Status
[July 2023] The Coprinopsis cinerea AmutBmut v2.0 genome was sequenced using PacBio and assembled with Flye. The gene models were predicted by Laszlo Nagy's group and imported into MycoCosm. The JGI Fungal Annotation Pipeline was used to provide functional annotation to the gene models and remove poor quaility models. The mitochondrial genome was assembled separately and is available in the download section.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 37.27 |
| Sequencing read coverage depth | 77.08x |
| # of contigs | 23 |
| # of scaffolds | 21 |
| # of scaffolds >= 2Kbp | 21 |
| Scaffold N50 | 5 |
| Scaffold L50 (Mbp) | 3.44 |
| # of gaps | 2 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 4.36, 3.99, 3.73 |
The RNA dataset includes data from Illumina and Pacbio reads.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 46498398 | 46324837 | 99.6% |
| Other | IsoSeq_hq_reads_HOTYG | 124971 | 124375 | 99.5% |
| Other | RNAseq_contigs | 46159 | 45324 | 98.2% |
| Gene Models | FilteredModels4 | |
| length (bp) of: | average | median |
| gene | 1991 | 1729 |
| transcript | 1675 | 1441 |
| exon | 284 | 165 |
| intron | 66 | 58 |
| description: | ||
| protein length (aa) | 454 | 373 |
| exons per gene | 5.90 | 5 |
| # of gene models | 13154 |
Collaborators
- Michael Freitag, Department of Biochemistry & Biophysics, Oregon State University
- Laszlo Nagy, Biological Research Centre, Szeged.
Links
- JGI PhyloGroup Portals: Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricales
Funding
The work conducted by the U.S. Department of Energy Joint Genome
Institute, a DOE Office of Science User Facility, is supported by
the Office of Science of the U.S. Department of Energy under
Contract No. DE-AC02-05CH11231.
