Functional Analysis of a Model Filamentous Fungus

模型丝状真菌的功能分析

• 批准号: 6876664
• 负责人: Jay C. Dunlap
• 金额: $ 177.23万
• 依托单位: DARTMOUTH COLLEGE
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-04-01 至 2009-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6876664
• 关键词: Neurospora; functional /structural genomics; fungal genetics

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.

描述（由申请人提供）：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（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 250,000 个物种组合的模型非酵母真菌。大多数脉孢菌基因在酵母中没有同源物，并且迄今为止，近 40% 的基因在任何生物体中都没有强同源物，这表明对这些基因功能的检查既新颖又信息丰富。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 脉孢菌基因组已完全测序（> 16 倍档案覆盖率），并且使用脉孢菌基因训练的程序进行自动注释，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分析以及将它们分发给整个科学界来追求系统性的基因破坏。通过主要关注注释和基因组学，我们将创建一个平台，用于以电子方式捕获社区反馈和有关现有注释的数据，同时构建和维护数据库以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能够对脉孢菌中近 11,000 个可区分的转录本进行转录分析。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整体影响；这些数据将通过网络通过结构提供。由于选择性剪接、选择性启动子和长反义转录本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生成 cDNA 文库，以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。总的来说，这项工作将有助于将基因组探索锚定在很大程度上未经探索的真菌系统发育王国中。