes from the conifer root rot pathogen Heterobasidion occidentale. Phytochemistry 82:158-165.

19. Tzelepis G, Melin P, Funck Jensen D, Stenlid J, Karlsson M (2012) Functional analysis of glycoside hydrolase family 18 and 20 genes in Neurospora crassa. Fungal Genetics and Biology 49:717-730. 

18. Olson Å, Aerts A, Asiegbu F, Belbahri L, Bouzid O, Broberg A, Canbäck B, Coutinho P, Cullen D, Dalman K, Deflorio G, van Diepen L, Dunand C, Duplessis S, Durling M, Gonthier P, Grimwood J, Fossdal C-G, Hansson D, Henrissat B, Hietala A, Himmelstrand K, Hoffmeister D, Högberg N, James T, Karlsson M, Kohler A, Kües U, Lee Y-H, Lin Y-C, Lind M, Lindquist E, Lombard V, Lucas S, Lundén K, Morin E, Murat C, Park J, Raffaello T, Rouzé P, Salamov A, Schmutz J, Solheim H, Ståhlberg J, Vélëz H, de Vries R, Wiebenga A, Woodward S, Yakovlev I, Garbelotto M, Martin F, Grigoriev I, Stenlid J (2012) Insight into trade-off between wood decay and parasitism from the genome of a fungal forest pathogen. New Phytologist 194:1001-1013.

17. Dubey M, Ubhayasekera W, Sandgren M, Funck Jensen D, 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:e36152. 

16. Mgbeahuruike A, Karlsson M, Asiegbu F (2012) Differential expression of two hydrophobin genes (Pgh1 and Pgh2) from the biological control agent Phlebiopsis gigantea. Fungal Biology 116:620-629.

15. Hosseini S, Karlsson M, Funck Jensen D, Heyman F (2012) Quantification of Phytophthora pisi DNA and RNA transcripts during in planta infection of pea. European Journal of Plant Pathology 132:455-468. 

14. Mgbeahuruike A, Sun H, Fransson P, Kasanen R, Daniel G, Karlsson M, Asiegbu F (2011) Screening of Phlebiopsis gigantea isolates for traits associated with biocontrol of the conifer pathogen Heterobasidion annosum. Biological Control 57:118-129. 

13. Ihrmark K, Asmail N, Ubhayasekera W, Melin P, Stenlid J, Karlsson M (2010) Comparative molecular evolution of Trichoderma chitinases in response to mycoparasitic interactions. Evolutionary Bioinformatics 6:1-26. 

12. Karlsson M, Stenlid J (2009) Comparative evolutionary histories of fungal chitinases. In: Pontarotti P (ed) Evolutionary Biology, Concept, Modeling, and Application. Springer-Verlag GmbH Berlin Heidelberg 323-338. 

11. Karlsson M, Stenlid J (2009) Evolution of family 18 glycoside hydrolases: Diversity, domain-structures and phylogenetic relationships. Journal of Molecular Microbiology and Biotechnology 16:208-223. 

10. Nygren C, Eberhardt U, Karlsson M, Parrent J, Lindahl B, Taylor A (2008) Growth on nitrate and occurrence of nitrate reductase-encoding genes in a phylogenetically diverse range of ectomycorrhizal fungi. New Phytologist 180:875-889. 

9. Wik L, Karlsson M, Johannesson H (2008) The evolutionary trajectory of the mating-type (mat) genes in Neurospora relates to reproductive behaviour of taxa. BMC Evolutionary Biology 8:109. 

8. Adomas A, Heller G, Olson Å, Osborne J, Karlsson M, Nahalkova J, van Zyl L, Sederoff R, Stenlid J, Finlay R, Asiegbu F (2008) Comparative analysis of transcript abundance in Pinus sylvestris roots after challenge with a saprotrophic, pathogenic or mutualistic fungus. Tree Physiology 28:885-897. 

7. Karlsson M, Stenlid J (2008) Comparative evolutionary histories of the fungal chitinase gene family reveal non-random size expansions and contractions due to adaptive natural selection. Evolutionary Bioinformatics 4:47-60. 

6. Karlsson M, Elfstrand M, Stenlid J, Olson Å (2008) A fungal cytochrome P450 is expressed during the interaction between the fungal pathogen Heterobasidion annosum sensu lato and conifer trees. DNA Sequence 19:115-120. 

5. Karlsson M, Nygren K, Johannesson H (2008) The evolution of the pheromonal signal system and its potential role for reproductive isolation in heterothallic Neurospora. Molecular Biology and Evolution 25:168-178. 

4. Karlsson M, Hietala A, Kvaalen H, Solheim H, Olson Å, Stenlid J, Fossdal C-G (2007) Quantification of host and pathogen DNA and RNA transcripts in the interaction of Norway spruce with Heterobasidion parviporum. Physiological and Molecular Plant Pathology 70:99-109. 

3. Karlsson M, Stenlid J, Olson Å (2007) Two hydrophobin genes from the conifer pathogen Heterobasidion annosum are expressed in aerial hyphae. Mycologia 99:227-231. 

2. Karlsson M, Stenlid J, Olson Å (2005) Identification of a superoxide dismutase gene from the conifer pathogen Heterobasidion annosum. Physiological and Molecular Plant Pathology 66:99-107. 

1. Karlsson M, Olson Å, Stenlid J (2003) Expressed sequences from the basidiomycetous tree pathogen Heterobasidion annosum during early infection of Scots pine. Fungal Genetics and Biology 39:51-59.