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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.
2010 Project Description
Draft genome sequences were completed for eight genomes of fungi in the family Clavicipitaceae, including the tall fescue symbiont (endophyte), Neotyphodium coenophialum, two isolates of the closely related fungus, Epichloe festucae, three ergot fungi, Claviceps purpurea, Claviceps fusiformis, and Claviceps paspali, and two other plant-associated Clavicipitaceae, Aciculosporium take and a newly discovered symbiont of Ipomoea asarifolia. Deep sequencing was conducted on mRNA (RNA-seq) from unstressed tall fescue plants with and without the symbiont, N. coenophialum, and material was collected for metabolomic and RNA-seq analysis of plants with and without N. coenophialum that were subjected to time periods of 1-7 days without watering.
The genome sizes of the two Epichloe festucae genomes were each 35 Mb. One of the E. festucae genomes gave 8142 gene predictions, and the other gave 8832 gene predictions. The Neotyphodium coenophialum genome was 95 Mb, and preliminary analysis indicates that the fungus is triploid, in keeping with its previous characterization as an interspecific hybrid with three ancestors. Genome sizes of the other Clavicipitaceae ranged from 27 Mb to 59 Mb, but the numbers of genes in each were comparable to E. festucae. Comparisons of these genomes indicated that the endophytes have especially unstable regions containing genes for biosynthesis of alkaloids that may cause livestock toxicosis or protect the host plants from insects. This result helps account for the chemotypic diversity of natural endophyte isolates.
The RNA-seq analysis of tall fescue indicated that the symbiont, N. coenophialum, induced higher expression of plant genes for ethylene biosynthesis and glutathione-S-transferase. These activities may precondition the plant to resist effects of water deficit, in part accounting for the beneficial effect of the symbiont on drought tolerance.
Arnaoudova E, Haws DC, Huggins P, Jaromczyk JW, Moore N, Schardl CL, Yoshida R (2010) Statistical phylogenetic tree analysis using differences of means. Frontiers in Neuroscience 4: 47 (12 pp)
Eaton CJ, Cox MP, Ambrose B, Becker M, Hesse U, Schardl CL, Scott B (2010) Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis. Plant Physiology 153: 1780-1794
Schardl CL (2010) The epichloae, symbionts of the grass subfamily Pooideae Annals of the Missouri Botanical Garden 97: 646-665
Schardl CL, Chen F (2010) Plant defences against herbivore attack. In Encyclopedia of Life Sciences. John Wiley & Sons, Ltd.
Zhang D-X, Nagabhyru P, Blankenship JD, Schardl CL (2010) Are loline alkaloid levels regulated in grass endophytes by gene expression or substrate availability? Plant Signaling & Behavior 5: 11