Status
Assembly v1 (September 2010) is a draft assembly of 454 and Sanger gDNA reads, and shredded Velvet contigs. The latter were assembled from Solexa gDNA reads. A total of 348 scaffolds and 50.8 Mbp were assembled using Newbler.
Summary statistics for the Wolfiporia cocos v1.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 50.48 |
| Sequencing read coverage depth | 40.48x |
| # of contigs | 2228 |
| # of scaffolds | 348 |
| # of scaffolds >= 2Kbp | 348 |
| Scaffold N50 | 7 |
| Scaffold L50 (Mbp) | 2.54 |
| # of gaps | 940 |
| % of scaffold length in gaps | 4.4% |
| Three largest Scaffolds (Mbp) | 5.11, 4.03, 3.94 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | ESTs | 1311441 | 1265180 | 96.5% |
| Other | EST contigs | 12377 | 11329 | 91.5% |
| Gene Models | FilteredModels2 | |
| length (bp) of: | average | median |
| gene | 2035 | 1634 |
| transcript | 1529 | 1262 |
| exon | 242 | 146 |
| intron | 97 | 57 |
| description: | ||
| protein length (aa) | 409 | 333 |
| exons per gene | 6.31 | 5 |
| # of gene models | 12746 |
Collaborators
- PI: Igor Grigoriev at DOE Joint Genome Institute
- David Hibbett at Clark U.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.
Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748
Floudas D, Binder M, Riley R, Barry K, Blanchette RA, Henrissat B, Martínez AT, Otillar R, Spatafora JW, Yadav JS, Aerts A, Benoit I, Boyd A, Carlson A, Copeland A, Coutinho PM, de Vries RP, Ferreira P, Findley K, Foster B, Gaskell J, Glotzer D, Górecki P, Heitman J, Hesse C, Hori C, Igarashi K, Jurgens JA, Kallen N, Kersten P, Kohler A, Kües U, Kumar TK, Kuo A, LaButti K, Larrondo LF, Lindquist E, Ling A, Lombard V, Lucas S, Lundell T, Martin R, McLaughlin DJ, Morgenstern I, Morin E, Murat C, Nagy LG, Nolan M, Ohm RA, Patyshakuliyeva A, Rokas A, Ruiz-Dueñas FJ, Sabat G, Salamov A, Samejima M, Schmutz J, Slot JC, St John F, Stenlid J, Sun H, Sun S, Syed K, Tsang A, Wiebenga A, Young D, Pisabarro A, Eastwood DC, Martin F, Cullen D, Grigoriev IV, Hibbett DS
The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes.
Science. 2012 Jun 29;336(6089):1715-9. doi: 10.1126/science.1221748
Links
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.
