Functional Analysis of a Model Filamentous Fungus

描述(申请人提供)：该计划项目中四个相互依赖的项目的总体目标是对粗糙脉孢菌进行功能基因组学、注释和表达分析，这种丝状真菌已经成为超过250,000种非酵母真菌的组合模式。大多数脉孢菌基因在酵母菌中没有同源基因，近40%的基因在任何生物体中到目前为止都没有很强的同源基因，这表明对这些基因的功能的研究将是新颖和有意义的。脉孢菌是真核生物基础研究的重要模型，与脉孢菌相关的真菌包括重要的动植物病原菌和产生抗生素、化学物质、酶和药物的工业菌株。 43Mb的脉孢子虫基因组已经完全测序(&gt；16倍的档案覆盖范围)，使用训练脉孢子虫基因的程序进行自动注释可以预测10,082个蛋白质。第一个项目将通过有针对性的基因替换、这些菌株的初步表型以及它们在整个科学界的分布来寻求对基因的系统性破坏。通过主要关注注释和基因组学，我们将创建一个以电子方式捕获社区反馈和有关现有注释的数据的平台，同时建立和维护一个数据库来捕获和显示有关表型的信息，依靠EST分析的数据来完善基因结构。基于寡核苷酸的微阵列将允许对脉孢子菌中近11,000个可区分的转录本进行转录图谱分析。这项工作将提供各种生长条件下基因表达的基线分析，然后开始分析新基因丢失的全球影响；这些数据将通过结构通过网络提供。由于选择性剪接、选择性启动子和长的反义转录本对脉孢子虫表达序列的整体复杂性有广泛的贡献，因此将从野生型和相关菌株中建立cDNA文库来记录这种复杂性以帮助注释。相关菌株的序列将驱动SNP图谱的组装。总体而言，这一努力将有助于在基本上未被探索的真菌系统发育王国内进行基因组探索。

DESCRIPTION (provided by applicant): The overall goal of the four interdependent projects in this Program Project is to carry out functional genomics, annotation, and expression analyses of Neurospora crassa, the filamentous fungus that has become a model for the assemblage of over 250,000 species of non-yeast fungi. Most Neurospora genes have no homologs in yeasts and nearly 40% have no strong homologs in any organism to date, suggesting that examination of the functions of these genes will both novel and informative. Neurospora is an important model for basic research in eukaryotes, and fungi allied to Neurospora include significant animal and plant pathogens and industrial strains yielding antibiotics, chemicals, enzymes, and pharmaceuticals. The 43 Mb Neurospora genome is completely sequenced (>16 fold archival coverage), and automated annotation using programs trained on Neurospora genes predict 10,082 proteins. The first Project will pursue the systematic disruption of genes through targeted gene replacements, preliminary phenotyping of these strains, and their distribution to the scientific community at large. Through a primary focus in Annotation and Genomics, we will produce a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes, relying on data from EST analyses to refine the gene structures. Oligonucleotide-based microarrays will allow Transcriptional Profiling of the nearly 11,000 distinguishable transcripts in Neurospora. This effort will provide a baseline analysis of gene expression under a variety of growth conditions, and later begin to analyze the global effects of loss of novel genes; these data will be made available through the web via structures. Since alternative splicing, alternative promoters, and long antisense transcripts contribute widely to the overall complexity of expressed sequences in Neurospora, cDNA libraries will be generated from wild type and related strains to document this complexity to aid in annotation. Sequences from related strains will drive assembly of a SNP map. Overall, this effort will help to anchor genomic exploration within the largely unexplored phylogenetic Kingdom of the Fungi.