Project groups

8-1.2 | GENOMIC ADAPTATION IN PATHOGENIC OOMYCETES

Project leader:
Prof. Dr. Marco Thines

Oomycetes are organisms known to few, yet they are distributed ubiquitously around the world. They have radiated in specific habitats over a wide range of climatic conditions, including deserts, rainforests and arctic and temperate regions of the world, and can be found in terrestrial, limnic and marine environments. They have adapted to a great variety of lifestyles – some are specialised saprophytes, others are parasites of animals, fungi, plants, seaweeds or diatoms. Some of the plant parasites have reached a stage of endophytism where they cannot be detected visually any more, but live in very close symbiosis with their host plants.

Plant pathogenic oomycetes are often associated with certain weather conditions and cause losses of billions of Euros each year and are pests of a great variety of crops, including potato, maize, sorghum, millet, lettuce, cocoa, sugarcane, mustard, peppers and many more. Only a fraction of the true biodiversity has so far been uncovered – despite of their economic importance – and new species, genera, and even families await their discovery. Especially the obligate plant parasitic oomycetes have evolved to a high degree of diversity, and hitherto unknown species distributed by global trade pose a serious threat to horticulture and agriculture.

The research conducted in our group spans a wide range of disciplines and topics including cell biology, ecology, evolutionary biology, genomics and plant-pathogen interactions of oomycetes. In addition, it includes the development and application of methods for exploiting the genetic information conserved in biological archives (with focus on herbaria).

Our aim is to gain a deeper knowledge of the evolutionary processes that have shaped oomycete diversity and their biotic interaction, and to use this information to investigate how these are shaped and influenced by climate conditions. Many Oomycetes show adaptation to specific climates and temperature regimes, and in plant pathogens climatic conditions are important for symptom development and are often used for disease forecasting. Thus our research offers a basis for understanding the reaction of this little-known, yet tremendously important, group of organisms to a changing climate.

In our research, we are networking with the most distinguished groups in oomycete research and cooperate with researchers from all over the world, in particular North America, Australia, East Asia and Europe.

 

Team

Dr. Youngjoon Choi, Researcher
Dr. Suchita Patel, Researcher
Dr. Sabine Telle, Researcher
Leila Kachour, Ph.D. student
Bagdevi Mishra, Ph.D. student
Bora Nam, Ph.D. student
Lisa Nigrelli, Ph.D. student
Rahul Sharma, Ph.D. student
Ali Tahir, Ph.D. student
Xiaojuan Xia, Ph.D. student

Publications

Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E., Thines, M., et al. (2010) : Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome. - Science, vol. 330, 1549-1551, DOI: 10.1126/science.1195203 

Choi, Y.-J., Thines, M., Runge, F., Hong, S.-B., Telle, S. & H.D. Shin (2011) : Evidence for high degrees of specialisation, evolutionary diversity, and morphological distinctiveness in the genus Bremia. - Fungal Biology 115(2): 102-111. 

Choi, Y.-J. & M. Thines (2011) : Morphological and molecular confirmation of Albugo resedae (Albuginales; Oomycota) as a distinct species from A. candida. - Mycological Progress 10(2): 143-148.

Choi, Y.-J., Shin, H.-D., Ploch, S. & M. Thines (2011) : Three new phylogenetic lineages are the closest relatives of the widespread species Albugo candida. - Fungal Biology 115(7): 598–607.

Choi, Y.-J., Thines, M. & H.-D. Shin (2011) : A new perspective on the evolution of white blister rusts: Albugo s.str. (Albuginales; Oomycota) is not restricted to Brassicales but also present on Fabales. - Organisms Diversity & Evolution 11(3): 193-199.

Choi, Y.-J., Thines, M., Han, J.-G. & H.-D. Shin (2011) : Mitochondrial phylogeny reveals intraspecific variation in Peronospora effusa, the spinach downy mildew pathogen. - The Journal of Microbiology 49(6): 1039-1043.

Choi, Y.-J., Thines, M., Tek, M.P. & H.-D. Shin (2012) : Morphological evidence supports the existence of multiple species in Pustula (Albuginaceae, Oomycota). - Nova Hedwigia 94: 181-194.

