Status
Version 3, September 2013. This is an improved version of the Schizophyllum commune genome. The original assembly was sequenced using Sanger technology and assembled using Arachne. In this improved assembly one primer walk round reduced the contig count from 276 to 72.
Summary statistics for the Schizophyllum commune v3.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 38.67 |
| Sequencing read coverage depth | 8.29x |
| # of contigs | 72 |
| # of scaffolds | 25 |
| # of scaffolds >= 2Kbp | 25 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 2.56 |
| # of gaps | 47 |
| % of scaffold length in gaps | 0.2% |
| Three largest Scaffolds (Mbp) | 4.46, 3.88, 3.54 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | All_conditions | 83121 | 61920 | 74.5% |
| Other | Rnnotator | 47007 | 34452 | 73.3% |
| Other | Three_conditions | 51144 | 40804 | 79.8% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1772 | 1500 |
| transcript | 1453 | 1235 |
| exon | 276 | 164 |
| intron | 77 | 55 |
| description: | ||
| protein length (aa) | 418 | 343 |
| exons per gene | 5.27 | 4 |
| # of gene models | 16319 |
Collaborators
- Robin Ohm, DOE Joint Genome Institute, USA
- Igor Grigoriev, DOE Joint Genome Institute, USA
- 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
Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wösten HA
Genome sequence of the model mushroom Schizophyllum commune.
Nat Biotechnol. 2010 Sep;28(9):957-63. doi: 10.1038/nbt.1643
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
Ohm RA, de Jong JF, Lugones LG, Aerts A, Kothe E, Stajich JE, de Vries RP, Record E, Levasseur A, Baker SE, Bartholomew KA, Coutinho PM, Erdmann S, Fowler TJ, Gathman AC, Lombard V, Henrissat B, Knabe N, Kües U, Lilly WW, Lindquist E, Lucas S, Magnuson JK, Piumi F, Raudaskoski M, Salamov A, Schmutz J, Schwarze FW, vanKuyk PA, Horton JS, Grigoriev IV, Wösten HA
Genome sequence of the model mushroom Schizophyllum commune.
Nat Biotechnol. 2010 Sep;28(9):957-63. doi: 10.1038/nbt.1643
Links
Schizophyllum commune reference strain H4-8:
- Schizophyllum commune H4-8 (reference strain, version 3, this portal)
- Schizophyllum commune H4-8 (reference strain, version 2, for archival use only)
- Schizophyllum commune H4-8 (reference strain, version 1, for archival use only)
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.
