Status
Dec 2013. The Auricularia subglabra TFB10046 SS–5 v2.0 genome was assembled using the Illumina and PacBio platforms and assembled with AllPathsLG version R41043 (Gnerre et al., 2010). The genome was annotated using the JGI annotation pipeline and custom analyses.
Summary statistics for the Auricularia subglabra SS-5 v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 76.85 |
| Sequencing read coverage depth | 95.8 |
| # of contigs | 2158 |
| # of scaffolds | 761 |
| # of scaffolds >= 2Kbp | 556 |
| Scaffold N50 | 37 |
| Scaffold L50 (Mbp) | 0.62 |
| # of gaps | 1397 |
| % of scaffold length in gaps | 13.3% |
| Three largest Scaffolds (Mbp) | 2.14, 2.12, 1.82 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| EstClusters | 454EstClusters | 14766 | 14179 | 96.0% |
| EstClusters | CombestEstClusters | 19163 | 19144 | 99.9% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1556 | 1281 |
| transcript | 1217 | 1026 |
| exon | 254 | 148 |
| intron | 91 | 55 |
| description: | ||
| protein length (aa) | 382 | 319 |
| exons per gene | 4.80 | 3 |
| # of gene models | 25459 |
Collaborators
- PI: Igor Grigoriev, DOE Joint Genome Institute
- David Hibbett, Hibbett lab at Clark University
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
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.
