Enabling a community to dissect an organism: overview of the Neurospora functional genomics project.
Jay C. Dunlap,Katherine A. Borkovich,Matthew R. Henn,Gloria E. Turner,Matthew S. Sachs,N. Louise Glass,Kevin McCluskey,Michael Plamann,James E. Galagan,Bruce W. Birren,Richard L. Weiss,Jeffrey P. Townsend,Jennifer J. Loros,Mary Anne Nelson,Randy Lambreghts,Hildur V. Colot,Gyungsoon Park,Patrick D. Collopy,Carol S. Ringelberg,Christopher M. Crew,Liubov Litvinkova,David DeCaprio,Heather M. Hood,Susan Curilla,Mi Shi,Matthew Crawford,Michael Koerhsen,Phil Montgomery,Lisa Larson,Matthew D. Pearson,Takao Kasuga,Chaoguang Tian,Meray Baştürkmen,Lorena Altamirano,Junhuan Xu +34 more
TLDR
CDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts, and drive the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes.Abstract:
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 acccomplish 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 nonyeast 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.read more
Citations
More filters
Journal ArticleDOI
Cellobiose Dehydrogenase and a Copper-Dependent Polysaccharide Monooxygenase Potentiate Cellulose Degradation by Neurospora crassa
TL;DR: Cellobiose dehydrogenases and proteins related to the polysaccharide monooxygenases described here are found throughout both ascomycete and basidiomycete fungi, suggesting that this model for oxidative cellulose degradation may be widespread throughout the fungal kingdom.
Journal ArticleDOI
Systems analysis of plant cell wall degradation by the model filamentous fungus Neurospora crassa
Chaoguang Tian,William T. Beeson,Anthony T. Iavarone,Jianping Sun,Michael A. Marletta,Jamie H. D. Cate,N. Louise Glass +6 more
TL;DR: The results show that the powerful tools available in N. crassa allow for a comprehensive system level understanding of plant cell wall degradation mechanisms used by a ubiquitous filamentous fungus.
Journal ArticleDOI
The Fungal Genetics Stock Center: a repository for 50 years of fungal genetics research
TL;DR: The Fungal Genetics Stock Center was established in 1960 to ensure that important strains used in early genetics research were available to subsequent generations of fungal geneticists and, as research came to depend on cloned genes, vectors and gene libraries, the FGSC included these materials.
Journal ArticleDOI
Efficient Gene Replacements in Toxoplasma gondii Strains Deficient for Nonhomologous End Joining
TL;DR: It is revealed that a significant KU-dependent NHEJ DNA repair pathway is present in Toxoplasma gondii, making this genetic background an efficient host for gene targeting to speed postgenome functional analysis and genetic dissection of parasite biology.
Journal ArticleDOI
Plant Cell Wall Deconstruction by Ascomycete Fungi
TL;DR: This review covers plant biomass degradation, from sensing, to transmission and modulation of signals, to activation of transcription factors and gene induction, to enzyme complement and function.
References
More filters
Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Proceedings Article
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Timothy L. Bailey,Charles Elkan +1 more
TL;DR: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.
Journal ArticleDOI
Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
Elizabeth A. Winzeler,Daniel D. Shoemaker,Anna Astromoff,Hong Liang,Keith Anderson,Bruno André,Rhonda Bangham,Rocío Benito,Jef D. Boeke,Howard Bussey,Angela M. Chu,Carla Connelly,Karen Davis,Fred S. Dietrich,Sally Dow,Mohamed El Bakkoury,Françoise Foury,Stephen H. Friend,Erik Gentalen,Guri Giaever,Johannes H. Hegemann,Ted Jones,Michael T. Laub,Hong Liao,Nicole Liebundguth,David J. Lockhart,Anca Lucau-Danila,Marc Lussier,Nasiha M'Rabet,Patrice Menard,Michael Mittmann,Chai Pai,Corinne Rebischung,José L. Revuelta,Linda Riles,Christopher J. Roberts,Petra Ross-Macdonald,Bart Scherens,Michael Snyder,Sharon Sookhai-Mahadeo,Reginald Storms,Steeve Veronneau,Marleen Voet,Guido Volckaert,Teresa R. Ward,Robert W. Wysocki,Grace Yen,Kexin Yu,Katja Zimmermann,Peter Philippsen,Mark Johnston,Ronald W. Davis +51 more
TL;DR: A total of 6925 Saccharomyces cerevisiae strains were constructed, by a high-throughput strategy, each with a precise deletion of one of 2026 ORFs (more than one-third of the ORFs in the genome), finding that 17 percent were essential for viability in rich medium.
Journal ArticleDOI
Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae.
TL;DR: Three new dominant drug resistance cassettes have unique antibiotic resistance phenotypes and do not affect growth when inserted into the ho locus, which make the cassettes ideally suited for creating S. cerevisiae strains with multiple mutations within a single strain.
Journal ArticleDOI
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
Related Papers (5)
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
Lessons from the Genome Sequence of Neurospora crassa: Tracing the Path from Genomic Blueprint to Multicellular Organism
Katherine A. Borkovich,Lisa A. Alex,Oded Yarden,Michael Freitag,Gloria E. Turner,Nick D. Read,Stephan Seiler,Deborah Bell-Pedersen,John V. Paietta,Nora Plesofsky,Michael Plamann,Marta Goodrich-Tanrikulu,Ulrich Schulte,Gertrud Mannhaupt,Frank E. Nargang,Alan Radford,Claude P. Selitrennikoff,James E. Galagan,Jay C. Dunlap,Jennifer J. Loros,David E. A. Catcheside,Hirokazu Inoue,Rodolfo Aramayo,Michael Polymenis,Eric U. Selker,Matthew S. Sachs,George A. Marzluf,Ian T. Paulsen,Rowland H. Davis,Daniel J. Ebbole,Alex Zelter,Eric R. Kalkman,Rebecca O’Rourke,Frederick J. Bowring,Jane Yeadon,Chizu Ishii,Keiichiro Suzuki,Wataru Sakai,Robert Pratt +38 more