Status
This draft was generated using a whole genome shotgun method. Genomic DNA was used to create six main libraries; four small insert (2 - 4 kb) pUC18 libraries, one medium insert (6 - 8 kb) pMCL200 library, and one large insert (35 - 40 kb) pCC1Fos library. A total of 611,025 end sequences were used in the assembly, corresponding to approximately 10.6X sequence depth.
Releases
- v2.0 (February 2005): A total of 611,025 paired sequence fragments (10.6X coverage) were assembled with the JGI assembler, JAZZ. The assembly contains 35.1 million base pairs of non-redundant sequence in 232 scaffolds greater than 1 Kbp. 90% of the assembly was in 21 scaffolds, while 50% was found in 8 scaffolds longer than 1.9 Mbp.
- v1.0 (February 2002): A total of 619,903 paired sequence fragments (10.5X coverage) were assembled with the JGI assembler, JAZZ. The assembly contains 29.6 million base pairs of non-repetitive sequence in 349 scaffolds greater than 3 kbp. 90% of the assembly was in 165 scaffolds. 50% was found in 45 scaffolds longer than 203 Kbp. Gene modeling and analysis were performed at the JGI and ORNL.
Summary statistics for the Phanerochaete chrysosporium
v3.0 release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 35.15 |
| Sequencing read coverage depth | 10.6x |
| # of contigs | 1253 |
| # of scaffolds | 232 |
| # of scaffolds >= 2Kbp | 204 |
| Scaffold N50 | 8 |
| Scaffold L50 (Mbp) | 1.91 |
| # of gaps | 1021 |
| % of scaffold length in gaps | 7.5% |
| Three largest Scaffolds (Mbp) | 3.27, 3.04, 2.44 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | EST_contigs | 68995 | 63043 | 91.4% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1684 | 1416 |
| transcript | 1401 | 1184 |
| exon | 259 | 157 |
| intron | 66 | 56 |
| description: | ||
| protein length (aa) | 408 | 332 |
| exons per gene | 5.41 | 4 |
| # of gene models | 13602 |
Collaborators
- Dan Cullen, PI, USDA, Forest Service, Forest Products Laboratory (Madison, WI, USA)
- Catholic University, Departmento de Genética Molecular y Microbiologíca, Facultad de Ciencias Biológicas, Pontifica Universidad Católica de Chile, Santiago, Chile and Millenium Institute for Fundamental and Applied (Santiago, Chile)
- Department of Physics, University of California, Berkeley (Berkeley, CA, USA)
- Novozyme Biotech, Inc. (Davis, CA, USA)
- Oak Ridge National Laboratory (Oak Ridge, TN, USA)
- Center National De La Recherche Scientifique (France)
- Department of Biological Sciences, Columbia University (New York, NA USA)
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Ohm RA, Riley R, Salamov A, Min B, Choi IG, Grigoriev IV
Genomics of wood-degrading fungi.
Fungal Genet Biol. 2014 Nov;72():82-90. doi: 10.1016/j.fgb.2014.05.001
Ohm RA, Riley R, Salamov A, Min B, Choi IG, Grigoriev IV
Genomics of wood-degrading fungi.
Fungal Genet Biol. 2014 Nov;72():82-90. doi: 10.1016/j.fgb.2014.05.001
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.
