Fungal Genome and Transcriptomes in Phytopathogenesis

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The Microbotryum violaceum fungal complex is an exciting system for examination of the ecology and evolution of host/pathogen interactions and can serve as a model for emerging infectious diseases in 'wild' non-agricultural environments where host heterogeneity provides an important contrast to heavily studied agricultural pathogens. Current genomics scale high-throughput technologies are invaluable for gaining insight into the complex systems and associated interactions that result in disease progression. This project will provide a genomics infrastructure necessary for the rational design of hypothesis driven inquiries into M. violaceum development and pathogenesis. A comprehensive and comparative view will be generated of the suites of genes that play significant roles in fungal development and successful infection. The specific objectives are to: (1) Sequence and assemble the complete genome of Microbotryum violaceum, which is estimated to be 25 Mb; (2) Annotate gene structure using computational methods; (3) Analyze gene transcription profiles late in infection; (4) Promptly release publicly all reads, assemblies, and annotation; and (5) Develop education, training and outreach programs. Broader impacts: Several research groups are prepared to use the genome sequence to analyze signaling leading to fungal development and disease production, host specificity, genes under positive selection, evolution of sex, and gene expression during infection. A website will be developed at the Broad Institute to disseminate the information on the genome of M. violaceum as well as allow comparison to other genomes, including Ustilago maydis, the causative agent of corn smut disease. These resources will be used by a community of scientists in the public and private sectors interested in basic fungal biology, host-parasite interactions, fungal evolution and the development of new methods for protecting agricultural crop plants from fungal diseases through a better understanding of the basic infection mechanism and disease process of obligate plant parasitic fungi. Furthermore, this project will provide educational opportunities for undergraduate students to participate in fungal genomics and bio-informatics research and broaden the participation in basic science by under-represented groups (specifically, African-Americans, women, Appalachians). An outreach mechanism will enhance the interest of such undergraduates in pursuing an advanced degree in the biological sciences.