Genome of Epichloe Festucae, a Model Endophyte of Grasses

Fungal mutualists are a ubiquitous and extremely important feature of plant ecology and agriculture. Epichloe species represent the most genetically tractable of plant-mutualistic fungi, and the best model for evolutionary transition from pathogenesis to mutualism. Together with their asexual derivatives (Neotyphodium species), they are seed-transmissible endophytes of grasses, provide dramatic benefits to their host plants, and are important to the ecology of their hosts in nature and in agriculture settings such as pastures. The evolutionary transition to mutualism is exemplified by Epichloe festucae, the ubiquitous symbiont of fine fescue grasses, which displays pathogenic and mutualistic states simultaneously on the same host plant. In their mutualistic states these endophytes cause profound changes in plant growth, persistence, and resistance to abiotic and biotic stresses. Their effects are remarkable considering that they constitute less than 0.5% of their host biomass. Thus, they have allure as model symbionts, but also present technical difficulties in studying the molecular biology underlying their host interactions. Genomic tools can transcend such technical difficulties. This proposal initiates endophyte genomics in order to search for genes that may be especially relevant to the mutualistic and pathogenic stages and developmental coordination with their hosts. Objective 1 is to sequence the E. festucae genome to 8x coverage by end-sequencing clones of a 4 kb sheared-fragment library. Objective 2 is application ofbioinformatic techniques for sequence contig assembly and gene discovery. The deliverable result will be publication of an annotated genomic sequence of the model endophyte, and identification of a set of putative genes predicted to include the great majority of those in the genome. Intellectual Merit: This is a large-scale gene discovery effort for a model bioprotective symbiont that also has an alternative, pathogenic life cycle. Genes identified may be unique to this and related endophytes or common with other fungi. This, and relationships of their predicted gene products, will suggest testable hypotheses with respect to gene functions in bioprotection, pathogenesis, and biosynthesis of secondary metabolites. This endophyte genome project will marry modern research techniques (genomics and bioinformatics) with. evolution, ecology and agriculture. Broader Impacts: Data generated from this study will rapidly be made accessible to the scientific community, and will be an important resource for comparative genome studies of fungi, particularly plant pathogens and mutualistic symbionts. The project will involve cross-training postdocs, graduate and undergraduate students in the biological and computer sciences. The trainees will learn high-throughput, robotic methods of generating biological data and the analysis of large data sets. There is an acute need for such cross-trained scientist in academics, government and industry. The investigators will actively recruit students from traditionally underrepresented minorities in ways that have proven successful in increasing their representation in recent years. The subject of this proposal is a model member of a group of fungi that have major economic impacts in agriculture. A negative economic impact is that some of these endophytes cause livestock toxicosis, estimated to cost the U.S. beef industry 5600 million annually, with additional impacts on other livestock and wildlife. But, a positive impact is that the endophytes provide a variety of fitness enhancements to the plants, improving longevity of pasture, turf, and conservation grass stands. The proposed research will go far in helping elucidate, thus address, the mechanisms of beneficial and detrimental endophyte effects.