Dunlap Jay C, Borkovich Katherine A, Henn Matthew R, Turner Gloria E, Sachs Matthew S, Glass N Louise, McCluskey Kevin, Plamann Michael, Galagan James E, Birren Bruce W, Weiss Richard L, Townsend Jeffrey P, Loros Jennifer J, Nelson Mary Anne, Lambreghts Randy, Colot Hildur V, Park Gyungsoon, Collopy Patrick, Ringelberg Carol, Crew Christopher, Litvinkova Liubov, DeCaprio Dave, Hood Heather M, Curilla Susan, Shi Mi, Crawford Matthew, Koerhsen Michael, Montgomery Phil, Larson Lisa, Pearson Matthew, Kasuga Takao, Tian Chaoguang, Baştürkmen Meray, Altamirano Lorena, Xu Junhuan
Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA.
Adv Genet. 2007;57:49-96. doi: 10.1016/S0065-2660(06)57002-6.
A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to accomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of non yeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed 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. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.
一个研究团队正在开展一项以丝状真菌粗糙脉孢菌为核心的功能基因组学项目，旨在开启对所有丝状真菌的功能基因组分析。这项工作中四个相互依存的项目的总体目标是完成对粗糙脉孢菌的功能基因组学、注释及表达分析。粗糙脉孢菌是一种丝状真菌，是超过25万种非酵母真菌群体的既定模型。基于已完全测序的43兆碱基的粗糙脉孢菌基因组，项目1通过靶向基因替换来系统地破坏基因，对突变菌株进行表型分析，并将它们分发给广大科学界。项目2主要聚焦于注释和生物信息学，开发了一个平台，用于以电子方式收集有关现有注释的群体反馈和数据，同时建立和维护一个数据库来捕获和展示有关表型的信息。项目3中创建的基于寡核苷酸的微阵列正用于收集粗糙脉孢菌在各种生长和发育条件下近11000个可区分转录本的基线表达数据，并最终开始分析项目1所创建菌株中缺失新基因的全局效应。项目4中生成的cDNA文库记录了粗糙脉孢菌表达序列的整体复杂性，包括可变剪接、可变启动子和反义转录本。此外，这些研究推动了一个目前由近300个标记组成的单核苷酸多态性（SNP）图谱的组装，这将大大加速基因的定位克隆。
