If you use data from this site in your work, please reference to Hegedus et al.
CopciDB is a community resource for the model mushroom Coprinopsis cinerea as well as other mushroom-forming fungi and intends to facilitate research and discussion on the Agaricomycetes, with special emphasis on fruiting body development. The database is built around high quality genomes of two C. cinerea strains (Okayama 7 and A43mutB43mut), which are widely used by laboratories working on these fascinating fungi around the world. CopciDB aims to provide a continuously updated gold standard resource for mycologists and a platform to develop research questions on mushrooms. It contains information on genes, expression patterns, orthology across the most frequently examined fruiting body forming species and evolutionary aspects; as well as tools for the analysis of genomic and protein sequences.
This fascinating group of fungi belong to the class Agaricomycetes in the Basidiomycota, the group of fungi that produces the most complex multicellular structures in the fungal kingdom, called fruiting bodies. Mushroom-forming fungi are used as model systems of basic biological phenomena, as healthy and sustainable food sources, efficient decomposers of lignocellulosic plant materials, or as mutualistic mycorrhizal partners of a wide range of plant species, to name just a few.
Inspired by similar websites for well-established model systems (such as yeastgenome.org, aspgd.org, candidagenome.org), this database focuses on the genomics and transcriptomics of Coprinopsis cinerea and related mushroom-forming fungi which are used as models of fruiting body development. Thus, it includes information on Agaricus bisporus (two strains), Agrocybe aegerita, Auricularia subglabra, Flammulina velutipes, Ganoderma sp., Grifola frondosa, Hypsizygus marmoreus, Lentinula edodes and Schizophyllum commune.
The site integrates genomic and transcriptomic information from a multitude of studies as well as information on gene orthology across species and evolutionary conservation.
The database is built around genomes of C. cinerea Okayama 7 (Stajich et al. 2010 PNAS) and C. cinerea A43mutB43mut pab1-1 #326 (Muraguchi et al. 2015 Plos One, later improved by Xie et al. 2020 FGB and Hegedus et al. 2024 bioRxiv). Both genomes are assembled at the chromosome level. Resequencing of the A43mutB43mut strain was made possible by a Community Sequencing Program of the Joint Genome Institute aiming to produce telomere-to-telomere genomes of important model fungi (led by Michael Freitag). For each gene/protein in the two genomes, gene pages (e.g. CC1G_12850) summarize the available information on the gene’s structure, function, expression and conservation, which can be browsed following corresponding tabs. Gene pages also provide information on orthologs in other important mushroom species.
Concerning the two C. cinerea strains, users will find more gene expression data for the A43mutB43mut strain from multiple recent studies of the development (including single-cell RNA-Seq) and lignocellulose degrading abilities of this species, whereas correspondence to published papers is easier to find in the Okayama 7 genome, because authors often refer to genes based on their systematic CC1G_XXXXX identifiers.
The Genome browser function allows viewing the assembly, with several additional tracks of expression data (Illumina, QuantSeq, Nanopore) using JBrowse.
Expression data from multiple studies have been integrated, including an ultra-low input RNA-Seq study of the early (primordial) development of C. cinerea (Varga et al <ref later>). Gene expression levels are shown as bar diagrams with variances, samples with similar conditions or belonging to one study grouped into single plots whenever possible.
The Search function provides quick access to similarity-based (Blast) or textual search results, such as for gene names (e.g. COP4) or conserved protein domains (e.g. IPR016024). Blast searches can be performed against the assemblies, gene-, transcript- and protein repertoires of both species.
The Downloads section provides snapshots of the annotated genomes of both C. cinerea strains for download and local use.
Annotations are provided for Carbohydrate-active genes (CAZymes) and transcription factors (TFs).
We appreciate the contributions of all people involved.