Functional Analysis of a Model Filamentous Fungus

项目描述（由申请人提供）：本项目中四个相互依赖的项目的总体目标是对粗糙脉孢菌（Neurospora crassa）进行功能基因组学、注释和表达分析，粗糙脉孢菌是一种丝状真菌，已成为超过25万种非酵母真菌集合的模型。大多数脉孢菌基因在酵母中没有同源物，近40%的基因在任何生物体中没有强同源物，这表明对这些基因功能的研究既新颖又有意义。脉孢菌是真核生物基础研究的重要模式，与脉孢菌相关的真菌包括重要的动物和植物病原体以及产生抗生素、化学品、酶和药物的工业菌株。 43 Mb脉孢菌基因组完全测序（>16倍存档覆盖率），使用在脉孢菌基因上训练的程序进行自动注释预测10，082种蛋白质。第一个项目将通过有针对性的基因替换、对这些菌株进行初步表型分析以及将其分发给广大科学界来系统地破坏基因。通过注释和基因组学的主要重点，我们将建立一个平台，用于电子捕获社区反馈和现有注释的数据，同时建立和维护一个数据库来捕获和显示表型信息，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菌中近11，000种可区分的转录本进行转录谱分析。这项工作将提供在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;这些数据将通过网络结构提供。由于选择性剪接、选择性启动子和长反义转录物对脉孢菌中表达序列的整体复杂性有广泛贡献，因此将从野生型和相关菌株产生cDNA文库以记录这种复杂性以帮助注释。来自相关菌株的序列将驱动SNP图谱的组装。总的来说，这一努力将有助于锚定基因组探索在很大程度上未开发的真菌系统发育王国。

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.