Fungal Genome and Transcriptomes in Phytopathogenesis

小菜蛾真菌复合体是一个研究寄主/病原体相互作用的生态学和进化的令人兴奋的系统，可以作为野生非农业环境中新出现的传染病的模型，在非农业环境中，寄主的异质性与大量研究的农业病原体形成了重要的对比。目前的基因组学规模的高通量技术对于洞察导致疾病进展的复杂系统和相关相互作用是非常宝贵的。该项目将为合理设计假说驱动的对紫罗兰的发育和发病机制的调查提供必要的基因组基础设施。将对在真菌发育和成功感染中发挥重要作用的基因组产生一个全面和比较的观点。其具体目标是：(1)测序和组装紫色微孢子菌的完整基因组，估计为25Mb；(2)使用计算方法对基因结构进行注释；(3)分析感染后期的基因转录谱；(4)迅速公布所有阅读、组装和注释；以及(5)制定教育、培训和推广计划。更广泛的影响：几个研究小组准备使用基因组序列来分析导致真菌发育和疾病产生的信号、宿主特异性、正选择下的基因、性别进化以及感染期间的基因表达。布罗德研究所将建立一个网站，以传播关于诸葛菜基因组的信息，并允许与其他基因组进行比较，包括玉米黑穗病的病原菌--玉米黑粉菌。这些资源将由公共和私营部门的科学家社区使用，他们对基础真菌生物学、宿主与寄生虫的相互作用、真菌进化以及通过更好地了解专性植物寄生真菌的基本感染机制和疾病过程来保护农作物免受真菌疾病影响的新方法的开发感兴趣。此外，该项目将为本科生提供参与真菌基因组学和生物信息学研究的教育机会，并扩大代表不足的群体(特别是非洲裔美国人、妇女、阿巴拉契亚人)对基础科学的参与。外展机制将提高这些本科生攻读生物科学高级学位的兴趣。

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.