Status
v2, September 2011. This is an improved version of the Serpula lacrymans 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 46 to 36.
Summary statistics for the Serpula lacrymans S7.9 v2.0
release are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 42.73 |
| Sequencing read coverage depth | 8 |
| # of contigs | 375 |
| # of scaffolds | 36 |
| # of scaffolds >= 2Kbp | 36 |
| Scaffold N50 | 6 |
| Scaffold L50 (Mbp) | 2.95 |
| # of gaps | 339 |
| % of scaffold length in gaps | 0.9% |
| Three largest Scaffolds (Mbp) | 5.71, 3.54, 3.27 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | Sanger ESTs | 751838 | 402772 | 53.6% |
| Other | Sanger Newbler-assembled clusters | 107971 | 67678 | 62.7% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1588 | 1304 |
| transcript | 1244 | 1023 |
| exon | 217 | 141 |
| intron | 75 | 58 |
| description: | ||
| protein length (aa) | 370 | 296 |
| exons per gene | 5.73 | 4 |
| # of gene models | 12789 |
Collaborators
- Daniel Eastwood,Warwick HRI, University of Warwick, Wellesbourne, UK.
- Nils Hogberg, Department of Forest Mycology & Pathology, Swedish University of Agricultural Sciences, UPPSALA, Sweden.
- Olaf Schmidt, Department of Wood Biology, University of Hamburg, Hamburg, Germany.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC
The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.
Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411
Eastwood DC, Floudas D, Binder M, Majcherczyk A, Schneider P, Aerts A, Asiegbu FO, Baker SE, Barry K, Bendiksby M, Blumentritt M, Coutinho PM, Cullen D, de Vries RP, Gathman A, Goodell B, Henrissat B, Ihrmark K, Kauserud H, Kohler A, LaButti K, Lapidus A, Lavin JL, Lee YH, Lindquist E, Lilly W, Lucas S, Morin E, Murat C, Oguiza JA, Park J, Pisabarro AG, Riley R, Rosling A, Salamov A, Schmidt O, Schmutz J, Skrede I, Stenlid J, Wiebenga A, Xie X, Kües U, Hibbett DS, Hoffmeister D, Högberg N, Martin F, Grigoriev IV, Watkinson SC
The plant cell wall-decomposing machinery underlies the functional diversity of forest fungi.
Science. 2011 Aug 5;333(6043):762-5. doi: 10.1126/science.1205411
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.
