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Protocols

MycoCosm specifications

Information


Unique identifier OMICS_01657
Name MycoCosm
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Allowed
Maintained Yes

Documentation


Maintainer


  • person_outline Igor V. Grigoriev

Publication for MycoCosm

MycoCosm citations

 (65)
library_books

The Hydrophobin Like OmSSP1 May Be an Effector in the Ericoid Mycorrhizal Symbiosis

2018
Front Plant Sci
PMCID: 5938622
PMID: 29765384
DOI: 10.3389/fpls.2018.00546

[…] 2 × 100 bp Illumina HiSeq sequencing (RNA-Seq) was performed by IGA Technology Services (Udine, Italy). Raw reads were trimmed and aligned to the respective reference transcripts available at the JGI MycoCosm database (http://genome.jgi-psf.org/programs/fungi/index.jsf) using CLC Genomics Workbench v6. For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.8 and the ma […]

library_books

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

2018
Sci Rep
PMCID: 5910433
PMID: 29679020
DOI: 10.1038/s41598-018-24686-4

[…] bly of RNA contigs. Reads were assembled into consensus sequences using Rnnotator (v. 3.3.2).Both genomes were annotated using the JGI Annotation Pipeline and made available via the JGI fungal portal MycoCosm. The genomes of Cadophora sp. and P. macropsinosa can be accessed at http://genome.jgi.doe.gov/Cadsp1 and http://genome.jgi.doe.gov/Perma1 respectively, and these Whole Genome Shotgun project […]

library_books

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors

2018
BMC Genomics
PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] .21 [] incorporated in Program to Assemble Spliced Alignments (PASA) pipeline v.2.0.2 [] to build a complete set of transcripts. Homologs from predicted proteins of H. irregulare TC 32–1 available in Mycocosm at Joint Genome Institute (JGI) portal (http://genome.jgi.doe.gov/Hetan2/Hetan2.home.html) were searched in the soft-masked assembly by Exonerate v.2.2.0 [] with protein2genome model. GeneMar […]

call_split

Genome Wide Analysis of Corynespora cassiicola Leaf Fall Disease Putative Effectors

2018
Front Microbiol
PMCID: 5840194
PMID: 29551995
DOI: 10.3389/fmicb.2018.00276
call_split See protocol

[…] e de novo assembled into consensus sequences using Rnnotator (Martin et al., ). The genome assembly was annotated using the JGI Annotation Pipeline and made available via the JGI fungal genome portal MycoCosm (jgi.doe.gov/fungi; Grigoriev et al., ). The Whole Genome Shotgun project of the reference isolate CCP has been deposited at DDBJ/ENA/GenBank under the accession NSJI00000000. The version des […]

library_books

A Near Complete Haplotype Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

2018
MBio
PMCID: 5821087
PMID: 29463659
DOI: 10.1128/mBio.02275-17

[…] with proteinortho v5.16 (-singles) () of all nonredundant candidate effectors with publicly available P. striiformis f. sp. tritici genomes. Pst-130 () and Pst-78 () protein sets were downloaded from MycoCosm (9 May 2017) (). Pst-0821, Pst-21, Pst-43, and Pst-887 were downloaded from yellowrust.com (30 March 2017) (). We performed a similar analysis to search for candidate effector orthologs in Pu […]

call_split

Molecular Networks of Postia placenta Involved in Degradation of Lignocellulosic Biomass Revealed from Metadata Analysis of Open Access Gene Expression Data

2018
PMCID: 5859471
PMID: 29559843
DOI: 10.7150/ijbs.22868
call_split See protocol

[…] ained statistically significant genes were analyzed by the supplier provided annotations Protein-ID and Best hit BlastP. Gene and protein level annotations of P. placenta MAD-698R were retrieved from MycoCosm (fungal genome repository) , . Custom linux based scripts were written to retrieve the annotations for differentially expressed gene list using KOG, GO and InterPro annotations of P. placenta […]

Citations

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MycoCosm institution(s)
US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
MycoCosm funding source(s)
Supported by Director, Office of Science, Office of Biological and Environmental Research, Life Sciences Division, US Department of Energy [DE-AC02-05CH11231].

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