Coprinopsis cinerea Genome Project
Coprinopsis cinerea (Coprinus cinereus) is a multicellular basidiomycete with a typical mushroom form that undergoes a complete sexual cycle. A higher fungus (Agaricales), C. cinerea is comprised of many cell types providing a window on the development of multicellularity within the fungal kingdom. The short life cycle and easy cultivation of C. cinerea facilitate extensive genetic and molecular analysis of this species. Such analyses will help to address questions such as whether the genes responsible for the multicellularity of C. cinerea are the progenitors of those in other multicellular organisms, or are innovations restricted to the fungal kingdom.
The Coprinopsis cinerea sequence project is part of the Broad Institute's Fungal Genome Initiative. Its goal is to release a 10X genome sequence coverage for Coprinopsis cinerea, strain Okayama 7 (#130). The Coprinopsis genome project is a partnership between the Broad Institute and the Coprinopsis research community. Genomic DNA for the genome project was provided by Patricia Pukkila at University of North Carolina. The Broad produced whole genome shotgun sequence from 4kb and 10kb plasmids and 40kb Fosmids. The resulting 10X assembly was made public July 2003. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the project accession AACS00000000.
What is Coprinopsis cinerea?
Coprinopsis cinerea is a multicellular basidiomycete with a typical mushroom form that undergoes a complete sexual cycle. Unlike most mushrooms, C. cinerea can complete its entire life cycle (2 weeks) in the laboratory. Its easy cultivation on simple defined media permits extensive genetic and molecular analysis. Spores of each mating type produce a monokaryotic mycelium. The fusion of compatible hyphae establishes a dikaryotic mycelium that forms a fruiting body - a miniature mushroom with three distinct tissues (gill, stalk, and cap). The primordium grows and the basidial cells of the hymenial layers in the gills initiate and complete nuclear fusion, meiosis, and haploid basidiospore formation. Spore maturation and active discharge from the cap are accompanied by elongation of the stalk and autodigestion of the remaining gill tissue.
Genomic analysis may reveal whether the genes responsible for the multicellularity of Coprinopsis cinerea are the progenitors of those in other multicellular organisms (e.g., nuclear receptors) or are innovations restricted to the fungal kingdom. Coprinopsis cinerea is a higher fungus (Agaricales) comprised of many cell types and, therefore, provides a window on the development of multicellularity within a single kingdom. The cells of this organism undergo coordinated developmental events not observed in unicellular fungi, including secondary and tertiary gill formation, cap expansion and autodigestion, active spore discharge, and stalk elongation, phototropism, and gravitropism.
The haploid genome size of C. cinerea is estimated at 37.5 Mb. The 13 chromosomes range in size from 1-5 Mb. Over 100 markers affecting mating type, hyphal growth, fruit body morphogenesis, and DNA repair have been assigned to 10 linkage groups. Coprinopsis cinerea is easily transformed by DNA, and targeted gene disruption is achieved in some instances. Both RFLP and RAPD markers are widely utilized. Duplicated genes frequently become methylated at CpG dinucleotides. Chromosome-specific cosmid libraries have been prepared for 8 of the 13 chromosomes. Both commercially prepared cDNA libraries and a cDNA library suitable for yeast two-hybrid screens are available. A partial contig map of the smallest chromosome (~1 Mb) has been assembled and its sequence is currently being determined.
Collaborators on the project include: Jason Stajich, Patricia Pukkila, Frederick Dietrich, Mark Farman, Allen C. Gathman, Patrick Hoegger, Sirdar Kilaru, Ursula Kues, Walt Lilly, Aaron Mackey, Hajime Muraguchi, Cathy Rehmeyer, Mario Stanke, Rajesh Velagapudi, Sarah K. Wilke, Mark Borodovsky, Roderick Guigo.
Data access and Citation
The genome assembly and annotation of Coprinopsis cinerea is available in Genbank.
For use of this data, please cite: Stajich JE et al., "Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus).", Proc Natl Acad Sci U S A, 2010 Jun 14;107(26):11889-94