Status
June 2013. The genome assembly of Schizophyllum commune Loenen D was sequenced using Illumina technology and assembled using AllPathsLG release version R42328. To assist in gene prediction, ESTs from the reference strain H4-8 were used.
Summary statistics for the Schizophyllum commune Loenen D
v1.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 35.88 |
| Sequencing read coverage depth | 112.3X |
| # of contigs | 1822 |
| # of scaffolds | 1774 |
| # of scaffolds >= 2Kbp | 1357 |
| Scaffold N50 | 194 |
| Scaffold L50 (Mbp) | 0.05 |
| # of gaps | 48 |
| % of scaffold length in gaps | 0.1% |
| Three largest Scaffolds (Mbp) | 0.32, 0.29, 0.27 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | All_conditions | 83121 | 19187 | 23.1% |
| Other | Three_conditions | 51144 | 12040 | 23.5% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 1708 | 1438 |
| transcript | 1370 | 1153 |
| exon | 247 | 148 |
| intron | 76 | 55 |
| description: | ||
| protein length (aa) | 435 | 363 |
| exons per gene | 5.55 | 4 |
| # of gene models | 13827 |
Collaborators
- Robin Ohm - DOE Joint Genome Institute, USA
- Luis Lugones - Utrecht University, The Netherlands
- Han Wösten - Utrecht University, The Netherlands
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Marian IM, Vonk PJ, Valdes ID, Barry K, Bostock B, Carver A, Daum C, Lerner H, Lipzen A, Park H, Schuller MBP, Tegelaar M, Tritt A, Schmutz J, Grimwood J, Lugones LG, Choi IG, Wösten HAB, Grigoriev IV, Ohm RA
The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune.
mBio. 2022 May 23;():e0062822. doi: 10.1128/mbio.00628-22
Marian IM, Vonk PJ, Valdes ID, Barry K, Bostock B, Carver A, Daum C, Lerner H, Lipzen A, Park H, Schuller MBP, Tegelaar M, Tritt A, Schmutz J, Grimwood J, Lugones LG, Choi IG, Wösten HAB, Grigoriev IV, Ohm RA
The Transcription Factor Roc1 Is a Key Regulator of Cellulose Degradation in the Wood-Decaying Mushroom Schizophyllum commune.
mBio. 2022 May 23;():e0062822. doi: 10.1128/mbio.00628-22
Links
Schizophyllum commune strains sequenced at JGI:
- Schizophyllum commune H4-8 (reference strain)
- Schizophyllum commune Tattone D
- Schizophyllum commune Loenen D (this portal)
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.
