About CopciDB

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.

News

Welcome

Welcome to CopciDB! We are happy that CopciDB was launched today, and hope it will provide a useful platform for researchers working on mushroom-forming fungi and fruiting body development.

 Current versions of available genomes in CopciDB:

C. cinerea Okayama 7 (annotation from Stajich et al. 2010 PNAS): 94 scaffolds (13 Chr + 81 U), 13 393 genes
C. cinerea A43mutB43mut pab1-1 #326 (annotation from Hegedus et al. 2024 bioRxiv): 21 scaffolds (13 Chr + 8 fragment), 13 617 genes.

List of currently integrated expression data:

  • Developmental time course of C. cinerea A43mutB43mut (Krizsan et al. 2019)
  • Transcriptional aspects of four developmental paths of C. cinerea A43mutB43mut (Xie et al. 2020)
  • Growth of C. cinerea A43mutB43mut on XX lignocellulosic, simple and complex carbon as well as F nitrogen sources (Hegedus et al in prep)
  • Expression profiling of the response of cinerea A43mutB43mut to various stress factors (Hegedus et al in prep)
  • Expression profiling of the life cycle of cinerea A43mutB43mut including basidiospore germination, oidiation, dark and light incubation and fruiting body development (Hegedus et al.)
  • C. cinerea A43mutB43mut challenges with Bacillus subtilis and E. coli (Kombrink et al. 2018)
  • Single-cell (ultra-low input) RNA-Seq data of the early development of C. cinerea A43mutB43mut (Varga et al. in prep)
  • Transcriptional profiling of early germ-tube outgrowth of C. cinerea A43mutB43mut (Lau et al. 2020)
  • C. cinerea Okayama7 challenged with fungivorous and bacterivorous nematodes and Gram+ and Gram- bacteria (Plaza et al. 2016)

 

The pages will be periodically updated with new annotations, expression data and others.

Posted May 01, 2024