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Genomics of Fungal Endophytes and Their Host Grasses
Department of Plant Pathology
Epichloe species and closely related Neotyphodium species are common symbionts of many temperate turf, forage and wild grasses, and provide a variety of fitness enhancements such as increased stress tolerance, as well as resistance to nematodes and insects. In addition, the Epichloe species, but not Neotyphodium species, sometimes can cause disease on the host plants. A survey of endophyte and host plant genes will enable studies of gene expression in response to each other and to stresses, as well as during pathogenic or mutualistic phases. Such studies will help reveal mechanisms underlying beneficial effects of endophytes, as well as the basis of fungal pathogenicity and suppression of pathogenicity.
2011 Project Description
Genomes of several more Epichloe species and a Neotyphodium species (endophytes) symbiotic with grasses were sequenced, as was the genome of a related symbiont from the dicotyledonous plant Ipomoea asarifolia (from the morning-glory family, Convolvulaceae). This brought the total number of sequenced genomes from plant-associated clavicipitaceous fungi to 14: E. amarillans, E. brachyelytri, E. festucae (2 isolates), E. glyceriae, E. typhina (2 isolates), N. coenophialum, N. gansuense, Aciculosporium take, Claviceps fusiformis, C. paspali, C. purpurea, and P. ipomoeae. All of these genomes, except that of N. coenophialum, were annotated to predict genes, which were compared between species and isolates. Then, the alkaloid biosynthesis genes were identified and compared.
Objective 2: This objective was completed previously.
Objective 3: Deep sequencing of expressed mRNA was conducted on plants with and without endophyte, including ovaries of Italian ryegrass (Lolium multiflorum), and vegetative tillers of tall fescue (Lolium arundinaceum = Festuca arundinacea). The mRNA samples from tall fescue included both unstressed and drought-stressed plants, to monitor both endophyte and plant gene expression changes in response to stress.
Objective 1: There were three gene clusters for the three alkaloid classes, ergolines, indole-diterpenes and lolines. In addition, the peramine biosynthesis gene was identified in several Epichloe and Neotyphodium species. A striking difference between the alkaloid gene clusters in Epichloe and Neotyphodium species and those in other Clavicipitaceae was that the former had very large blocks of repetitive DNA throughout each cluster. These repeats appeared to be involved in destabilizing genes in the clusters, leading to considerable variation in alkaloid profiles of different endophytes.
Objective 2: Together with data from objective 3, the expressed sequence tags were mapped onto the E. festucae genome as a tool for annotating the endophyte genomes by refining the sets of gene models.
Objective 3: Plant genes that responded to drought stress, and were upregulated to a greater extent in endophyte-symbiotic plants than in asymbiotic plants, included those for biosynthesis of the plant stress hormone, jasmonic acid, as well as genes for detoxification of reactive oxygen species.
Fleetwood D.J., Khan A.K., Johnson R.D., Young C.A., Mittal S., Wrenn R.E., Hesse U., Foster S.J., Schardl C.L., Scott B. (2011) Abundant degenerate miniature inverted-repeat transposable elements in genomes of epichloid fungal endophytes of grasses. Genome Biology and Evolution 3:1253-1264. DOI: 10.1093/gbe/evr098.
Florea S., Machado C., Andreeva K., Schardl C.L. (2011) Elimination of marker genes from transformed filamentous fungi by unselected transient transfection with a Cre-expressing plasmid, in: A. M. Pirttila and S. Sorvari (Eds.), Prospects and applications for plant-associated microbes. A laboratory manual, part B: fungi, Karhukopio OY, Turku, Finland. pp. 146-149.
Steiner U., Leibner S., Schardl C.L., Leuchtmann A., Leistner E. (2011) Periglandula, a new fungal genus within the Clavicipitaceae and its association with Convolvulaceae. Mycologia 103:1133-1145. DOI: 10.3852/11-031.