Understanding the biological characteristics of the invasive properties of fungal pathogens in plants is an important step towards developing more sustainable solutions for their elimination. These microscopic fungi cause highly destructive diseases commonly known as “rusts” in several agronomically important crops such as wheat, soy, coffee and poplar. In a new study, an international consortium of researchers from the INRA centres in Nancy and Versailles, the Université Henri Poincaré – Nancy 1 and a joint team from the CNRS and Université d’Aix – Marseille sequenced and conducted a comparative analysis of the genomes of wheat and poplar rust fungi. These diseases are caused by biotrophic fungi1, which feed off the host plant without killing it. The rust significantly weakens the infested plants and seriously reduces crop yields. Growth and reproduction of these rust fungi depend entirely on the plants which they parasite.
Sequencing of the genomes of the fungi responsible for wheat steam rust (Puccinia graminis f. sp. tritici) and poplar leaf rust (Melampsora larici-populina) has significantly contributed to understanding the parasitic nature of rust.
Rust genomes are large in size and contain a very large repertoire of genes (over 16,000 in the two fungi). Over half are new genes previously unidentified in other plant pathogens. Rust fungi genomes, for example, present a specific ability to secrete over a thousand different effector-like proteins (most of which occur only in rust fungi). These effectors are small, secreted proteins believed to be capable of suppressing the defence systems of plants during infection. The genomes of Melampsora larici-populina and Puccinia graminis also contain a massive proliferation of transposable elements2 which have contributed to innovation in rusts, notably by facilitating the appearance of new genes as the pathogens coevolve with the host plants.
Rusts are very difficult to study due to their obligate biotrophic lifestyle. Few varieties of rust fungi can be isolated and artificially maintained in a laboratory. The sequencing of these two genomes therefore represents an important breakthrough in the study of plant pathology, given the impact of foliar diseases in crops of major agronomical interest. The results of this study are expected to further understanding of the mechanisms behind the evolution of biotrophy.
Zoom: poplar rust
Poplar is an important crop in Europe’s wood industry and an increasingly common product in the energy sectors. Melampsora larici-populina, the causal agent of poplar rust, is the primary impediment to further expansion of poplar production. The disease causes significant damage to poplar plantations and can lower annual yield growth by up to 50% in trees in man-made plantations. In just a few decades, the causal agent of foliar disease has successfully bypassed resistance mechanisms in nearly every poplar cultivar used in plantations. As such, a better understanding of the genetic characteristics of this disease is urgently needed to develop cultivars with durable immunities to rust. After the sequencing of the poplar genome in 20063, sequencing of the poplar rust genome should make it possible to identify the triggering factors of the disease and to observe how these factors evolve to suppress immunity in trees.
On the basis of this knowledge, it will be possible to develop more effective, environmentally-sustainable methods of combating the disease by breeding resistant trees.
Rust disease in poplar leaf.
©Benjamin Petre/INRA
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Zoom: wheat stem rust
Puccinia graminis f. sp. tritici, the causal agent of black rust in wheat stem, has caused large-scale epidemics in wheat crops around the world. The use of resistant wheat varieties since the mid 20th century has successfully reduced the impact of the disease. However the appearance of the highly virulent Ug99 strain of the fungus in Uganda in 1999 and later in South Africa, Yemen and Iran poses a threat to worldwide production, as 85% of the wheat varieties grown in major production zones are vulnerable to this strain (as are 90% of the varieties sown in the Middle East, Central Asia and the Indian subcontinent – the most vulnerable zones). In response, an international programme to fight the disease was reactivated4. Sequencing of the wheat stem rust genome therefore represents an important step towards understanding the mechanism s involved in overcoming resistance in wheat to the disease, and towards identifying the effectors which manipulate a plant’s immune system. This crucial breakthrough in the field of fungal genomics is expected to help breed new wheat varieties to fight the Ug99 strain and other new and aggressive strains of the fungus.
Black rust in wheat plants.
© Marc Fouchard/INRA
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1Fungi can also be necrotrophic (they kill the host plant) or hemibiotrophic (they feed off the living plant and later become necrotrophic).
2Also known as a transposon, a transposable element is a sequence of DNA capable of moving and multiplying within a genome autonomously.
3http://www.nancy.inra.fr/la_science_et_vous/genome_du_peuplier
4http://www.globalrust.org/
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Reference:
Obligate biotrophy features unraveled by the genomic analysis of rust fungi. PNAS advanced online version of 2 May 2011:
doi 10.1073/pnas.1019315108
Sébastien Duplessisa, Christina A. Cuomob, Yao-Cheng Linc, Andrea Aertsd, Emilie Tisseranta, Claire Veneault-Fourreya, David L. Jolye, Stéphane Hacquarda, Joëlle Amselemf, Brandi L. Cantarelg, Readman Chiuh, Pedro M. Coutinhog, Nicolas Feaue, Matthew Fieldh, Pascal Freya, Eric Gelhayea, Jonathan Goldbergb, Manfred G. Grabherrb, Chinnappa D. Kodirab, Annegret Kohlera, Ursula Küesi, Erika A. Lindquistd, Susan M. Lucasd, Rohit Magoj, Evan Maucelib, Emmanuelle Morina, Claude Murata, Jasmyn L. Pangilinand, Robert Parkk, Matthew Pearsonb, Hadi Quesnevillef, Nicolas Rouhiera, Sharadha Sakthikumarb, Asaf A. Salamovd, Jeremy Schmutzd, Benjamin Sellesa, Harris Shapirod, Philippe Tanguaye, Gerald A. Tuskanl,d, Bernard Henrissatg, Yves Van de Peerc, Pierre Rouzéc, Jeffrey G. Ellisj, Peter N. Doddsj, Jacqueline E. Scheinh, Shaobin Zhongm, Richard C. Hameline, Igor V. Grigorievd, Les J. Szabon,m, and Francis Martina
aUnité Mixte de Recherche 1136, INRA/Nancy Université, Interactions Arbres/Micro-organismes, Centre de Nancy, 54280 Champenoux, France; bBroad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142; cDepartment of Plant Systems Biology, VIB, B-9052 Ghent, Belgium; dUS Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; eNatural Resources Canada, Ste-Foy, QC, Canada G1V 4C7; fINRA, Unité de Recherche Génomique Info, 78026 Versailles Cedex, France; gUnité Mixte de Recherche 6098, CNRS–Universités Aix-Marseille I and II, Marseille, France; hGenome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6 Canada; iDivision of Molecular Wood Biotechnology and Technical Mycology, Büsgen-Institute, University of Göttingen, Büsgenweg, 37077 Göttingen, Germany; jCommonwealth Scientific and Industrial Research Organization, Plant Industry, Canberra, ACT 2601, Australia; kPlant Breeding Institute Cobbitty, University of Sydney, Camden, NSW 2570, Australia; lBiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6422; mDepartment of Plant Pathology, University of Minnesota, St. Paul, MN 55108; nCereal Disease Laboratory, Agricultural Research Service, US Department of Agriculture, St. Paul, MN 55108
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