Choi, Y.J., Han, K.S., Park, Y.H. & H.D. Shin (2014) : First Report of White Blister Rust Caused by Albugo candida on Wasabi in Korea. - Plant Disease, DOI: 10.1094/PDIS-12-13-1259-PDN

Glynou, K., Ali, T., Buch, A.K, Kia, S.H., Ploch, S., Xia, X, Celik, A., Thines, M & J.G. Macia-Vicente (2015) : The local environment determines the assembly of root endophytic fungi at a continental scale. - Enviromental Microbiology, doi:10.1111/1462-2920.13112.

Guerrero, Y., Hofmann, T.A., Williams, C., Thines, M. & M. Piepenbring (2011) : Asterotexis cucurbitacearum, a poorly known pathogen of Cucurbitaceae new to Costa Rica, Grenada and Panama. - Mycology 2: 87-90.

Hulvey, J., Telle, S., Nigrelli, L., Lamour, K. & M. Thines (2010) : Salisapiliaceae - A new family of oomycetes from marsh grass litter of southeastern North America. - Persoonia 25: 109–116.

Lamour, K.H., Mudge, J., ... Sharma, R. et. al. (2012) : Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. - Molecular Plant-Microbe Interactions 25: 1350-1360.

Levesque, C.A., Brouwer, H., Cano, L., Hamilton, J.P., Holt, C., Huitema, E., Raffaele, S., Robideau, G.P., Thines, M., Win, J., Zerillo, M.M., Beakes, G.W., Boore, J.L., Busam, D., Dumas, B., Ferriera, S., Fuerstenberg, S.I., Gachon, C.M., Gaulin, E., Govers, F., Grenville-Briggs, L., Horner, N., Hostetler, J., Jiang, R.H., Johnson, J., Krajaejun, T., Lin, H., Meijer, H.J., Moore, B., Morris, P., Phuntmart, V., Puiu, D., Shetty, J., Stajich, J.E., Tripathy, S., Wawra, S., van West, P., Whitty, B.R., Coutinho, P.M., Henrissat, B., Martin, F., Thomas, P.D., Tyler, B.M., De Vries, R.P., Kamoun, S., Yandell, M., Tisserat, N. & C.R. Buell (2010) : Genome sequence of the necrotrophic plant pathogen, Pythium ultimum, reveals original pathogenicity mechanisms and effector repertoire. - Genome Biology 11:R73.

Mirzaee, M.R., Ploch, S., Runge, F., Telle, S., Nigrelli, L. & M. Thines (2013) : A new presumably widespread species of Albugo parasitic to Strigosella spp. (Brassicaceae). - Mycological Progress 12 (1): 45-52.

Nigrelli, L. & M. Thines (2013) : Tropical oomycetes in the German Bight: Climate warming or overlooked diversity? - Fungal Ecology 6: 152-160.

Ploch, S. & M. Thines (2011) : Obligate biotrophic pathogens of the genus Albugo are widespread as asymptomatic endophytes in natural populations of Brassicaceae. - Molecular Ecology 20: 3692-3699.

Ploch, S., Telle, S., Choi, Y.-J., Cunnington, J., Priest, M., Rost, C., Shin, H.-D. & M. Thines (2011) : The molecular phylogeny of the white blister rust genus Pustula reveals a case of underestimated biodiversity with several undescribed species on ornamentals and crop plants. - Fungal Biology 115: 214-219.

Ploch, S., Choi, Y.-J., Rost, C., Shin, H.-D., Schilling, E. & M. Thines (2010) : Evolution of diversity in Albugo is driven by high host specificity and multiple speciation events on closely related Brassicaceae. - Molecular Phylogenetics and Evolution 57: 812–820.

Quesada-Ocampo, L.M., Granke, L.L., Olsen, J., Gutting, H.C., Runge, F., Thines, M., Lebeda, A. & M.K. Hausbeck (2012) : The Genetic Structure of Pseudoperonospora cubensis Populations. - Plant Disease 96: 1459-1470. 

Raffaele, S., Farrer, R.A., Cano, L.M., Studholme, D.J., MacLean, D., Thines, M. et al. (2010) : Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage. - Science 330, 1540-1543, DOI:10.1126/science.1193070
Link to Publication

Reimer, D., Pos, K.M., Thines, M., Grün, P. & H.B. Bode (2011) : A natural prodrug activation mechanism in nonribosomal peptide synthesis. - Nature Chemical Biology 7: 888-890.

