Status
[December 2018] The Schizophyllum commune 227.1 genome was sequenced using Illumina, assembled with SPAdes (v3.12.0), and annotated using the JGI Annotation Pipeline. Mitochondrial genome was assembled separately and is available on the Download page.
Summary statistics for the Schizophyllum commune 227.1
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 38.32 |
| Sequencing read coverage depth | 169.43x |
| # of contigs | 1131 |
| # of scaffolds | 1000 |
| # of scaffolds >= 2Kbp | 776 |
| Scaffold N50 | 70 |
| Scaffold L50 (Mbp) | 0.15 |
| # of gaps | 131 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 0.69, 0.61, 0.56 |
Note: The following EST alignment statistics reflect
alignment of reference strain H4-8 RNAseq to the strain 227.1
assembly. Based on poor mapping, H4-8 EST contig assemblies were
included only as fgenesh_kg training data when determining the
final 227.1 FilteredModels2 annotation.
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | ESTclusters | 83121 | 16538 | 19.9% |
| Ests | est.fasta | 860951048 | 547673893 | 63.6% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1760 | 1494 |
| transcript | 1408 | 1196 |
| exon | 244 | 147 |
| intron | 76 | 55 |
| description: | ||
| protein length (aa) | 450 | 377 |
| exons per gene | 5.76 | 5 |
| # of gene models | 13547 |
Collaborators
- Robin A. Ohm, Utrecht University, The Netherlands
Links
- JGI PhyloGroup Portals: Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Schizophyllum
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.
