MycoCosm portal: gearing up for 1000 fungal genomes

By Igor V. Grigoriev, Roman Nikitin, S. Haridas, A. Kuo, R. Ohm, Robert Otillar, R. Riley, A. Salamov, Xu Zhao, Frank Korzeniewski and 4 more. 2013

1,343 citations recorded by the source corpus.

MycoCosm is a fungal genomics portal (http://jgi.doe.gov/fungi), developed by the US Department of Energy Joint Genome Institute to support integration, analysis and dissemination of fungal genome sequences and other ‘omics’ data by providing interactive web-based tools. MycoCosm also promotes and facilitates user community participation through the nomination of new species of fungi for sequencing, and the annotation and analysis of resulting data. By efficiently filling gaps in the Fungal Tree of Life, MycoCosm will help address important problems associated with energy and the environment, taking advantage of growing fungal genomics resources.

Subfields: Cell Biology, Molecular Biology, Plant Science

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

1. R. Blanchette
2. D. Hibbett

In Molecular Biology

1. Martin Steinegger
2. Johannes Söding
3. Milot Mirdita
4. Jinbo Xu
5. Francis Martin
6. Bernard Henrissat
7. Vincent Lombard
8. Clovis Galiez

In Plant Science

1. Vincent Lombard
2. Bernard Henrissat
3. Christoph Bleidorn
4. Francis Martin
5. R. Blanchette
6. D. Hibbett

Citations in the corpus

• Uniclust databases of clustered and deeply annotated protein sequences and alignments (2016, methodology): “gz: archive containing three files with Pfam, SCOP, and PDB annotations, each formatted as tab-separated lists with nine columns: (1,2) identifiers for query and target, (3-5, 6-8) domain start and end-position and total sequence length for both UniProt and database sequence, (9) HHblits E-value.”
• Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists (2015, neutral): “22 and 23 ).”
• PHI-base: the pathogen–host interactions database (2019, background): “and to the thousands of fungal genomes and hundreds of protist genomes in the MycoCosm database provided by the Joint Genome Institute (JGI) (44).”
• Computed structures of core eukaryotic protein complexes (2021, neutral): “To mitigate the first three challenges, we chose to predict protein complexes for the yeast Saccharomyces cerevisiae as the starting point because there are a large number of fungal genomes (16), the genome is relatively small (6000 genes in total), and there is relatively little mRNA splicing (17).”
• Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi (2014, background): “Genome assemblies and annotations for the organisms used in this study are available via the JGI Genome Portal MycoCosm (http://jgi.doe. gov/fungi; see also Table S1).”
• Third generation sequencing: technology and its potential impact on evolutionary biodiversity research (2016, background): “…massive sequencing of genomes from organisms all over the tree of life is envisaged by different consortia, many of them driven by research questions in the field of evolution (e.g., GIGA Consortium of Scientists, 2014; Grigoriev et al., 2014; i5K Consortium, 2013; Koepfli, Paten, & O’Brien, 2015).”