Rost, C. & M. Thines (2012) : A new species of Pustula (Oomycetes, Albuginales) is the causal agent of sunflower white rust. - Mycological Progress 11: 351-359.

Runge, F. & M. Thines : Host matrix has major impact on the morphology of Pseudoperonospora cubensis. - European Journal of Plant Pathology 129: 147–156.

Runge, F. & M. Thines (2012) : Reevaluation of Host Specificity of the Closely Related Species Pseudoperonospora humuli and P. cubensis. - Plant Disease 96: 55-61.

Runge, F., Choi, Y.-J. & M. Thines (2011) : Phylogenetic investigations in the genus Pseudoperonospora reveal overlooked species and cryptic diversity in the P. cubensis species cluster. - European Journal of Plant Pathology 129:135–146.

Runge, F., Ndambi, B. & M. Thines (2012) : Which Morphological Characteristics Are Most Influenced by the Host Matrix in Downy Mildews? A Case Study in Pseudoperonospora cubensis. -  PLoS One: e44863.

Runge, F., Telle, S., Ploch, S., Savory, E., Day, B., Sharma, R. & M. Thines (2011) : The inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora. - IMA Fungus 2: 163-171.

Schornack, S., van Damme, M., Bozkurt, T.O., Cano, L.M., Smoker, M., Thines, M., Gaulin, E., Kamoun, S. & E. Huitema (2010) : Ancient class of translocated oomycete effectors targets the host nucleus. - PNAS 107(40): 17421-17426.

Schroder, S., Telle, S., Nick, P. & M. Thines (2011) : Cryptic diversity of Plasmopara viticola (Oomycota, Peronosporaceae) in North America. Organisms Diversity & Evolution 11(1): 3-7.

Spring, O., Thines, M., Wolf, S. & R. Zipper (2011) : PCR-based detection of sunflower white blister rust (Pustula helianthicola C. Rost & Thines) in soil samples and asymptomatic host tissue. - European Journal of Plant Pathology 131: 519-527.

Telle, S. & M. Thines (2012) : Reclassification of an enigmatic downy mildew species on lovegrass (Eragrostis) to the new genus Eraphthora, with a key to the genera of the Peronosporaceae. - Mycological Progress 11(1): 121-129.

Telle, S., Shivas, R.G., Ryley, M.J. & M. Thines (2011) : Molecular phylogenetic analysis of Peronosclerospora (Oomycetes) reveals cryptic species and genetically distinct species parasitic to maize. European Journal of Plant Pathology, DOI 10.1007/s10658-011-9772-8.

Thines, M. & S. Kamoun (2010) : Oomycete-plant coevolution: Recent advances and future prospects. - Current Opinion in Plant Biology 13: 427-433.

Thines, M. & V. Kummer (2013) : Diversity and species boundaries in floricolous downy mildews. - Mycological Progress 12: 321-329.

Thines, M. (2010) : Evolutionary history and diversity of white blister rusts (Albuginales). - Polish Botanical Journal 2010 55(2): 259-264.

Thines, M. (2011) : Recent outbreaks of downy mildew on grape ivy (Parthenocissus tricuspidata, Vitaceae) in Germany are caused by a new species of Plasmopara. - Mycological Progress 10(4): 415-422.

Thines, M., Runge, F., Telle, S. & H. Voglmayr (2010) : Phylogenetic investigations in the downy mildew genus Bremia reveal several distinct lineages and a species with a presumably exceptional wide host range. - European Journal of Plant Pathology 128:81-89.

Trigiano, R.N., Wadl, P.A., Dean, D., Hadziabdic, D., Scheffler, B.E., Runge, F., Telle, S., Thines, M., Ristaino, J. & O. Spring (2012) : Ten polymorphic microsatellite loci identified from a small insert genomic library for Peronospora tabacina. - Mycologia 104: 633-640.

Yoshida, K., Schuenemann, V.J., Cano, L.M., Pais, M., Mishra, B., Sharma, R., Lanz, C., Martin, F.N., Kamoun, S., Krause, J., Thines, M., Weigel, D. & H.A. Burbano (2013) : The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. - eLife, doi 10.7554/elife.00731.